Identification In cases where more than one name applies to a single unit, several identifications should be formed and flagged as preferred. Relationships between differently identified sub-units of the unit can be specified by means of the IdentificationRole. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Identification:2001-09-21T16-00-00Z jatorre@gmail.com DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com IdentificationDate TaxonName GBIF - Concatenated scientific name, preferrably formed in accordance with a Code of Nomenclature, i. e. a monomial, bionomial, or trinomial plus author(s) or author team(s) and - where relevant - year, or the name of a cultivar or cultivar group, or a hybrid formula, as fully as possible. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:TaxonName:2001-09-21T16-00-00Z jatorre@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com TaxonName FirstEpithet GBIF - The first epithet in a botanical name combination (species epithet or the epithet of the subdivision of a genus. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:FirstEpithet:2001-09-21T16-00-00Z jatorre@gmail.com FirstEpithet FirstEpithet Genus GBIF test - Genus www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Genus:2001-09-21T16-00-00Z jatorre@gmail.com Genus InfraspecificEpithet GBIF - The final epithet of a botanical name of infraspecific rank. AppInfo Nothing found. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:InfraspecificEpithet:2001-09-21T16-00-00Z jatorre@gmail.com InfraspecificEpithet InfraspecificEpithet TaxonIdentified psiblast_input_alignment Input Alignment File for PSI-BLAST Restart (-B option) bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:psiblast_input_alignment:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr Alignment Sequence alignment genopole.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:Alignment:2001-09-21T16-00-00Z carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content CpGAnnotation Annotations about nucleotidic CpG patterns www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CpGAnnotation:2007-01-15T15-14-14Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Sequence Score CpG Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Percentaje Ratio ElementString ElementString object for string arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementString:2006-03-21T11-52-03Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Value WeightedAminoAcidSequences Contains an object with its id and namespace (ProteinID) and a list of all the AA sequences found corresponding to this proteinID cgl.imim.es urn:lsid:biomoby.org:objectclass:WeightedAminoAcidSequences:2008-07-07T15-39-06Z jflo@imim.es AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length WeightedObject 'Object with integer'. cgl.imim.es urn:lsid:biomoby.org:objectclass:WeightedObject:2008-07-07T15-38-58Z jflo@imim.es Repetitions Description WeightedObject AminoAcidSequence GCP_Evidence An evidence indicates reliability of a feature or simply documents its authoritative origin. The core of an evidence is its source which can be anything (because it is an Entity). Usual evidence sources are BiblioReferences, Studies and OntologyTerms. GCP_Evidence records its "supporting source" directly in the form of the GCP_SimpleIdentifier from which it inherits. In this case, the MOBY namespace should hint at the type of object that is the supporting source (e.g. NCBI_Pubmed" probably indicates a bibliographic citation; IRIS_Study probably means ICIS Study data in the International Rice Information System) such that the end user can retrieve the source document or data type with another pertinent web service call. - curator. The person who keeps the data related to evidence. This is modeled as a GCP_SimpleIdentifier identifying a GCP_Person - evidenceCode. A GCP_SimpleIdentifier identifying a suitable GCP_OntologyTerm (generally, derived from the Gene Ontology evidence code ontology). - score. Indicator of the reliability of the evidence (which is usually a numeric value between 0 and 1, but also other types of Value are allowed - e.g. an ontology term value) www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Evidence:2008-10-14T03-21-03Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name evidenceCode score curator Source Source data type contains information about the taxID, the genotype and original genomic molecule. itag.sol urn:lsid:biomoby.org:objectclass:Source:2008-03-12T16-28-59Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com taxID String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com genotype name Ace_Text data format for assembly information genome.imim.es urn:lsid:biomoby.org:objectclass:Ace_Text:2006-05-19T12-49-02Z akerhornou@imim.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content snp_genotype Snp Genotypes www.hapmap.org urn:lsid:biomoby.org:objectclass:snp_genotype:2001-09-21T16-00-00Z hapmap@hapmap.edu snp_allele Snp Allele www.hapmap.org urn:lsid:biomoby.org:objectclass:snp_allele:2001-09-21T16-00-00Z hapmap@hapmap.edu DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length allele1 allele2 Organism An organism object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Organism:2006-03-01T18-35-20Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com PDF placeholder for pdf types www.renci.org urn:lsid:biomoby.org:objectclass:PDF:2007-03-28T13-51-47Z jdr0887@renci.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content FASTA_Text Fasta report. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:FASTA_Text:2001-09-21T16-00-00Z enrique.deandres@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Dummy_data test data for practicing service development coding.plantpath.ksu.edu urn:lsid:biomoby.org:objectclass:Dummy_data:2006-09-13T21-12-58Z jcn@ksu.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FASTA_Text Fasta report. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:FASTA_Text:2001-09-21T16-00-00Z enrique.deandres@pcm.uam.es dummy_FASTA_Text amirna artificial microRNA cshl.edu urn:lsid:biomoby.org:objectclass:amirna:2007-05-23T20-06-10Z leotta@cshl.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com loop_144 amirna_id target_seq mirna_long mirna_pattern Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com energy optimal_energy Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com mutations score FASTA_NA_multi Nucleic multiple FASTA entries genopole.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:FASTA_NA_multi:2001-09-21T16-00-00Z carrere@toulouse.inra.fr FASTA_NA NA sequence in FASTA format bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:FASTA_NA:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SeqDescription Sequence Description. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SeqDescription:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description CDNALibrary A cDNA Library eva.mpg.de urn:lsid:biomoby.org:objectclass:CDNALibrary:2001-09-21T16-00-00Z hoehndorf@eva.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com id RestrictAnnotation Annotations about restriction enzyme cleavage sites. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RestrictAnnotation:2007-01-15T15-05-51Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev Chart1D Provides data for plotting a one dimensional graph. Contains one or more GraphSeries1D objects as well as a chart title, chart description and an axis label. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Chart1D:2008-05-11T12-21-48Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com title description dimension1_axis_label GraphSeries1D Contains one or more GraphPoint1D objects to plot a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeries1D:2008-05-11T12-21-45Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com dimension1 GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com EmailAddress An e-mail address moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:EmailAddress:2007-04-06T18-47-52Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com address HMM_Text HMM profile. inb.bsc.es urn:lsid:biomoby.org:objectclass:HMM_Text:2007-01-19T15-52-38Z rroyo@lsi.upc.edu Consensus_Sequence_Text Consensus sequences reflect the most common choice of base or amino acid at each position of a series of related DNA, RNA or protein sequences. inb.bsc.es urn:lsid:biomoby.org:objectclass:Consensus_Sequence_Text:2007-01-19T15-51-18Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content b64_Encoded_Postscript Base 64 encoded Postscript image bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:b64_Encoded_Postscript:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content tigr-xml TIGRXML formatted file bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:tigr-xml:2007-07-23T12-48-40Z Jerome.Gouzy@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPdefinitionList-XML An iHOPdefinitionList XML document from iHOP web services cnio.es urn:lsid:biomoby.org:objectclass:iHOPdefinitionList-XML:2007-04-14T12-57-55Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SubElement SubElement data type that can hold different kind of information about certain regions, like exons. itag.sol urn:lsid:biomoby.org:objectclass:SubElement:2008-03-12T16-11-00Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start stop strand Evidence Evidence data type that can hold different kind of score objects. itag.sol urn:lsid:biomoby.org:objectclass:Evidence:2008-03-12T16-03-48Z joecker@mpiz-koeln.mpg.de Evidence iHOPactionVerb An action verb used by iHOP services to label text fragments cnio.es urn:lsid:biomoby.org:objectclass:iHOPactionVerb:2007-04-14T12-58-05Z jmfernandez@cnio.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com verbId String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com class iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content Predotar_result Result from Predotar with or without PlantID result genoplante-info.infobiogen.fr urn:lsid:biomoby.org:objectclass:Predotar_result:2001-09-21T16-00-00Z gpsupport@infobiogen.fr Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MIT_Score ER_Score Plast_Score Other_Score String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Compartment CompartmentPrediction The results of a compartment prediction program e.g. TargetP or Predotar atidb.org urn:lsid:biomoby.org:objectclass:CompartmentPrediction:2001-09-21T16-00-00Z matthew.couchman@bbsrc.ac.uk compartment c_score m_score o_score s_score GatheringSite Elements describing the field events that created the unit and their location. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:GatheringSite:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Locality Original locality data as appearing on a label or in an original entry. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Locality:2001-09-21T16-00-00Z jatorre@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com LocalityText Locality Coordinates Element that allows the recording of the latitude and longitude of a recording or collecting position. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Coordinates:2001-09-21T16-00-00Z jatorre@gmail.com CoordinatesText LongitudeDecimal Maps to Darwin Core 2: Longitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LongitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com LongitudeDecimal LongitudeDecimal LatitudeDecimal Maps to Darwin Core 2: Latitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LatitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com LatitudeDecimal LatitudeDecimal SpatialDatum Mathematical surface on which the mapping and coordinate system used for the geocodes of the record are based www.mncn.csic.es urn:lsid:biomoby.org:objectclass:SpatialDatum:2001-09-21T16-00-00Z jatorre@gmail.com SpatialDatum SpatialDatum Coordinates GetzJob A getz job. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GetzJob:2006-03-01T18-35-57Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Query A query object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Query:2006-03-01T18-35-19Z pieter.neerincx@gmail.com query Field A database field name. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Field:2006-03-01T18-35-18Z pieter.neerincx@gmail.com field HSSP_Text HSSP plain text. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:HSSP_Text:2007-01-11T09-56-16Z inb@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ScoredMotifAnnotatedAASequence Scored motif annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotatedAASequence:2007-01-12T12-54-19Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ScoredMotifAnnotation Scored Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotation:2007-01-12T12-54-17Z rroyo@lsi.upc.edu MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start AC ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score Annotations SpatialDatum Mathematical surface on which the mapping and coordinate system used for the geocodes of the record are based www.mncn.csic.es urn:lsid:biomoby.org:objectclass:SpatialDatum:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SpatialDatum InterProScanResult An InterProScan Result atidb.org urn:lsid:biomoby.org:objectclass:InterProScanResult:2009-06-23T18-07-06Z sean.walsh@bbsrc.ac.uk Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Length Match_End String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com InterPro_Match_Description Checksum Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com E-value Method Match_Name Match_Start Date Match_Accession InterPro_Match_Accession Sequence_Id Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Tree Phylogenetic tree www.phytome.org urn:lsid:biomoby.org:objectclass:Tree:2001-09-21T16-00-00Z dlu@email.unc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content LongitudeDecimal Maps to Darwin Core 2: Longitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LongitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com LongitudeDecimal Signature_cleave_table Table showing the predicted cleavage sites in a sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Signature_cleave_table:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Start End Score MaturePeptide PredictedSNP Predicted SNP with base change and confidence www.weigelworld.org urn:lsid:biomoby.org:objectclass:PredictedSNP:2006-06-27T14-35-08Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome Position Strain base_ref base_var Confidence GCG8 Text formatted in 'GCG8' format www.illuminae.com urn:lsid:biomoby.org:objectclass:GCG8:2007-02-13T17-50-30Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Ontology_Term A generic object for representing ontology terms and their definitions. The namespace will tell you which ontology is being referred to, and the id will tell you which node in that ontology is represented by the object. There should be no need to further specify this object by making ontology-specific versions of it, since this should be done by specifying the NAMESPACE, rather than an ISA extension of this object (please!). www.illuminae.com urn:lsid:biomoby.org:objectclass:Ontology_Term:2006-12-08T13-41-31Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Definition Term nsSNP_genomic Contains three string values: strand, condon_pos, allele icapture.ubc.ca urn:lsid:biomoby.org:objectclass:nsSNP_genomic:2006-03-31T20-48-50Z ycsong@student.cs.uwaterloo.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Strand Codon_Pos Allele GCP_GermplasmSet GCP_GermplasmSet is simply any collection of germplasm objects of a specified type (inferred by the namespace of its primary identifier, since it indirectly inherits from GCP_SimpleIdentifier via GCP_Entity). The list of germplasm is identified indirectly by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmSet:2008-10-14T03-22-00Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies germplasm Email An e-mail address object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Email:2006-03-01T18-35-14Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com URL An Universal Resource Locater (URL). www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:URL:2006-03-01T18-35-11Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com b64_encoded_PDB PDB compressed in zlib and encoded in base 64 bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:b64_encoded_PDB:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content EMBL Text formatted in 'EMBL' format www.illuminae.com urn:lsid:biomoby.org:objectclass:EMBL:2007-02-13T17-50-12Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description BLAST-Report A parent node for all of the different types of Blast reports bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:BLAST-Report:2006-07-06T21-23-16Z markw@illuminae.com Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Pizza_InterestingPizza Any pizza that has at least 3 toppings. Note that this is a cardinality constraint on the hasTopping property and NOT a qualified cardinality constraint (QCR). A QCR would specify from which class the members in this relationship must be. eg has at least 3 toppings from PizzaTopping. This is currently not supported in OWL. c.fr urn:lsid:biomoby.org:objectclass:Pizza_InterestingPizza:2011-10-14T15-17-17Z j@c.fr Pizza_Pizza no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_Pizza:2011-10-14T15-17-11Z j@c.fr Pizza_DomainConcept no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DomainConcept:2011-10-14T15-16-56Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pizza_PizzaBase no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_PizzaBase:2011-10-14T15-16-59Z j@c.fr hasBase ProbMolWeightAnnotation Annotations about de novo peptide sequence inferred by PepNovo www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbMolWeightAnnotation:2007-01-15T14-54-34Z inb@pcm.uam.es MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length DeNovoPeptide Probability RecordBasis An indication of what the unit record describes. Note that the element SourceReference provides for the case that the record is based on a publication. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:RecordBasis:2001-09-21T16-00-00Z jatorre@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com RecordBasis Tropgene_locus data types containing locus and allele identifiers tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:Tropgene_locus:2001-09-21T16-00-00Z m.ruiz@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com allele geneSNP SNPs and AA-changes in genes www.weigelworld.org urn:lsid:biomoby.org:objectclass:geneSNP:2006-06-19T16-50-56Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome pos aa_pos strain codon_ref aa_ref codon_var aa_var aa_change PDB-Text PDB format report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PDB-Text:2006-10-04T14-19-35Z moby-services@mmb.pcb.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_Phenotype GCP_Phenotype data is modeled as a GCP_FeatureWithObjectValue in which the feature_type is "phenotype", the value_type is "ontology" and the feature values is a cartesian cross product of GCP_OntologyTerms from three ontologies: 1. Plant Ontology 2. Phenotype Attribute 3. Phenotype Attribute Value specified by GCP_SimpleIdentifiers identifying the GCP_OntologyTerms for each. The GCP_FeatureWithObjectValue inherits from GCP_SimpleIdentifier which can point to the GCP_OntologyTerm designating the phenotype itself, in a shared catalog (such as one under development by members of the International Rice Functional Genomics Consortium). For example: <GCP_Phenotype namespace="IRFGC_Mutant" id="0000006" > <GCP_SimpleIdentifier ...articleName="feature_type" >phenotype</GCP_SimpleIdentifier> <GCP_SimpleIdentifier ...articleName="value_type" >ontology</GCP_SimpleIdentifier> ... <MOBY:Collection ...articleName="values" > <GCP_SimpleIdentifier namespace="PO" id="0020040" ...>Basal Leaf Sheath</GCP_SimpleIdentifier> <GCP_SimpleIdentifier namespace="PATO" id="0000033"...>Color</GCP_SimpleIdentifier> <GCP_SimpleIdentifier ...>Purple</GCP_SimpleIdentifier> </GCP_SimpleIdentifier> ... </GCP_Phenotype> www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Phenotype:2008-10-14T03-22-13Z r.bruskiewich@cgiar.org GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values PIR Text formatted in 'PIR' format www.illuminae.com urn:lsid:biomoby.org:objectclass:PIR:2007-02-14T19-34-02Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content zPDB a WIP of a compacted and encoded PDB file prot3.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:zPDB:2001-09-21T16-00-00Z yanwong@ebgm.jussieu.fr text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Sample This is a sample object cegen.upf.es urn:lsid:biomoby.org:objectclass:Sample:2001-09-21T16-00-00Z josep.alegre@upf.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com code Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com affectation FASTA_NA NA sequence in FASTA format bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:FASTA_NA:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GenericFeature Generic feature in a sequence database with start and end positions www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericFeature:2006-06-27T13-55-21Z stephan.ossowski@tuebingen.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Feature Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Start End BasicGFF3SequenceFeature An object containing all components necessary to represent a simple GFF-compliant sequence feature (the content is NOT validated against the GFF specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:BasicGFF3SequenceFeature:2006-04-27T19-04-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com type source seqid Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start end Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score strand phase multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com value key column9_tag_value IG Text formatted in 'IG' format www.illuminae.com urn:lsid:biomoby.org:objectclass:IG:2007-02-13T17-50-54Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_GeneProduct A GCP_GeneProduct is a wrapper defining molecular biological products in living cells, whose function can be characterized using GCP_OntologyTerms specifying Gene Ontology (GO) terms. These are partitioned in this data type as molecularFunctions, biologicalProcesses and cellularCompartments attributes identified by the corresponding sets of GCP_SimpleIdentifier objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeneProduct:2008-10-14T03-22-45Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name molecularFunctions cellularCompartments biologicalProcesses GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies Alignment Sequence alignment genopole.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:Alignment:2001-09-21T16-00-00Z carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_EmbeddedMap The GCP_EmbeddedMap is a kind of GCP_MapFeature that encapsulates an sourceMap Map for positioning onto another parent Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EmbeddedMap:2008-10-14T03-21-40Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name sourceMap GCP_MapFeature A GCP_MapFeature models a kind of GCP_Feature that has a coordinate position on a coordinate-dimensioned space called a map, which is identified by a GCP_SimpleIdentifier (see GCP_Map below). The MapFeature class is subclassed into domain specific map feature concepts such as biological GenomicFeature and geographical Location classes. By definition, a MapFeature belongs to only one map; however, the point, interval or space located by the map feature may be mapped onto more than one map, and may have many associated characteristics, which are generally retrievable by suitable web services using the MOBY namespace and identifier associated with the GCP_MapFeature. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapFeature:2008-10-14T03-21-39Z r.bruskiewich@cgiar.org map GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Compseq_Text The text consists of: Header information and comments are preceeded by a '#' character at the start of the line. The Word size and the Total count are then given on separate lines, The headers of the columns of results are preceeded by a '#' The results columns are: the sub-sequence word, the observed frequency, the expected frequency (which will be read from the input file if one is given, else it is a simple inverse of the number of words of the size specified that can be constructed), the ratio of the observed to expected frequency. After a blank line at the end, the results of 'Other' words is given - this is the number of words with a sequence which has IUPAC ambiguity codes or other unusual characters in. Example: ------------------------------------------ # # compseq example # # The Expected frequencies are calculated on the (false) assumption that every # word has equal frequency. # # The input sequences are: # HSFAU Word size 2 Total count 517 # # Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency # AA 45 0.0870406 0.0625000 1.3926499 AC 20 0.0386847 0.0625000 0.6189555 AG 45 0.0870406 0.0625000 1.3926499 AT 14 0.0270793 0.0625000 0.4332689 CA 34 0.0657640 0.0625000 1.0522244 CC 43 0.0831721 0.0625000 1.3307544 CG 25 0.0483559 0.0625000 0.7736944 CT 37 0.0715667 0.0625000 1.1450677 GA 31 0.0599613 0.0625000 0.9593810 GC 43 0.0831721 0.0625000 1.3307544 GG 46 0.0889749 0.0625000 1.4235977 GT 28 0.0541586 0.0625000 0.8665377 TA 15 0.0290135 0.0625000 0.4642166 TC 33 0.0638298 0.0625000 1.0212766 TG 32 0.0618956 0.0625000 0.9903288 TT 26 0.0502901 0.0625000 0.8046422 Other 0 0.0000000 0.0000000 10000000000.0000000 ------------------------------- mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Compseq_Text:2007-03-14T17-17-45Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FASTA_pep FASTA format for short peptide sequences. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:FASTA_pep:2007-01-12T13-55-00Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content TEST FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:TEST:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content RemapOutput Output obtained by running remap and contains the locations where enzymes cut in the sequence, as well as: * The list of enzymes that cut the sequence and match the required criteria. * The list of enzymes that cut the sequence and fail the MINCUTS criteria. * The list of enzymes that cut the sequence and fail the MAXCUTS criteria. * The list of enzymes that do not cut the sequence but which match all the required criteria. * The number of enzymes that cut the sequence and fail the SITELEN, BLUNT, STICKY, COMMERCIAL, AMBIGUOUS criteria. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:RemapOutput:2007-03-15T19-47-10Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content TaxonTCS Taxon concept in TCS format. www.gbif.org urn:lsid:biomoby.org:objectclass:TaxonTCS:2006-08-21T08-51-47Z fdcastillo@gbif.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com NameRef Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Scientific Name AccordingTo TaxonRelationship Defines a relation between two taxon concepts. www.gbif.org urn:lsid:biomoby.org:objectclass:TaxonRelationship:2006-08-21T08-46-28Z fdcastillo@gbif.org BriefTaxonConcept Brief description of a taxon returned by the GBIFGetTaxonConcepts. www.gbif.org urn:lsid:biomoby.org:objectclass:BriefTaxonConcept:2006-08-08T09-24-41Z fdelcastillo@gbif.org Key CanonicalName Accepted PublicationKey TaxonFrom Relationship TaxonTo Relationships TreeCon Text formatted in 'TreeCon' format www.illuminae.com urn:lsid:biomoby.org:objectclass:TreeCon:2007-02-13T17-54-53Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Jackknifernon Text formatted in 'jackknifernon' format www.illuminae.com urn:lsid:biomoby.org:objectclass:Jackknifernon:2007-02-13T17-51-43Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Trait_Details ICIS Property/Trait Information www.iris.irri.org urn:lsid:biomoby.org:objectclass:Trait_Details:2001-09-21T16-00-00Z mulat@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com trait_desc Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com num_studies trait_abbr trait_id trait_name GeneticElement GeneticElement including name, type, start, stop, strand (0 for forward, 1 for reverse), and description; use name for element identifier (like 'exon_1'), type for the element class (like 'exon') mips.gsf.de urn:lsid:biomoby.org:objectclass:GeneticElement:2006-06-14T11-45-25Z Octave.Noubibou@gsf.de Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com strand String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description name type stop start ElementXYData Coordinates <x,y>. inb.bsc.es urn:lsid:biomoby.org:objectclass:ElementXYData:2007-01-12T14-48-45Z rroyo@lsi.upc.edu Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Key Value DDBJ_flat_file DDBJ flat file xml.ddbj.nig.ac.jp urn:lsid:biomoby.org:objectclass:DDBJ_flat_file:2008-02-14T02-30-12Z ykuwana@genes.nig.ac.jp text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content AvailableMaterial Object containing information about available material gabi.rzpd.de urn:lsid:biomoby.org:objectclass:AvailableMaterial:2006-06-28T08-38-28Z neigenfi@rzpd.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Url AdditionalInformation simple_key_value_pair Basic key/value pair object for key/value pairs with a 1:1 relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:simple_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com value key SequenceFeatureTable text representation of the feature table for a sequence. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:SequenceFeatureTable:2007-03-15T19-36-23Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FunCat MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:FunCat:2008-06-13T11-27-52Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Testak Tetsing, will be removed soon... samples.jmoby.net urn:lsid:biomoby.org:objectclass:Testak:2006-09-27T10-49-46Z martin.senger@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com 5strand 3strand TaxonScientificName Full taxon name. skofic.net urn:lsid:biomoby.org:objectclass:TaxonScientificName:2001-09-21T16-00-00Z info@skofic.net Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name MappedFeature Sequence mapped to a feature of a sequence database www.weigelworld.org urn:lsid:biomoby.org:objectclass:MappedFeature:2006-06-27T14-04-15Z stephan.ossowski@tuebingen.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Orientation Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Mismatches TargetSequence GenericFeature Generic feature in a sequence database with start and end positions www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericFeature:2006-06-27T13-55-21Z stephan.ossowski@tuebingen.mpg.de Feature Start End SeqDB LutefiskAnnotation Annotations about de novo peptide sequence inferred by Lutefisk www.pcm.uam.es urn:lsid:biomoby.org:objectclass:LutefiskAnnotation:2007-01-15T15-02-17Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length LutefiskPeptide Rank Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Prc PevzScr Quality IntScr X-corr EquicktandemAnnotatedNASequence Nucleotidic sequence with annotations about tandem repeats. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EquicktandemAnnotatedNASequence:2007-01-15T15-09-06Z inb@pcm.uam.es AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description EquicktandemAnnotation Annotations about tandem repeats. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EquicktandemAnnotation:2007-01-15T15-06-46Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Score Size Count Annotations SchematikonMotifSupport Support and unique support for a Schematikon structure motif schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonMotifSupport:2001-09-21T16-00-00Z boris.steipe@utoronto.ca Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com UniqueSupport Support Regex This object can carry a regular expression. It can also say what kind of regular expression is carried. Additionally, it can contain some flags that may not be (in some regular expression languages) put directly in the regular expression. The only mandatory member is the regular expression itself ("regex"). The other members are: "format" specifies what language/format/engine is the "regex" for; typical values are Java, Perl, POSIX. "case_insensitive" is a flag that enables case-insensitive matching. "multiline_mode" is a flag that enables multiline mode. In multiline mode the expressions ^ and $ match just after or just before, respectively, a line terminator or the end of the input. "dotall_mode" is a flag that enables dotall mode. In dotall mode, the expression . matches any character, including a line terminator (in Perl, this mode is called single-line mode). "literal_mode" is a flag that enables literal parsing of the pattern. When this flag is specified then the input string that specifies the pattern is treated as a sequence of literal characters. Metacharacters or escape sequences in the input sequence will be given no special meaning. "comments" is a human-readable text explaining what this regular expression means. samples.jmoby.net urn:lsid:biomoby.org:objectclass:Regex:2001-09-21T16-00-00Z martin.senger@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com regex format Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca case_insensitive multiline_mode dotall_mode literal_mode comments iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Allele A lightweight object representing an Allele. The namespace and id should indicate the specific Allele being described. The contained String object is a human-readable description of the Allele in whatever form is most appropriate (e.g. the phenotype). bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Allele:2006-06-29T16-47-03Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description abwur_test Test datatype www.ab.wur.nl urn:lsid:biomoby.org:objectclass:abwur_test:2008-02-01T10-28-47Z mark.fiers@wur.nl text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com constraintDefinition GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org name ProfitOutput Output obtained by running profit: The output contains a a list of three columns. The first column is the name of the matching sequence found. The second is the start position in the sequence of the match. The third column (after the word 'Percentage:') is the percentage of the maximum possible score (sum of the highest value at each position in the frequency matrix). mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:ProfitOutput:2007-03-15T20-03-29Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ElementImage_Encoded Image_Encoded belonging to an Array. inb.bsc.es urn:lsid:biomoby.org:objectclass:ElementImage_Encoded:2007-01-12T14-52-29Z atorrano@lsi.upc.edu Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com mimeType rawdata Value MEGA Text formatted in 'MEGA' format www.illuminae.com urn:lsid:biomoby.org:objectclass:MEGA:2007-02-13T17-52-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PrositeDoc_Text Prosite plain text. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:PrositeDoc_Text:2007-01-11T10-24-12Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Nexusnon Text formatted in 'Nexusnon' format www.illuminae.com urn:lsid:biomoby.org:objectclass:Nexusnon:2007-02-13T17-53-56Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Equick_tandem_repeat Header and table showing the potential tandem repeats scanned in a sequence by means of runEMBOSSEquicktandem service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Equick_tandem_repeat:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com From To Hitcount Threshold Maxrepeat Equick_tandem_table Table showing the potential tandem repeats scanned in a sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Equick_tandem_table:2001-09-21T16-00-00Z inb@pcm.uam.es Start End Score Size Count iANT_entry_db-xml iANT entry collection (iANT::DB::Entry) xml file. This xml format describes a collection of entries (sequence with annotations) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT_entry_db-xml:2007-11-08T15-38-13Z Sebastien.Carrere@toulouse.inra.fr iANT-xml iANT xml file (entry, feature, db_entry, db_features) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT-xml:2007-07-18T12-58-41Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_Variate Variates are the dependent (measured) variables applied to a studyGCP_Study objects dereference their variates via a MOBY:Collection of GCP_SimpleIdentifier objects that resolve to GCP_Variate objects. GCP_Variate inherits most of its functionality from GCP_Feature. Variate property, scale and method are as per GCP_Factor narrative above. GCP_Variate reports its dataRange as a GCP_Constraint. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Variate:2008-10-14T03-22-47Z r.bruskiewich@cgiar.org GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values dataRange iANT_BLAST_Text Blast text report in iANT format bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:iANT_BLAST_Text:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com blast_report GCP_GenomicFeature A GCP_GenomicFeature is a kind of GCP_MapFeature that describes characterized segment of biological genetic information, corresponding to a DNA segment in the genome or a derivative thereof (see also the full GCP domain model description of a GenomicFeature). Being a GCP_MapFeature, a GCP_GenomicFeature generally embodies a suitable map position, identity and semantics as recorded by GCP_Feature articleNames. Basic general semantics (i.e. "I am a gene locus feature") is usually recorded in type article of the feature, but additional semantics may be recorded either in the specific values of the feature or in its supportingEvidence. How to split this semantics up is still a matter of evolving best practices. One might, for example, use the values field to connect a gene structure to its various other associated feature objects (e.g. structure parts - exons, utr's etc. - and products - transcripts, gene products - but use the supportingEvidence article to connect to more extensive annotation (such as detection protocol or sequence database citation). A GCP_GenomicFeature can report its assigned molecular genomicFeatureVariants, both identified by GCP_SimpleIdentifiers. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenomicFeature:2008-10-14T03-21-56Z r.bruskiewich@cgiar.org GCP_MapFeature A GCP_MapFeature models a kind of GCP_Feature that has a coordinate position on a coordinate-dimensioned space called a map, which is identified by a GCP_SimpleIdentifier (see GCP_Map below). The MapFeature class is subclassed into domain specific map feature concepts such as biological GenomicFeature and geographical Location classes. By definition, a MapFeature belongs to only one map; however, the point, interval or space located by the map feature may be mapped onto more than one map, and may have many associated characteristics, which are generally retrievable by suitable web services using the MOBY namespace and identifier associated with the GCP_MapFeature. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapFeature:2008-10-14T03-21-39Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name map GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values genomicFeatureVariants VirtualPrimerPair Two Primers and parameters for a virtual PCR www.weigelworld.org urn:lsid:biomoby.org:objectclass:VirtualPrimerPair:2006-06-27T18-45-27Z stephan.ossowski@tuebingen.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com FivePrimer ThreePrimer SeqDB Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Mismatches MaxDistance DCCP_Text DCCP plain text. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:DCCP_Text:2007-01-15T15-22-55Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FASTA_AA_multi Proteic multiple FASTA entries bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:FASTA_AA_multi:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr FASTA_AA AA sequence in FASTA format bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:FASTA_AA:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_Content Large or complex (binary) publication content of GCP_BiblioReference instances is wrapped by the GCP_Content class, which is a kind of GCP_Feature with a body which can be an object of any data type extending the MOBY:Object data type. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Content:2008-10-14T03-22-56Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type body OccurrenceRecord Brief description of a taxon returned by the GBIFGetTaxonConcepts. www.gbif.org urn:lsid:biomoby.org:objectclass:OccurrenceRecord:2006-08-15T13-00-00Z fdcastillo@gbif.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com InstitutionCode ScientificName Country BasisOfRecord Latitude Longitude CMLSpectUrl A url to a CMLSpect XML file, see http://www.xml-cml.org/ www.ab.wur.nl urn:lsid:biomoby.org:objectclass:CMLSpectUrl:2008-02-14T15-54-28Z mark.fiers@wur.nl String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Url Id Name DASGFF Contains annotations across a segment in xml format cnio.es urn:lsid:biomoby.org:objectclass:DASGFF:2007-07-19T14-37-49Z jmrodriguez@cnio.es text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DeletionPrediction Deletion prediction with core (high confidence) and boundaries (lower confidence) www.weigelworld.org urn:lsid:biomoby.org:objectclass:DeletionPrediction:2006-06-26T15-47-35Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome Boundary strain Core NDB-Text NDB text. inb.bsc.es urn:lsid:biomoby.org:objectclass:NDB-Text:2007-01-12T12-56-16Z rroyo@lsi.upc.edu text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Clustalw_Evaluated_Text Evaluation of a Clustalw_Text (Clustalw multiple sequence alignment) in ascii format. inb.bsc.es urn:lsid:biomoby.org:objectclass:Clustalw_Evaluated_Text:2007-04-19T14-50-25Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com iHOPchemicalCompound An chemical compound used by iHOP services to label text fragments cnio.es urn:lsid:biomoby.org:objectclass:iHOPchemicalCompound:2007-04-14T12-58-07Z jmfernandez@cnio.es iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SigcleaveAnnotatedAASequence Aminoacid sequence with annotations about signal cleavage sites www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SigcleaveAnnotatedAASequence:2007-01-15T15-24-24Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length SigcleaveAnnotation Annotations about protein signal cleavage sites www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SigcleaveAnnotation:2007-01-15T15-23-30Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score MaturePeptide Annotations TaxonRelationship Defines a relation between two taxon concepts. www.gbif.org urn:lsid:biomoby.org:objectclass:TaxonRelationship:2006-08-21T08-46-28Z fdcastillo@gbif.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com BriefTaxonConcept Brief description of a taxon returned by the GBIFGetTaxonConcepts. www.gbif.org urn:lsid:biomoby.org:objectclass:BriefTaxonConcept:2006-08-08T09-24-41Z fdelcastillo@gbif.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Key CanonicalName Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Accepted PublicationKey TaxonFrom Relationship TaxonTo gene_ref adds synonyms to the parent icapture.ubc.ca urn:lsid:biomoby.org:objectclass:gene_ref:2006-11-07T14-42-45Z ycsong@student.cs.uwaterloo.ca gene Contains string values, which represents gene name, description and summary icapture.ubc.ca urn:lsid:biomoby.org:objectclass:gene:2006-04-02T17-17-58Z ycsong@student.cs.uwaterloo.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com description name summary synonyms iHOPabstract-XML An iHOPabstract XML document from iHOP web services cnio.es urn:lsid:biomoby.org:objectclass:iHOPabstract-XML:2007-04-14T12-57-54Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MGIS_id Accession ID in MGIS (http://mgis.grinfo.net) bioinfo.inibap.org urn:lsid:biomoby.org:objectclass:MGIS_id:2001-09-21T16-00-00Z m.rouard@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com vernacularName OrderedMatrix A matrix that is is completely ordered. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:OrderedMatrix:2007-04-24T21-29-05Z ekawas@mrl.icapture.ubc.ca Matrix_row an item in a row of a matrix, where the key is the position of the item in the row and the value is the value of the item in the matrix at that particular position mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Matrix_row:2007-04-24T21-21-57Z ekawas@mrl.icapture.ubc.ca simple_key_value_pair Basic key/value pair object for key/value pairs with a 1:1 relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:simple_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com value key item Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com row_position Matrix_row Matrix Matrix object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Matrix:2006-03-21T11-48-31Z inb@pcm.uam.es testout Test output object www.iris.irri.org urn:lsid:biomoby.org:objectclass:testout:2001-09-21T16-00-00Z mulat@cgiar.org Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com gid String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com dvalue scaleid tmethid TropGENE_Diversity_Matrix Complete disjunctive tables for diversity analysis : accessions per row, alleles in column, coded in 0/1 with 2 columns per allele (one for presence, one for absence) tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:TropGENE_Diversity_Matrix:2001-09-21T16-00-00Z manuel.ruiz@cirad.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content AlleleAssociation This is a alleleAssociation object cegen.upf.es urn:lsid:biomoby.org:objectclass:AlleleAssociation:2001-09-21T16-00-00Z josep.alegre@upf.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com snp Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com pValue validity Wildcard_Query Text Query for IRIS which allows wildcards www.iris.irri.org urn:lsid:biomoby.org:objectclass:Wildcard_Query:2001-09-21T16-00-00Z mulat@cgiar.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com end_row start_row String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com germplasm_name MSF Multiple Sequence Format genopole.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:MSF:2001-09-21T16-00-00Z carrere@toulouse.inra.fr Alignment Sequence alignment genopole.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:Alignment:2001-09-21T16-00-00Z carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Query A query object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Query:2006-03-01T18-35-19Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com iHOPfoundSymbols It is basically a list of found symbols using services ... cnio.es urn:lsid:biomoby.org:objectclass:iHOPfoundSymbols:2007-04-14T12-58-02Z jmfernandez@cnio.es iHOPsymbol It is an iHOP symbol of a gene or protein, supported by evidences cnio.es urn:lsid:biomoby.org:objectclass:iHOPsymbol:2007-04-14T12-58-00Z jmfernandez@cnio.es iHOPevidence It is an iHOP evidence of a gene or protein name cnio.es urn:lsid:biomoby.org:objectclass:iHOPevidence:2007-04-14T12-57-58Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com organism iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content homolog synonym description symbol Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca truncatedList GFF3 Generic Feature Format File type 3 (SequenceOntology compliant GFF format) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF3:2001-09-21T16-00-00Z markw@illuminae.com GFF Generic Feature Format File (of any subtype) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com AC ID PPSearchReport PPSearch report, motif annotated sequences. inb.bsc.es urn:lsid:biomoby.org:objectclass:PPSearchReport:2007-01-12T12-54-26Z rroyo@lsi.upc.edu MotifAnnotatedAASequence Motif annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotatedAASequence:2007-01-12T12-54-24Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start AC ID Annotations TotalHits AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description XCMSSetSerializedUrl A url to an R Serialized XCMSSet object www.ab.wur.nl urn:lsid:biomoby.org:objectclass:XCMSSetSerializedUrl:2008-02-14T15-55-28Z mark.fiers@wur.nl Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Url Id Name Annotated_KO_Term KEGG ontology term mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_KO_Term:2008-06-13T11-26-24Z joecker@mpiz-koeln.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com description KO_Term KEGG ontology term mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:KO_Term:2008-06-13T11-25-35Z joecker@mpiz-koeln.mpg.de Pattern Pattern in prosite format. inb.bsc.es urn:lsid:biomoby.org:objectclass:Pattern:2007-01-12T12-52-18Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content OrganismsShortName Short name for organisms test.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:OrganismsShortName:2007-10-15T13-30-52Z sebastien.letort@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DataBase A database object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:DataBase:2006-03-01T18-35-12Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com LutefiskReport De Novo peptides reported by Lutefisk service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:LutefiskReport:2007-01-15T15-05-21Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MW MWTolerance FragIonTolerance IonOffset Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com ChargeState CysResMass IonsWindow ExtThreshold ExtNumber Gaps PeakWidth DataThreshold IonsResidue CterminalMass NterminalMass NterminalTagMass CterminalTagMass String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceTag LutefiskAnnotatedAASequence De novo peptide sequence with Lutefisk annotations www.pcm.uam.es urn:lsid:biomoby.org:objectclass:LutefiskAnnotatedAASequence:2007-01-15T15-02-45Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length LutefiskAnnotation Annotations about de novo peptide sequence inferred by Lutefisk www.pcm.uam.es urn:lsid:biomoby.org:objectclass:LutefiskAnnotation:2007-01-15T15-02-17Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start LutefiskPeptide Rank Prc PevzScr Quality IntScr X-corr Annotations AnnotatedSequence PepinfoReport Collection of featured sequences. inb.bsc.es urn:lsid:biomoby.org:objectclass:PepinfoReport:2007-01-12T12-52-57Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com FeatureAASequence It's an AA sequence with an associated feature value as a array of floats mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:FeatureAASequence:2006-10-05T15-08-40Z moby-services@mmb.pcb.ub.es ArrayFloat ArrayFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayFloat:2006-03-21T11-50-38Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Element feature AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length Tiny Small Aliphatic Aromatic Non-polar Polar Charged Positive Negative Hydropathy_KD Hydropathy_OHM Consensus Meta_Alignment_Text Meta-alignment text report genome.imim.es urn:lsid:biomoby.org:objectclass:Meta_Alignment_Text:2006-03-21T21-49-03Z akerhornou@imim.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SigcleaveReport Protein signal cleavage sites reported by runEmbossSigcleaveFromID service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SigcleaveReport:2007-01-15T15-26-06Z inb@pcm.uam.es SigcleaveAnnotatedAASequence Aminoacid sequence with annotations about signal cleavage sites www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SigcleaveAnnotatedAASequence:2007-01-15T15-24-24Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length SigcleaveAnnotation Annotations about protein signal cleavage sites www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SigcleaveAnnotation:2007-01-15T15-23-30Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score MaturePeptide Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits GappedDNASequence A DNA sequence with hyphens that represent gaps, e.g. as found in a sequence alignment moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:GappedDNASequence:2007-07-30T22-40-36Z gordonp@ucalgary.ca DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length RNASequence Lightweight representation an RNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:RNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length iANT_entry-xml iANT entry (iANT::Entry) xml file. This xml format describes an entry (sequence with annotations) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT_entry-xml:2007-10-30T14-24-25Z Sebastien.Carrere@toulouse.inra.fr iANT-xml iANT xml file (entry, feature, db_entry, db_features) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT-xml:2007-07-18T12-58-41Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GazOutput Output of the Gazeteer program - lat and long cipotato.org urn:lsid:biomoby.org:objectclass:GazOutput:2007-05-04T14-32-37Z r.simon@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com LatLong Chart3D Provides data for plotting a three dimensional graph. Contains one or more GraphSeries3D objects as well as a chart title, chart description and labels for the axis. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Chart3D:2008-05-11T12-21-51Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com title description dimension1_axis_label dimension2_axis_label dimension3_axis_label GraphSeries3D Contains one or more GraphPoint3D objects to plot a three dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeries3D:2008-05-11T12-21-47Z pieter.neerincx@gmail.com GraphPoint3D GraphPoint2D with an additional Float object for the third dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint3D:2008-05-11T12-21-44Z pieter.neerincx@gmail.com GraphPoint2D GraphPoint1D with an additional Float object for the second dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint2D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com dimension2 dimension3 dimension1 GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com GFF Generic Feature Format File (of any subtype) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content RenciNucleotideSequence Nucleotide sequence in RENCI format workflow.renci.unc.edu urn:lsid:biomoby.org:objectclass:RenciNucleotideSequence:2006-12-06T15-54-30Z nassar@renci.org RenciSequence Sequence in Renci format (FASTA format variant) workflow.renci.unc.edu urn:lsid:biomoby.org:objectclass:RenciSequence:2006-12-06T14-52-48Z nassar@renci.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com seq CpGAnnotatedNASequence Nucleotidic sequence with annotations about CpG patterns www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CpGAnnotatedNASequence:2007-01-15T15-15-43Z inb@pcm.uam.es AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description CpGAnnotation Annotations about nucleotidic CpG patterns www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CpGAnnotation:2007-01-15T15-14-14Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Sequence Score CpG Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Percentaje Ratio Annotations ColiCard ColiCard text format used in the CCDB database for describing genes found in E.coli, http://redpoll.pharmacy.ualberta.ca/CCDB/ ualberta.ca urn:lsid:biomoby.org:objectclass:ColiCard:2007-09-21T21-19-49Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ByoDynTarget Byodyn target argument for a simulation, it contains a float and a list of strings cbbl.imim.es urn:lsid:biomoby.org:objectclass:ByoDynTarget:2008-06-13T14-39-34Z jflo@imim.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com time String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com argument ByoDynOEDParameter Additional parameter used for a ByoDyn simulation of type OptimalExperimentalDesign cbbl.imim.es urn:lsid:biomoby.org:objectclass:ByoDynOEDParameter:2008-06-18T09-53-15Z jflo@imim.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com targetSpecies identifiabilityCriteria sensitivityParameters ByoDynTarget Byodyn target argument for a simulation, it contains a float and a list of strings cbbl.imim.es urn:lsid:biomoby.org:objectclass:ByoDynTarget:2008-06-13T14-39-34Z jflo@imim.es Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com time argument target Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com OEDResolution RenciAminoAcidSequence Amino acid sequence in RENCI format workflow.renci.unc.edu urn:lsid:biomoby.org:objectclass:RenciAminoAcidSequence:2006-12-06T15-56-34Z nassar@renci.org RenciSequence Sequence in Renci format (FASTA format variant) workflow.renci.unc.edu urn:lsid:biomoby.org:objectclass:RenciSequence:2006-12-06T14-52-48Z nassar@renci.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com seq RNAStructML RNAStructML is a XML schema for representing RNA secondary structure information. www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:RNAStructML:2008-03-12T09-12-52Z web@uni-bielefeld.de BioDom BioDOM is a JAVA library for converting native non-XML output from various bioinformatic tools to XML formats that can be validated against XMLSchemas. www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:BioDom:2008-03-04T11-47-16Z web@uni-bielefeld.de text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPrelatedInfo Information related to an iHOP symbol: sentences showing interaction evidences related to the symbol or sentences used to define the symbol inside iHOP system cnio.es urn:lsid:biomoby.org:objectclass:iHOPrelatedInfo:2007-04-14T12-58-19Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPsymbol It is an iHOP symbol of a gene or protein, supported by evidences cnio.es urn:lsid:biomoby.org:objectclass:iHOPsymbol:2007-04-14T12-58-00Z jmfernandez@cnio.es iHOPevidence It is an iHOP evidence of a gene or protein name cnio.es urn:lsid:biomoby.org:objectclass:iHOPevidence:2007-04-14T12-57-58Z jmfernandez@cnio.es organism iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content homolog synonym description symbol iHOPsentence It is a manuscript abstract sentence, composed by iHOPTextFragments (or children of iHOPTextFragments) cnio.es urn:lsid:biomoby.org:objectclass:iHOPsentence:2007-04-14T12-58-12Z jmfernandez@cnio.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com sentenceNumber iHOPpmid Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com journalImpact date sentencePiece sentence GIFFormatImage An image in Graphics Interchange Format (typically a drawing, with lossless compression, but a maximum of 256 colours) moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:GIFFormatImage:2007-04-18T15-04-58Z gordonp@ucalgary.ca WebFormatImage A 2D visual representation in a format whsoe rendering is supported by the major Web browsers moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:WebFormatImage:2007-04-10T23-22-43Z gordonp@ucalgary.ca Image A 2 dimensional visual element moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Image:2007-04-10T23-19-22Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content StrideOutput the result of a Stride process prot3.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:StrideOutput:2001-09-21T16-00-00Z yanwong@ebgm.jussieu.fr String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com STR SEQ ProbIDAnnotatedAASequence De novo peptide sequence with ProbID annotations www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbIDAnnotatedAASequence:2007-01-15T14-57-39Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ProbIDAnnotation Annotations about de novo peptide sequence inferred by ProbID www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbIDAnnotation:2007-01-15T14-56-39Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start ProbIDPeptide ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com PosteriorProb MatchedIons BayScore ZScore Annotations TropGENE_Distance_Matrix distance matrix built from a Musa TropGENE_Diversity_Matrix object tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:TropGENE_Distance_Matrix:2001-09-21T16-00-00Z david.baux@cirad.fr String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Matrix DNASequenceWithGFFFeatures A DNA Sequence including GFF-style features. HINT: the id attribute of this object should be equivalent to the 'reference' String component of each contained BasicGFFSequenceFeature object, or it wont make much sense. www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequenceWithGFFFeatures:2001-09-21T16-00-00Z markw@illuminae.com BasicGFFSequenceFeature An object containing all components necessary to represent a simple GFF-compliant sequence feature (the content is NOT validated against the GFF specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:BasicGFFSequenceFeature:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com reference source method Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start stop Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score strand frame phase multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com value key column9_tag_value feature DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length HitPosition Biomoby object consisting of a MapPosition object (A position on a genetic map. Can be used to denote a sequence ID and its start and stop co-ordinates with respect to another sequence to which it is aligned), an Object object (to denote the orientation of this sequence with respect to the sequence to which it is aligned) and a String object (to denote the corresponding cigar like line of the alignment). * Cigar like line (CLL): A compact way to represent the alignment between 2 sequences. It defines the sequence of matches(M), substitutions/mismatches(S), insertions(I) or deletions(D) on the second sequence with respect to the first based on this alignment. In addition, the presence of introns(N) between High Scoring Pairs (HSPs) of a hit obtained from an alignment of the two sequences by BLAT/BLAST etc. can also be represented. For example: * 8M2S50M would be 8 matches followed by 2 substitutions (mismatches)and finally 50 matches * 30M400N30M would be two HSPs of 30 matches each seperated by an intron of length 400 bp * 2M1I25M1D6M would be 2 matches, an insertion in the hit, 25 matches, a gap in the hit and 6 matches. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:HitPosition:2008-04-20T13-58-30Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com cll MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end strand HMMPfam_Report Reports the results of searching a sequence against a HMM database. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:HMMPfam_Report:2006-03-21T11-44-54Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Header Sequences Domains Stockholm_Text Multiple sequence alignment in Stockholm format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Stockholm_Text:2006-03-21T11-44-50Z inb@pcm.uam.es Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com content Alignments LabeledExtractData This represents a labeled extract. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:LabeledExtractData:2006-07-31T13-38-28Z cs01cb@csd.abdn.ac.uk MeasuredBioMaterialData This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:MeasuredBioMaterialData:2006-07-31T13-32-39Z cs01cb@csd.abdn.ac.uk Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com isPooled Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com remainingQuantity originalQuantity String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name description LabelData This represents a labeling compund use to label extracts. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:LabelData:2006-07-31T13-36-59Z cs01cb@csd.abdn.ac.uk name description label HAMAP_Family HAMAP database complete entry bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:HAMAP_Family:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com swissprot-flatfile a formatted plaintext swissprot flatfile bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:swissprot-flatfile:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content description clustal-aln-formatted-text Clustalw aln format bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:clustal-aln-formatted-text:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr alignment MatchingPattern Pattern created from several sequences. inb.bsc.es urn:lsid:biomoby.org:objectclass:MatchingPattern:2007-01-12T12-57-01Z rroyo@lsi.upc.edu Pattern Pattern in prosite format. inb.bsc.es urn:lsid:biomoby.org:objectclass:Pattern:2007-01-12T12-52-18Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Hits SeqHits Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Fitness BioDom BioDOM is a JAVA library for converting native non-XML output from various bioinformatic tools to XML formats that can be validated against XMLSchemas. www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:BioDom:2008-03-04T11-47-16Z web@uni-bielefeld.de text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content sequence_alignment_msf sequence alignment msf www.renci.org urn:lsid:biomoby.org:objectclass:sequence_alignment_msf:2007-03-06T13-37-30Z jdr0887@renci.org sequence_alignment sequence alignment www.renci.org urn:lsid:biomoby.org:objectclass:sequence_alignment:2007-02-15T17-14-22Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPdefinitionList Results related to an iHOP symbol: sentences used to define the symbol inside iHOP system cnio.es urn:lsid:biomoby.org:objectclass:iHOPdefinitionList:2007-04-14T12-58-21Z jmfernandez@cnio.es iHOPrelatedInfo Information related to an iHOP symbol: sentences showing interaction evidences related to the symbol or sentences used to define the symbol inside iHOP system cnio.es urn:lsid:biomoby.org:objectclass:iHOPrelatedInfo:2007-04-14T12-58-19Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPsymbol It is an iHOP symbol of a gene or protein, supported by evidences cnio.es urn:lsid:biomoby.org:objectclass:iHOPsymbol:2007-04-14T12-58-00Z jmfernandez@cnio.es iHOPevidence It is an iHOP evidence of a gene or protein name cnio.es urn:lsid:biomoby.org:objectclass:iHOPevidence:2007-04-14T12-57-58Z jmfernandez@cnio.es organism iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content homolog synonym description symbol iHOPsentence It is a manuscript abstract sentence, composed by iHOPTextFragments (or children of iHOPTextFragments) cnio.es urn:lsid:biomoby.org:objectclass:iHOPsentence:2007-04-14T12-58-12Z jmfernandez@cnio.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com sentenceNumber iHOPpmid Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com journalImpact date sentencePiece sentence EquicktandemReport Potential tandem repeats reported by runEmbossEquicktandemFromID service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EquicktandemReport:2007-01-15T15-09-54Z inb@pcm.uam.es EquicktandemAnnotatedNASequence Nucleotidic sequence with annotations about tandem repeats. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EquicktandemAnnotatedNASequence:2007-01-15T15-09-06Z inb@pcm.uam.es AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description EquicktandemAnnotation Annotations about tandem repeats. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EquicktandemAnnotation:2007-01-15T15-06-46Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Score Size Count Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits AnnotatedStructure Annotated structure: domains and fragments. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedStructure:2006-10-05T10-03-02Z moby-services@mmb.pcb.ub.es PDB-Text PDB format report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PDB-Text:2006-10-04T14-19-35Z moby-services@mmb.pcb.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Source StructureDomain Information on structure domains mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureDomain:2006-10-05T09-59-53Z moby-services@mmb.pcb.ub.es Name StructureBoundaries Information on structure boundaries of segments, fragments, domains, etc. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureBoundaries:2006-10-05T09-10-02Z moby-services@mmb.pcb.ub.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com End Start Chain Segments StructureDomains StructureFragment Information on structure fragment boundaries mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureFragment:2006-10-05T09-47-10Z moby-services@mmb.pcb.ub.es NumResidues StructureFragments MatrixFloat MatrixFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:MatrixFloat:2006-03-21T11-50-45Z inb@pcm.uam.es Matrix Matrix object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Matrix:2006-03-21T11-48-31Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ArrayFloat ArrayFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayFloat:2006-03-21T11-50-38Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Key ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Element Array swissprot-flatfile a formatted plaintext swissprot flatfile bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:swissprot-flatfile:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BooleanQueryString QueryString object specific for boolean queries. Operators are AND, OR and NOT. Hence they must be in uppercase to be interpreted as operator. Parenthesis can be provided using round brackets. For example: (abc AND gene) NOT musculus. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:BooleanQueryString:2008-01-10T16-15-56Z pieter.neerincx@gmail.com QueryString A Query object with a String containing a query. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:QueryString:2008-01-10T16-15-54Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com query Query A query object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Query:2006-03-01T18-35-19Z pieter.neerincx@gmail.com OligoQualityClassThresholds An object containing OligoQualityThresholds objects for primary and secondary hits. Primary hits are (near) perfect hits that can cause maximum signal in a hybridization experiment. Secondary hits are imperfect hits that cause a significant amount of noise in a hybridization experiment and should not be ignored. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoQualityClassThresholds:2008-03-07T16-34-45Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com OligoQualityThresholds An object containing several threshold values used to calculate whether a piece of a transcript can cause signal by binding to an oligo or not. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoQualityThresholds:2008-03-07T16-34-43Z pieter.neerincx@gmail.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com mismatches contiguous_stretch Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com free_energy percent_identity primary_hits secondary_hits ENSEMBLHomolog ENSEMBL Homolog information. inb.bsc.es urn:lsid:biomoby.org:objectclass:ENSEMBLHomolog:2007-01-12T12-52-21Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Type Description Genus Species Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Start End Strand Name GCP_Polygon A GeoPolygon is a GeoLinearFeature with a closed path (first equal last point). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Polygon:2008-10-14T03-23-05Z r.bruskiewich@cgiar.org GCP_GeoLinearFeature A GeoLinearFeature is a set of line segments defined by two or more GeoPoints. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoLinearFeature:2008-10-14T03-23-03Z r.bruskiewich@cgiar.org GCP_GeoPosition Constrains GCP_MapPosition to be more GIS like. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints geographicalProjection geographicalDatum GCP_GeoPoint A GeoPoint is a GeoPosition that has singular latitude, longitude and elevation point coordinates. It may belong to a GCP_LinearFeature object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPoint:2008-10-14T03-22-34Z r.bruskiewich@cgiar.org linearFeature latitude longitude elevation vertices text_html report in HTML format genome.imim.es urn:lsid:biomoby.org:objectclass:text_html:2006-03-22T11-03-31Z akerhornou@imim.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Stockholm_Text Multiple sequence alignment in Stockholm format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Stockholm_Text:2006-03-21T11-44-50Z inb@pcm.uam.es Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GenefarmBiochemicalFunction a biochemical function urgi.infobiogen.fr urn:lsid:biomoby.org:objectclass:GenefarmBiochemicalFunction:2006-09-05T15-56-00Z urgi-contact@versailles.inra.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com TFscan_Text runEMBOSSTFscan output. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TFscan_Text:2001-09-21T16-00-00Z inb@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Distance_Matrix Formalisation of a distance matrix genome.imim.es urn:lsid:biomoby.org:objectclass:Distance_Matrix:2006-03-22T14-25-20Z akerhornou@imim.es MatrixFloat MatrixFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:MatrixFloat:2006-03-21T11-50-45Z inb@pcm.uam.es Matrix Matrix object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Matrix:2006-03-21T11-48-31Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ArrayFloat ArrayFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayFloat:2006-03-21T11-50-38Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Key ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Element Array MatrixString MatrixString object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:MatrixString:2006-03-21T11-52-31Z inb@pcm.uam.es Key ArrayString ArrayString object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayString:2006-03-21T11-52-20Z inb@pcm.uam.es Key ElementString ElementString object for string arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementString:2006-03-21T11-52-03Z inb@pcm.uam.es Key String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Value Element Array Label CommentedObject Description of an object identified by 'id' in 'namespace' mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:CommentedObject:2006-10-05T10-15-26Z moby-services@mmb.pcb.ub.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description SO_VDJ_gene Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). cirad.fr urn:lsid:biomoby.org:objectclass:SO_VDJ_gene:2009-08-18T08-46-32Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment:2009-08-18T08-46-10Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight glycoImage Any of several image types that illustrate glycan structures ccrc.uga.edu urn:lsid:biomoby.org:objectclass:glycoImage:2008-02-15T02-39-46Z will@ccrc.uga.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com imageData GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de NCBI_Blast_XML XML formatted NCBI Blast report www.illuminae.com urn:lsid:biomoby.org:objectclass:NCBI_Blast_XML:2001-09-21T16-00-00Z markw@illuminae.com text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FASTA-Report An FASTA alignment Report bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:FASTA-Report:2006-07-06T22-09-38Z markw@illuminae.com Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MegaMergerReport A report of the actions of megamerger. Any actions that require a choice between using regions of the two sequences where they have a mismatch is marked with the word WARNING!. The sequence in these regions is written out in uppercase. All other regions of the output sequence are written in lowercase. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MegaMergerReport:2007-03-15T19-22-01Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ArrayInteger ArrayInteger object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayInteger:2006-03-21T11-52-11Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementInteger ElementInteger object for integer arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementInteger:2006-03-21T11-51-55Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Value Element GCP_Passport GCP_Passport is simply a list of GCP_SimpleFeature objects identifying and reporting descriptor data about a GCP_accession. The GCP_SimpleFeature type designates the passport descriptor controlled vocabulary name from pertinent GCP ontology. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Passport:2008-10-14T03-23-17Z r.bruskiewich@cgiar.org GCP_FeatureSet A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_FeatureSet:2008-10-14T03-22-22Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type features accession GI_Gene A GeneIlluminater gene object. Contains a gene symbol and a gene name where the symbol is the abbreviated form of the name. Gene names and symbols can be placed in a certain namespace to denote the status of the gene and the organisation who assigned this status (Namespaces are labelled [Organisation]_[Statuslike] like for example HGNC_Approved, HGNC_Pending, HGNC_Reserved, HGNC_Withdrawn, UniProt_Name, UniProt_Synomym, UniProt_OLN, UniProt_ORF) GeneIlluminator analyses synomyms and homonyms and clusters symbols for the same gene. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GI_Gene:2007-10-31T17-32-47Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com symbol name GCP_NameSpace GCP_NameSpace extends GCP_Identifier (so it can itself be identified) but forms an aggregation of related components which are related instances of GCP_Identifier. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_NameSpace:2008-10-14T03-23-02Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description components PSIBLAST_Text PSIBLAST report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PSIBLAST_Text:2006-10-06T09-53-04Z moby-services@mmb.pcb.ub.es BLAST-Text PSIBLAST report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:BLAST-Text:2001-09-21T16-00-00Z gelpi@bq.ub.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MotifAnnotatedAASequence Motif annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotatedAASequence:2007-01-12T12-54-24Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start AC ID Annotations LabelData This represents a labeling compund use to label extracts. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:LabelData:2006-07-31T13-36-59Z cs01cb@csd.abdn.ac.uk Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name description tableRow A row of data for a tabular object moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:tableRow:2007-06-21T15-47-03Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com cell MGIS_Query Evaluation and characterization criteria available in MGIS (http://mgis.grinfo.net) bioinfo.inibap.org urn:lsid:biomoby.org:objectclass:MGIS_Query:2001-09-21T16-00-00Z m.rouard@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Characterization_Pulp_In_Fruit Characterization_Pulp_Colour_At_Maturity Characterization_Presence_Of_Seeds_With_Source_Of_Pollen Characterization_Fruit_Shape Characterization_Fruit_General_Shape Characterization_Number_Of_Suckers Characterization_Development_Of_Suckers Characterization_Bunch_Shape Characterization_Rachis_Type Characterization_Rachis_Position Characterization_Male_Bud_Type Characterization_Mature_Fruit_Peel_Colour Characterization_Number_Of_Fruits Characterization_Fruit_Length Characterization_Pseudostem_Height Characterization_Dwarfism Abiotic_stress_Hightemp Abiotic_stress_Manganesetox Abiotic_stress_Soilacidity Abiotic_stress_Winds Abiotic_stress_Mineraldef Abiotic_stress_Flooding Abiotic_stress_Drought Abiotic_stress_Lowtemp Biotic_stress_cosmopolites Biotic_stress_Pratylenchusgood Biotic_stress_Pratylenchuscof Biotic_stress_Radopholus Biotic_stress_pseudomonas Biotic_stress_Fusarium Biotic_stress_Blacksig Biotic_stress_Yellowsig mcpd:ORIGCTY mcpd:COLLCODE GCP_IdentifierSet The GCP domain model <em>IdentifierSet</em> is modeled in MOBY simply as labeled <em>MOBY:Collections</em> of <em>GCP_SimpleIdentifiers</em>. They can belong to any (and different) namespaces. For example, a list of synonyms for an instance of Germplasm is an <em>IdentifierSet</em>. <em>IdentifierSet</em> extends from <em>GCP_SimpleIdentifier</em> hence its <b>name</b>, <em>MOBY:nameSpace</em> and <em>MOBY:nameSpace</em> can be used to identify its context (e.g. as the <b>synonyms</b> <em>IdentifierSet</em> of an <em>Germplasm</em> object). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_IdentifierSet:2008-10-14T03-20-58Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name identifiers GlycoCT_condenced Sequence object for carbohydrates or glyco-conjugates in GlycoCT (Condenced version) encoding. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoCT_condenced:2008-02-28T13-55-41Z r.ranzinger@dkfz.de GlycoSequence Object that can store a carbohydrate or a glyco-conjugate sequence. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoSequence:2008-02-14T14-51-57Z r.ranzinger@dkfz.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequence GCP_Organization A GCP_LegalEntity specific to an organization entity recognized in legal terms as having a legal personality (i.e. able to own property, liable for legal prosecution, etc.) www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Organization:2008-10-14T03-21-55Z r.bruskiewich@cgiar.org GCP_LegalEntity GCP_LegalEntity represents a general subclass for any GCP_Entity recognized in legal terms as having a legal personality (i.e. ability to have human behaviour as an individual or in aggregate, able to own property, liable for legal prosecution, etc.). This includes both person and organization. - contactingDetails. A LegalEntity obviously has details relating to its localization in the human world. For efficiency, we treat instances of another moby data type, GCP_ContactingDetails, as a subclass of GCP_Identifier, and referencing these details from GCP_LegalEntity using the pertinent GCP_SimpleIdentifier. A LegalEntity may have several such contactingDetails. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LegalEntity:2008-10-14T03-21-54Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies contactingDetails CpGReport Regions rich in CpG pattern reported by runEmbossCpGreportFromID service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CpGReport:2007-01-15T15-16-30Z inb@pcm.uam.es CpGAnnotatedNASequence Nucleotidic sequence with annotations about CpG patterns www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CpGAnnotatedNASequence:2007-01-15T15-15-43Z inb@pcm.uam.es AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description CpGAnnotation Annotations about nucleotidic CpG patterns www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CpGAnnotation:2007-01-15T15-14-14Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Sequence Score CpG Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Percentaje Ratio Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits GraphSeries3D Contains one or more GraphPoint3D objects to plot a three dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeries3D:2008-05-11T12-21-47Z pieter.neerincx@gmail.com GraphPoint3D GraphPoint2D with an additional Float object for the third dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint3D:2008-05-11T12-21-44Z pieter.neerincx@gmail.com GraphPoint2D GraphPoint1D with an additional Float object for the second dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint2D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com dimension2 dimension3 dimension1 GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com MSCmlspectUrl A url to a cmlspect file containing peak information from a MassSpec experiment ab.wur.nl urn:lsid:biomoby.org:objectclass:MSCmlspectUrl:2008-04-08T12-08-47Z mark.fiers@wur.nl String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Url SampleId ExperimentId GCP_RelatedAccessions GCP_RelatedAccession is modeled as a special type of GCP_MaintenanceNeighbourhood which is the set of all GCP_Accession objects that share a common biological ancestral source (e.g. as a single specified sample in a collecting mission, through direct linkages of donations between genebanks). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_RelatedAccessions:2008-10-14T03-22-57Z r.bruskiewich@cgiar.org GCP_MaintenanceNeighbourhood A GCP_MaintenanceNeighbourhood is a GCP_GermplasmNeighbourhood striving to conserve biological diversity in a set of Germplasm. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MaintenanceNeighbourhood:2008-10-14T03-22-03Z r.bruskiewich@cgiar.org GCP_GermplasmNeighbourhood GCP_GermplasmNeighbourhood is a kind of GCP_GermplasmSet which has a formal biological or management role (see GCP domain model descriptions). Such a set is formally established by source_germplasm (modeled as a set of GCP_SimpleIdentifiers identifying GCP_Germplasm objects) and (generally) belongs to a specified germplasm_collection (also specified by a GCP_SimpleIdentifiers). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmNeighbourhood:2008-10-14T03-22-01Z r.bruskiewich@cgiar.org GCP_GermplasmSet GCP_GermplasmSet is simply any collection of germplasm objects of a specified type (inferred by the namespace of its primary identifier, since it indirectly inherits from GCP_SimpleIdentifier via GCP_Entity). The list of germplasm is identified indirectly by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmSet:2008-10-14T03-22-00Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies germplasm germplasmCollection sourceGermplasm accessions GCP_RNAComplex A GCP_RNAComplex is a GCP_GeneProduct composed of a functional aggregation of GCP_RNASequence objects, which are identified by a set of GCP_SimpleIdentifier objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_RNAComplex:2008-10-14T03-23-22Z r.bruskiewich@cgiar.org GCP_GeneProduct A GCP_GeneProduct is a wrapper defining molecular biological products in living cells, whose function can be characterized using GCP_OntologyTerms specifying Gene Ontology (GO) terms. These are partitioned in this data type as molecularFunctions, biologicalProcesses and cellularCompartments attributes identified by the corresponding sets of GCP_SimpleIdentifier objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeneProduct:2008-10-14T03-22-45Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name molecularFunctions cellularCompartments biologicalProcesses GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies RNASequences GraphPoint2D GraphPoint1D with an additional Float object for the second dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint2D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com dimension2 ProbeId Material placed on a spot on microarray to represent a biological sequence. The ProbeID comes from KOME database, e,g, AU088561, 002-168-D12. typeOfMicroArray is e.g. cDNA, oligo. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:ProbeId:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com FeatureAASequence It's an AA sequence with an associated feature value as a array of floats mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:FeatureAASequence:2006-10-05T15-08-40Z moby-services@mmb.pcb.ub.es ArrayFloat ArrayFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayFloat:2006-03-21T11-50-38Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Element feature AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length PropertySequence Symbolic sequence based is a given property mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PropertySequence:2006-10-04T13-55-48Z moby-services@mmb.pcb.ub.es GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length description CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length MeasuredBioMaterialData This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:MeasuredBioMaterialData:2006-07-31T13-32-39Z cs01cb@csd.abdn.ac.uk Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com isPooled Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com remainingQuantity originalQuantity String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name description FeatureAnnotation Feature Annotation (from Uniprot database). inb.bsc.es urn:lsid:biomoby.org:objectclass:FeatureAnnotation:2006-12-11T04-48-32Z rroyo@lsi.upc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Type Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com End Start Status Id Description Evidence Ref FSOLV_Text Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:FSOLV_Text:2006-03-15T17-38-22Z gelpi@bq.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Metabolite Small organic molecule that participates in a metabolism. cdk.sourceforge.net urn:lsid:biomoby.org:objectclass:Metabolite:2007-10-09T18-24-00Z egon.willighagen@wur.nl Molecule Concept of a chemical molecule, such a metabolite. The molecule is represented in Chemical Markup Language. org.openscience.cdk urn:lsid:biomoby.org:objectclass:Molecule:2007-09-21T16-43-52Z egonw@users.sf.net Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceChromatogram A data series representing the intensities of various DNA bases detected in a sequencing experiment for a given DNA sample. Also known as a sequence trace, it is usually graphically represented as a graph of curved peaks, which each nucleotide given a different colour (hence the term chomatogram) moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:SequenceChromatogram:2007-04-10T22-36-13Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content InvertedComplementRepeat This datatype represents a sequence of nucleotides that is the reversed complement of another sequence further downstream. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:InvertedComplementRepeat:2007-04-16T19-37-28Z ekawas@mrl.icapture.ubc.ca Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com gaps NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length matches score Staden Text formatted in 'Staden' format www.illuminae.com urn:lsid:biomoby.org:objectclass:Staden:2007-02-13T17-54-18Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com CodcmpReport_Text Codcmp report. inb.bsc.es urn:lsid:biomoby.org:objectclass:CodcmpReport_Text:2007-01-23T10-31-28Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content EquicktandemAnnotation Annotations about tandem repeats. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EquicktandemAnnotation:2007-01-15T15-06-46Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start Score Size Count WeightedObject 'Object with integer'. cgl.imim.es urn:lsid:biomoby.org:objectclass:WeightedObject:2008-07-07T15-38-58Z jflo@imim.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Repetitions String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description Nexus_Text phylogenetic tree format bioinfo.inibap.org urn:lsid:biomoby.org:objectclass:Nexus_Text:2006-11-28T07-10-13Z m.rouard@cgiar.org text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FirstEpithet GBIF - The first epithet in a botanical name combination (species epithet or the epithet of the subdivision of a genus. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:FirstEpithet:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com FirstEpithet GCP_GenomicFeatureDetector GCP_GenomicFeatures may be detected by a GenomicFeatureAssay that uses a specific set of genetic information embodied in experimental reagents or computation inputs. The object describing this specific set of biological information is modeled by the GCP_GenomicFeatureDetector data type, which inherits its full documentation capacity from GCP_Entity. A GCP_GenomicFeatureDetector can report the assays to which it is applied, the genomicFeatures it detects and their characterized molecular detectedVariants. All of these are dereferenced by GCP_SimpleIdentifiers. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenomicFeatureDetector:2008-10-14T03-22-23Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies detectedVariants assays ProteinTable A Protein Table (*.ptt) file contains the location, strand, length, ID, generic name, COG assignation and functional annotation for every predicted protein in whole genomes. These protein table files can also be obtained from NCBI's ftp site: ftp://ftp.ncbi.nih.gov/genomes/ ualberta.ca urn:lsid:biomoby.org:objectclass:ProteinTable:2007-08-28T22-11-58Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length GB Sequence in GENBANK format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:GB:2001-09-21T16-00-00Z inb@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FastaConsensiFromGroup Fasta da base do projeto biofoco. www.condor.genoma.cenargen.embrapa.br urn:lsid:biomoby.org:objectclass:FastaConsensiFromGroup:2001-09-21T16-00-00Z mcosta@cenargen.embrapa.br Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com projectName groupCod fasta date autor SixPackOutput text representing SixPack output that contains protein sequence open reading frames mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:SixPackOutput:2007-03-15T19-26-07Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GraphSeries1D Contains one or more GraphPoint1D objects to plot a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeries1D:2008-05-11T12-21-45Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com dimension1 GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com ENSEMBLHomology ENSEMBL Homology information and list of homologs. inb.bsc.es urn:lsid:biomoby.org:objectclass:ENSEMBLHomology:2007-01-12T14-46-42Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description ENSEMBLHomolog ENSEMBL Homolog information. inb.bsc.es urn:lsid:biomoby.org:objectclass:ENSEMBLHomolog:2007-01-12T12-52-21Z rroyo@lsi.upc.edu Type Description Genus Species Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Start End Strand Name Homologs snp_allele Snp Allele www.hapmap.org urn:lsid:biomoby.org:objectclass:snp_allele:2001-09-21T16-00-00Z hapmap@hapmap.edu DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length PatmatdbReport Patmatdb report. inb.bsc.es urn:lsid:biomoby.org:objectclass:PatmatdbReport:2007-01-12T12-55-26Z rroyo@lsi.upc.edu ScoredMotifAnnotatedAASequence Scored motif annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotatedAASequence:2007-01-12T12-54-19Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ScoredMotifAnnotation Scored Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotation:2007-01-12T12-54-17Z rroyo@lsi.upc.edu MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start AC ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits ArrayString ArrayString object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayString:2006-03-21T11-52-20Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementString ElementString object for string arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementString:2006-03-21T11-52-03Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Value Element text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SO_TNA An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_TNA:2009-08-18T08-41-41Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com gene Contains string values, which represents gene name, description and summary icapture.ubc.ca urn:lsid:biomoby.org:objectclass:gene:2006-04-02T17-17-58Z ycsong@student.cs.uwaterloo.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com description name summary table Tabular (row-based) data moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:table:2007-06-25T23-20-32Z gordonp@ucalgary.ca tableRow A row of data for a tabular object moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:tableRow:2007-06-21T15-47-03Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com cell row CommentedDNASequence Represents a DNA Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedDNASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length glycoSVG An uncompressed svg representation of a glcyan structure ccrc.uga.edu urn:lsid:biomoby.org:objectclass:glycoSVG:2008-02-15T02-42-43Z will@ccrc.uga.edu glycoImage Any of several image types that illustrate glycan structures ccrc.uga.edu urn:lsid:biomoby.org:objectclass:glycoImage:2008-02-15T02-39-46Z will@ccrc.uga.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com imageData GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length OligoRecord Biomoby object containing one or more OligoHit objects and an Integer object for the length of the oligo. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoRecord:2008-04-20T13-58-32Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com length OligoHit Biomoby object consisting of a HitPosition object and a Moby CrossReference Information Block (CRIB). The CRIB lists evidence for gene expression of the sequence in the HitPosition object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoHit:2008-04-20T13-58-31Z pieter.neerincx@gmail.com HitPosition Biomoby object consisting of a MapPosition object (A position on a genetic map. Can be used to denote a sequence ID and its start and stop co-ordinates with respect to another sequence to which it is aligned), an Object object (to denote the orientation of this sequence with respect to the sequence to which it is aligned) and a String object (to denote the corresponding cigar like line of the alignment). * Cigar like line (CLL): A compact way to represent the alignment between 2 sequences. It defines the sequence of matches(M), substitutions/mismatches(S), insertions(I) or deletions(D) on the second sequence with respect to the first based on this alignment. In addition, the presence of introns(N) between High Scoring Pairs (HSPs) of a hit obtained from an alignment of the two sequences by BLAT/BLAST etc. can also be represented. For example: * 8M2S50M would be 8 matches followed by 2 substitutions (mismatches)and finally 50 matches * 30M400N30M would be two HSPs of 30 matches each seperated by an intron of length 400 bp * 2M1I25M1D6M would be 2 matches, an insertion in the hit, 25 matches, a gap in the hit and 6 matches. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:HitPosition:2008-04-20T13-58-30Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com cll MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end strand hit_position oligo_hit text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BasicClone Basic container for clone information www.gabipd.org urn:lsid:biomoby.org:objectclass:BasicClone:2008-03-07T14-14-03Z Neigenfind@mpimp-golm.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com AccessPageUrl Identifier Kind NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Sequence Scored_acronym_string Any text with a score or ranking associated, with possible acronym for keyword www.inblosam.com urn:lsid:biomoby.org:objectclass:Scored_acronym_string:2001-09-21T16-00-00Z michael@inblosam.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score string_component String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com acronym LINUCS Sequence object for carbohydrates or glyco-conjugates in LINUCS encoding. www.glycome-db.org urn:lsid:biomoby.org:objectclass:LINUCS:2008-02-28T13-56-29Z r.ranzinger@dkfz.de GlycoSequence Object that can store a carbohydrate or a glyco-conjugate sequence. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoSequence:2008-02-14T14-51-57Z r.ranzinger@dkfz.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequence GCP_Ontology When a user requires the retrieval of full details about a Demeter OntologyTerm or its subclasses, the system will return a subclass of GCP_Entity that fully documents it. This will include articles for the name, description and namespace attributes from the superclass GCP_SimpleIdentifier and GCP_Identifier that serve as the concept name, definition and parent ontology, respectively. The GCP_Entity also synonyms covers all concept alias names and database cross references. Of course, since GCP_OntologyTerm is a kind of GCP_Entity, it may also have a primary_citation supporting its definition, plus other pertinent annotation. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Ontology:2008-10-14T03-23-23Z r.bruskiewich@cgiar.org GCP_NameSpace GCP_NameSpace extends GCP_Identifier (so it can itself be identified) but forms an aggregation of related components which are related instances of GCP_Identifier. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_NameSpace:2008-10-14T03-23-02Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description components GCP_OntologyTerm A fully documented GCP_OntologyTerm object is a simply specialised kind of GCP_Entity documenting an abstract concept, belonging to a GCP hosted ontology (itself identified by a GCP_SimpleIdentifier). The name, description and namespace attributes of the superclass GCP_SimpleIdentifier and GCP_Identifier serve as the concept name, definition and parent ontology, respectively. The GCP_Entity synonyms covers all concept alias names and database cross references. Of course, since GCP_OntologyTerm is a kind of GCP_Entity, it may also have a primary_citation supporting its definition, plus other pertinent annotation. *Note: Generally speaking, MOBY services only need to to use GCP_SimpleIdentifier references to GCP_OntologyTerm instances, not the full GCP_OntologyTerm, except when the full ontology term definition (GCP_OntologyTerm) is requested by the end user for display in their application. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_OntologyTerm:2008-10-14T03-22-44Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies root Region Region data type contains information about any genomic sequence and its elements, e.x. annotations. itag.sol urn:lsid:biomoby.org:objectclass:Region:2008-03-12T16-33-08Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length GFF2 Generic Feature Format File type 2 (revised Sanger specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF2:2001-09-21T16-00-00Z markw@illuminae.com GFF Generic Feature Format File (of any subtype) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content EmageReport Gene expression annotations from Emage database. www.cnb.uam.es urn:lsid:biomoby.org:objectclass:EmageReport:2007-11-19T12-06-54Z natalia@cnb.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EmageAnnotation Annotations about gene expression from EMAGE database mapped on the image www.cnb.uam.es urn:lsid:biomoby.org:objectclass:EmageAnnotation:2007-11-19T12-06-12Z natalia@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com ExpressionLevel ExpressionPattern Description Component Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es mimeType rawdata GeneSymbol GeneName ExpressionNotes EmageAnnotation b64_encoded_jpeg Base 64 encoded JPEG-format image www.illuminae.com urn:lsid:biomoby.org:objectclass:b64_encoded_jpeg:2001-09-21T16-00-00Z markw@illuminae.com text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content InteractionMethod We represent an interaction method with this object pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:InteractionMethod:2001-09-21T16-00-00Z jmfernandez@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com shortlabel term definition Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome DDBJ_Accession DDBJ accession number xml.ddbj.nig.ac.jp urn:lsid:biomoby.org:objectclass:DDBJ_Accession:2008-02-14T02-30-01Z ykuwana@genes.nig.ac.jp text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GlycoCT_xml Sequence object for carbohydrates or glyco-conjugates in GlycoCT (XML version) encoding. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoCT_xml:2008-02-28T13-54-49Z r.ranzinger@dkfz.de GlycoSequence Object that can store a carbohydrate or a glyco-conjugate sequence. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoSequence:2008-02-14T14-51-57Z r.ranzinger@dkfz.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequence GeneInfo Characteristics of gene. The annotation string should always have namespace NCBI_Acc and an ID. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:GeneInfo:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp GeneId LocusID from KOME database. e.g. RO3-AC079887-30020F. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:GeneId:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length sequence Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp end start chromosome position annotation orthologGene FASTA_Base_Quality_multi sequences base quality data in FASTA format genome.imim.es urn:lsid:biomoby.org:objectclass:FASTA_Base_Quality_multi:2006-05-03T09-02-44Z akerhornou@imim.es FASTA_Base_Quality Sequence base quality data in FASTA format genome.imim.es urn:lsid:biomoby.org:objectclass:FASTA_Base_Quality:2006-05-03T09-02-34Z akerhornou@imim.es FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content EBI_WUBlast_XML Blast result from EBI WUBlast mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:EBI_WUBlast_XML:2007-12-17T15-31-55Z joecker@mpiz-koeln.mpg.de text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SimpleAnnotatedJPEGImage An image with descriptive text www.illuminae.com urn:lsid:biomoby.org:objectclass:SimpleAnnotatedJPEGImage:2001-09-21T16-00-00Z markw@illuminae.com b64_encoded_jpeg Base 64 encoded JPEG-format image www.illuminae.com urn:lsid:biomoby.org:objectclass:b64_encoded_jpeg:2001-09-21T16-00-00Z markw@illuminae.com text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Description NCut_Input Text formatted that contains a representation of distances among homologous sequences pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:NCut_Input:2001-09-21T16-00-00Z jmrc@cnb.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iANT_feature-xml iANT feature xml file. This xml format describe the result of a program (blast,predotar,genomethreader, etc...). iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT_feature-xml:2007-07-18T13-11-30Z Sebastien.Carrere@toulouse.inra.fr iANT-xml iANT xml file (entry, feature, db_entry, db_features) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT-xml:2007-07-18T12-58-41Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BLAST-Text PSIBLAST report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:BLAST-Text:2001-09-21T16-00-00Z gelpi@bq.ub.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ArrayXYData An Array of <x,y> coordinates. inb.bsc.es urn:lsid:biomoby.org:objectclass:ArrayXYData:2007-01-12T14-48-52Z rroyo@lsi.upc.edu Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com xtitle ytitle title plot_title ElementXYData Coordinates <x,y>. inb.bsc.es urn:lsid:biomoby.org:objectclass:ElementXYData:2007-01-12T14-48-45Z rroyo@lsi.upc.edu Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Key Value elements Phylip_Text Multiple sequence alignment in Phylip format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Phylip_Text:2006-03-21T11-49-12Z inb@pcm.uam.es Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Cap3Report CAP3 Sequence Assembly Program output format. iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:Cap3Report:2007-10-30T14-24-38Z Sebastien.Carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Nj_Tree Neighbour joining tree built from a TropGENE_Distance_Matrix object bioinfo.inibap.org urn:lsid:biomoby.org:objectclass:Nj_Tree:2001-09-21T16-00-00Z david.baux@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Nexus Tree MSEicPdfUrl Link to a PDFed image of an EIC (Extracted Ion Chromatogram) of an alignment, possible generated by XCMS. www.ab.wur.nl urn:lsid:biomoby.org:objectclass:MSEicPdfUrl:2008-02-05T13-31-09Z mark.fiers@wur.nl Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name ExperimentId Url PHD_Text Text Report from PHD program (Secondary structure and accesibility predictions) mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PHD_Text:2006-10-04T15-13-29Z moby-services@mmb.pcb.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content OligoTargetSpecificity Biomoby object consisting of two Object objects: one for transcriptome target specificity of the oligo, the other for genome target specificity. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoTargetSpecificity:2008-04-20T13-58-33Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com genome transcriptome GlycanScore Object to store a score for a glycan object. For example, the similarity score of Glycan id G00012 from KEGG GLYCAN. rings.t.soka.ac.jp urn:lsid:biomoby.org:objectclass:GlycanScore:2008-02-15T01-56-40Z kkiyoko@soka.ac.jp GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score GCP_SimpleCitation GCP_SimpleCitation is generally as per the Demeter model except that the date, journal source and author list attributes are modeled as simple MOBY Strings. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleCitation:2008-10-14T03-21-13Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com source date authorList GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org name valueString type ACEDB Text formatted in 'ACEDB' format www.illuminae.com urn:lsid:biomoby.org:objectclass:ACEDB:2007-02-13T17-49-36Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ABISequenceChromatogram A raw trace file coming from (or formatted as if from) an Applied Biosystems sequencing machine moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:ABISequenceChromatogram:2007-04-10T22-56-22Z gordonp@ucalgary.ca SequenceChromatogram A data series representing the intensities of various DNA bases detected in a sequencing experiment for a given DNA sample. Also known as a sequence trace, it is usually graphically represented as a graph of curved peaks, which each nucleotide given a different colour (hence the term chomatogram) moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:SequenceChromatogram:2007-04-10T22-36-13Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPunknownEvidence An imprecise evidence used by iHOP services to label text fragments cnio.es urn:lsid:biomoby.org:objectclass:iHOPunknownEvidence:2007-04-14T12-58-09Z jmfernandez@cnio.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com simple_key_value_pair Basic key/value pair object for key/value pairs with a 1:1 relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:simple_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com value key feature accession-code Accession Code for DrugBank http://redpoll.pharmacy.ualberta.ca/drugbank/ ualberta.ca urn:lsid:biomoby.org:objectclass:accession-code:2007-07-09T18-54-09Z biomoby@dhx.ath.cx text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GlycoSequence Object that can store a carbohydrate or a glyco-conjugate sequence. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoSequence:2008-02-14T14-51-57Z r.ranzinger@dkfz.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequence String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Newick_Text phylogenetic tree in Newick format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Newick_Text:2001-09-21T16-00-00Z inb@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content TransmembraneReport Transmembrane spanning regions predicted by runEmbossTmapSequence service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TransmembraneReport:2007-01-15T15-11-48Z inb@pcm.uam.es TransmembraneAnnotatedAASequence Aminoacid sequence with annotations about transmembrane regions www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TransmembraneAnnotatedAASequence:2007-01-15T15-10-30Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length TransmembraneAnnotation Annotations about transmembrane fragments www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TransmembraneAnnotation:2007-01-15T14-53-36Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start TransmembraneNumber TransmembraneFragment Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits Author A manuscript author (used by iHOP services) cnio.es urn:lsid:biomoby.org:objectclass:Author:2007-04-14T12-58-10Z jmfernandez@cnio.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com surname name b64_encoded_ppm Base 64 encoded Portable-Pixmap format image test_toppred.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:b64_encoded_ppm:2007-10-03T12-26-59Z sebastien.letort@toulouse.inra.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GeneExpressionReport Gene expression annotations. www.cnb.uam.es urn:lsid:biomoby.org:objectclass:GeneExpressionReport:2008-04-07T13-53-29Z natalia@cnb.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GeneExpressionAnnotation Annotations about gene expression www.cnb.uam.es urn:lsid:biomoby.org:objectclass:GeneExpressionAnnotation:2008-04-07T13-53-07Z natalia@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com GeneSymbol Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es mimeType rawdata GeneName Component Description ExpressionPattern ExpressionLevel ExpressionNotes GeneExpressionAnnotation HFormat-text HFormat Text bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:HFormat-text:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content TargetCondition Experimental result under treatment type or growth conditions for microarray experiment. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:TargetCondition:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ratio TranscriptionUnit Fundamental unit in considering gene. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:TranscriptionUnit:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp ProbeId Material placed on a spot on microarray to represent a biological sequence. The ProbeID comes from KOME database, e,g, AU088561, 002-168-D12. typeOfMicroArray is e.g. cDNA, oligo. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:ProbeId:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com probeid GeneId LocusID from KOME database. e.g. RO3-AC079887-30020F. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:GeneId:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp b64_Encoded_PNG Base 64 encoded PNG-format image bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:b64_Encoded_PNG:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPsentence It is a manuscript abstract sentence, composed by iHOPTextFragments (or children of iHOPTextFragments) cnio.es urn:lsid:biomoby.org:objectclass:iHOPsentence:2007-04-14T12-58-12Z jmfernandez@cnio.es iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com sentenceNumber iHOPpmid Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com journalImpact date sentencePiece glycoPNG Image of a carbohydrates or glyco-conjugates in PNG format. The binary data of the PNG is BASE64 encoded. www.glycome-db.org urn:lsid:biomoby.org:objectclass:glycoPNG:2008-02-28T13-58-45Z r.ranzinger@dkfz.de glycoImage Any of several image types that illustrate glycan structures ccrc.uga.edu urn:lsid:biomoby.org:objectclass:glycoImage:2008-02-15T02-39-46Z will@ccrc.uga.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com imageData GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ABI_Encoded Trace data in ABI format genome.imim.es urn:lsid:biomoby.org:objectclass:ABI_Encoded:2006-05-17T12-51-53Z akerhornou@imim.es Chromatogram_Encoded Generic trace binary data object genome.imim.es urn:lsid:biomoby.org:objectclass:Chromatogram_Encoded:2006-05-16T14-51-50Z akerhornou@imim.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com rawdata MotifMatrix Prosite motif matrix. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifMatrix:2007-01-12T12-56-20Z rroyo@lsi.upc.edu text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DIGDescription A concept description in DIG format eva.mpg.de urn:lsid:biomoby.org:objectclass:DIGDescription:2001-09-21T16-00-00Z hoehndorf@eva.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com description VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Equick_tandem_table Table showing the potential tandem repeats scanned in a sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Equick_tandem_table:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Start End Score Size Count sequence_alignment sequence alignment www.renci.org urn:lsid:biomoby.org:objectclass:sequence_alignment:2007-02-15T17-14-22Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iANT-xml iANT xml file (entry, feature, db_entry, db_features) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT-xml:2007-07-18T12-58-41Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ArrayFloat ArrayFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayFloat:2006-03-21T11-50-38Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Element GCP_ContactingDetails GCP_ContactingDetails represents the details of a GCP_LegalEntity relating to its localization in the human world. A GCP_LegalEntity may be located in multiple sites in the world, each of a distinct type specified by a SimpleOntologyTerm (e.g. Home, Office, etc. for Persons; Headquarters, In-Country Offices, etc. for Organizations, ). ContactingDetails obviously include information like address and an associated postalCode. GCP_ContactingDetails points to the GCP_OntologyTerm defined jurisdiction via GCP_SimpleIdentifiers. The jurisdiction of a ContactingDetail location is the local (village and/or municipality), subnational (regional) and national (country) geopolitical jurisdictions within which the address is located. The address and the communicationDetails are modeled as MOBY:String collection. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_ContactingDetails:2008-10-14T03-21-44Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com communicationDetails GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org name version description jurisdiction address GCP_SimpleClade The GCP_SimpleClade provides a lightweight version of the Clade interface, only with identification and the corresponding tree file format (e.g. Newick, NHX, phyloxml) is modeled using a GCP_SimpleFeature (whose type specifies the tree document format provided), which models the tree as publication Content. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleClade:2008-10-14T03-21-15Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type tree GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description Global_Keyword A namespace for keywords; one keyword only mips.gsf.de urn:lsid:biomoby.org:objectclass:Global_Keyword:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com FamilyBLOCKAnnotation Family BLOCK Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:FamilyBLOCKAnnotation:2006-12-11T15-44-09Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com AC Strand Combined_Evalue Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Num_blocks Description BLOCKAnnotation BLOCK Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:BLOCKAnnotation:2006-12-11T15-43-56Z rroyo@lsi.upc.edu AC Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Frame BLOCK_Evalue Blocks PlasMapperTextMap Text formatted in PlasMapper TextMap format http://wishart.biology.ualberta.ca/PlasMapper/ ualberta.ca urn:lsid:biomoby.org:objectclass:PlasMapperTextMap:2007-07-17T20-10-50Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Annotated_FunCat MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_FunCat:2008-06-13T11-28-28Z joecker@mpiz-koeln.mpg.de FunCat MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:FunCat:2008-06-13T11-27-52Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com mimeType rawdata CodonUsageTableExtended_text Table reporting several statistical measures of codon usage for a given set of sequences moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:CodonUsageTableExtended_text:2006-10-23T22-09-16Z gordonp@ucalgary.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content RefSeq_Text RefSeq plain text sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RefSeq_Text:2007-01-11T10-31-17Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SchematikonSegmentID Schematikon protein structure segment ID schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonSegmentID:2001-09-21T16-00-00Z boris.steipe@utoronto.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ID CathDomainDescription_XML CATH Domain Description. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CathDomainDescription_XML:2007-01-12T11-34-37Z inb@pcm.uam.es text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Friend Objeto Pessoa www.ucb.br urn:lsid:biomoby.org:objectclass:Friend:2001-09-21T16-00-00Z glopes@ucb.br Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Idade String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Nome GCG Text formatted in 'GCG' format www.illuminae.com urn:lsid:biomoby.org:objectclass:GCG:2007-02-13T17-50-39Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SequenceDescription_Text brief text describing the sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SequenceDescription_Text:2007-01-15T15-28-11Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PMUT_Text PMUT report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PMUT_Text:2006-03-28T13-37-11Z gelpi@bq.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Zip_Encoded A Zip file encoded in Base-64. inb.bsc.es urn:lsid:biomoby.org:objectclass:Zip_Encoded:2007-09-27T10-45-05Z romina.royo@bsc.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com rawdata mimeTypte SpecimenUnit A container for all data referring to a unit (specimen or observation record) www.mncn.csic.es urn:lsid:biomoby.org:objectclass:SpecimenUnit:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com RecordBasis An indication of what the unit record describes. Note that the element SourceReference provides for the case that the record is based on a publication. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:RecordBasis:2001-09-21T16-00-00Z jatorre@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com RecordBasis RecordBasis GatheringSite Elements describing the field events that created the unit and their location. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:GatheringSite:2001-09-21T16-00-00Z jatorre@gmail.com Locality Original locality data as appearing on a label or in an original entry. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Locality:2001-09-21T16-00-00Z jatorre@gmail.com LocalityText Locality Coordinates Element that allows the recording of the latitude and longitude of a recording or collecting position. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Coordinates:2001-09-21T16-00-00Z jatorre@gmail.com CoordinatesText LongitudeDecimal Maps to Darwin Core 2: Longitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LongitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com LongitudeDecimal LongitudeDecimal LatitudeDecimal Maps to Darwin Core 2: Latitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LatitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com LatitudeDecimal LatitudeDecimal SpatialDatum Mathematical surface on which the mapping and coordinate system used for the geocodes of the record are based www.mncn.csic.es urn:lsid:biomoby.org:objectclass:SpatialDatum:2001-09-21T16-00-00Z jatorre@gmail.com SpatialDatum SpatialDatum Coordinates GatheringSite GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length GenericSequence Identification In cases where more than one name applies to a single unit, several identifications should be formed and flagged as preferred. Relationships between differently identified sub-units of the unit can be specified by means of the IdentificationRole. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Identification:2001-09-21T16-00-00Z jatorre@gmail.com DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com IdentificationDate TaxonName GBIF - Concatenated scientific name, preferrably formed in accordance with a Code of Nomenclature, i. e. a monomial, bionomial, or trinomial plus author(s) or author team(s) and - where relevant - year, or the name of a cultivar or cultivar group, or a hybrid formula, as fully as possible. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:TaxonName:2001-09-21T16-00-00Z jatorre@gmail.com TaxonName FirstEpithet GBIF - The first epithet in a botanical name combination (species epithet or the epithet of the subdivision of a genus. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:FirstEpithet:2001-09-21T16-00-00Z jatorre@gmail.com FirstEpithet FirstEpithet Genus GBIF test - Genus www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Genus:2001-09-21T16-00-00Z jatorre@gmail.com Genus InfraspecificEpithet GBIF - The final epithet of a botanical name of infraspecific rank. AppInfo Nothing found. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:InfraspecificEpithet:2001-09-21T16-00-00Z jatorre@gmail.com InfraspecificEpithet InfraspecificEpithet TaxonIdentified Identification iHOPevidence It is an iHOP evidence of a gene or protein name cnio.es urn:lsid:biomoby.org:objectclass:iHOPevidence:2007-04-14T12-57-58Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com organism iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content Clade A clade from the NCBI_Taxonomy. Contains a String object describing the name of the clade. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Clade:2007-10-31T17-32-51Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name Password A generic password object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Password:2006-03-01T18-35-15Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Field A database field name. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Field:2006-03-01T18-35-18Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pepstats_Text Pepstats report. inb.bsc.es urn:lsid:biomoby.org:objectclass:Pepstats_Text:2007-01-19T16-11-47Z rroyo@lsi.upc.edu text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Clustalw_Text Clustalw multiple sequence alignment report. org.inab.upc urn:lsid:biomoby.org:objectclass:Clustalw_Text:2006-02-28T12-39-01Z rroyo@lsi.upc.edu Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_GermplasmStudy GCP_GermplasmStudy is a kind of Study that characterises a GCP_GermplasmSet of germplasm (identified for retrieval by a GCP_SimpleIdentifier) and documenting growthConditions and treatments as MOBY:Collections of GCP_SimpleFeature objects (with feature types defined by a suitable ontology). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmStudy:2008-10-14T03-21-32Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name treatments GCP_Study GCP_Study, inherits from GCP_Entity and records general meta-data (but not the data contents) of a study. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Study:2008-10-14T03-21-28Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies project investigators factors variates effects germplasm growthConditions Frequencies Lightweight object containing the string value representing the genotype and the allele frequencies obtained from the HapMap project. icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Frequencies:2006-08-18T03-26-18Z youngcsong@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Frequency PepNovoReport De Novo peptides reported by PepNovo service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:PepNovoReport:2007-01-15T14-55-49Z inb@pcm.uam.es ProbMolWeightsAnnotatedAASequence De novo peptide sequence with annotations about mw and probability www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbMolWeightsAnnotatedAASequence:2007-01-15T14-55-25Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ProbMolWeightAnnotation Annotations about de novo peptide sequence inferred by PepNovo www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbMolWeightAnnotation:2007-01-15T14-54-34Z inb@pcm.uam.es MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight DeNovoPeptide Probability Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits GCP_HoldingInstitute GCP_HoldingInstitute is an organization that has one more more instances of GCP_GermplasmCollection, dereferenced by GCP_SimpleIdentifiers. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_HoldingInstitute:2008-10-14T03-22-27Z r.bruskiewich@cgiar.org GCP_Organization A GCP_LegalEntity specific to an organization entity recognized in legal terms as having a legal personality (i.e. able to own property, liable for legal prosecution, etc.) www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Organization:2008-10-14T03-21-55Z r.bruskiewich@cgiar.org GCP_LegalEntity GCP_LegalEntity represents a general subclass for any GCP_Entity recognized in legal terms as having a legal personality (i.e. ability to have human behaviour as an individual or in aggregate, able to own property, liable for legal prosecution, etc.). This includes both person and organization. - contactingDetails. A LegalEntity obviously has details relating to its localization in the human world. For efficiency, we treat instances of another moby data type, GCP_ContactingDetails, as a subclass of GCP_Identifier, and referencing these details from GCP_LegalEntity using the pertinent GCP_SimpleIdentifier. A LegalEntity may have several such contactingDetails. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LegalEntity:2008-10-14T03-21-54Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies contactingDetails collections ProbIDReport De Novo peptides reported by ProbID service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbIDReport:2007-01-15T14-59-35Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ProbIDAnnotatedAASequence De novo peptide sequence with ProbID annotations www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbIDAnnotatedAASequence:2007-01-15T14-57-39Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ProbIDAnnotation Annotations about de novo peptide sequence inferred by ProbID www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbIDAnnotation:2007-01-15T14-56-39Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start ProbIDPeptide ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com PosteriorProb MatchedIons BayScore ZScore Annotations AnnotatedSequence JPEGFormatImage An image in Joint Photographic Experts Group format (typically a photograph, with lossy compression) moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:JPEGFormatImage:2007-04-18T15-02-29Z gordonp@ucalgary.ca WebFormatImage A 2D visual representation in a format whsoe rendering is supported by the major Web browsers moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:WebFormatImage:2007-04-10T23-22-43Z gordonp@ucalgary.ca Image A 2 dimensional visual element moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Image:2007-04-10T23-19-22Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SwissProt_Text Swiss-Prot plain text sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SwissProt_Text:2007-01-12T10-54-09Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_GermplasmCollection GCP_GermplasmCollection is simply a set of germplasm, or rather, GCP_GermplasmNeighbourhood, that are managed by some legal entity, the owner, designated as the GCP_HoldingInstitute. The stocks of a GCP_GermplasmCollection are identified by GCP_SimpleIdentifiers that should resolve to those GCP_GermplasmNeighbourhood entries in the collection. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmCollection:2008-10-14T03-20-59Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name owner stocks GeneId LocusID from KOME database. e.g. RO3-AC079887-30020F. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:GeneId:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MSCmlspect A cmlspect file containing peak information from a MassSpec experiment ab.wur.nl urn:lsid:biomoby.org:objectclass:MSCmlspect:2008-05-29T09-02-53Z mark.fiers@wur.nl String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ExperimentId SampleId CmlSpect Annotated_EC_Number EC number mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_EC_Number:2008-06-13T11-24-52Z joecker@mpiz-koeln.mpg.de EC_Number EC number mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:EC_Number:2008-06-13T11-23-05Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description KCF Sequence object for carbohydrates or glyco-conjugates in KCF format. rings.t.soka.ac.jp urn:lsid:biomoby.org:objectclass:KCF:2008-05-09T05-26-50Z kkiyoko@soka.ac.jp GlycoSequence Object that can store a carbohydrate or a glyco-conjugate sequence. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoSequence:2008-02-14T14-51-57Z r.ranzinger@dkfz.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequence AlignedDNASeqs DNA sequences that have been aligned according to some method and similarity measure moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AlignedDNASeqs:2007-07-30T22-48-58Z gordonp@ucalgary.ca AlignedSequences A set of sequences (AA or DNA) that have been aligned according to some method and similarity measure moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AlignedSequences:2007-07-30T22-43-30Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GappedDNASequence A DNA sequence with hyphens that represent gaps, e.g. as found in a sequence alignment moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:GappedDNASequence:2007-07-30T22-40-36Z gordonp@ucalgary.ca DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length sequence GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com NCBI_Blast_XML_Gif XML formatted NCBI Blast report with a graphical display of the hits mips.gsf.de urn:lsid:biomoby.org:objectclass:NCBI_Blast_XML_Gif:2001-09-21T16-00-00Z D.Haase@gsf.de b64_encoded_gif Base 64 encoded GIF-format image www.illuminae.com urn:lsid:biomoby.org:objectclass:b64_encoded_gif:2001-09-21T16-00-00Z markw@illuminae.com text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content hitGraph NCBI_Blast_XML XML formatted NCBI Blast report www.illuminae.com urn:lsid:biomoby.org:objectclass:NCBI_Blast_XML:2001-09-21T16-00-00Z markw@illuminae.com text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com iHOPinteractionList Results related to an iHOP symbol: sentences showing interaction evidences related to the symbol cnio.es urn:lsid:biomoby.org:objectclass:iHOPinteractionList:2007-04-14T12-58-22Z jmfernandez@cnio.es iHOPrelatedInfo Information related to an iHOP symbol: sentences showing interaction evidences related to the symbol or sentences used to define the symbol inside iHOP system cnio.es urn:lsid:biomoby.org:objectclass:iHOPrelatedInfo:2007-04-14T12-58-19Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPsymbol It is an iHOP symbol of a gene or protein, supported by evidences cnio.es urn:lsid:biomoby.org:objectclass:iHOPsymbol:2007-04-14T12-58-00Z jmfernandez@cnio.es iHOPevidence It is an iHOP evidence of a gene or protein name cnio.es urn:lsid:biomoby.org:objectclass:iHOPevidence:2007-04-14T12-57-58Z jmfernandez@cnio.es organism iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content homolog synonym description symbol iHOPsentence It is a manuscript abstract sentence, composed by iHOPTextFragments (or children of iHOPTextFragments) cnio.es urn:lsid:biomoby.org:objectclass:iHOPsentence:2007-04-14T12-58-12Z jmfernandez@cnio.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com sentenceNumber iHOPpmid Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com journalImpact date sentencePiece sentence AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length StructureFragment Information on structure fragment boundaries mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureFragment:2006-10-05T09-47-10Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com NumResidues StructureBoundaries Information on structure boundaries of segments, fragments, domains, etc. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureBoundaries:2006-10-05T09-10-02Z moby-services@mmb.pcb.ub.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Chain codon_usage_table codon usage table www.renci.org urn:lsid:biomoby.org:objectclass:codon_usage_table:2007-02-19T22-27-21Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content User A generic user object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:User:2006-03-01T18-35-16Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Email An e-mail address object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Email:2006-03-01T18-35-14Z pieter.neerincx@gmail.com email Password A generic password object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Password:2006-03-01T18-35-15Z pieter.neerincx@gmail.com password InterProScanResult_Raw InterProScan result file in raw format bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:InterProScanResult_Raw:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ShiftYPredictionReport A report of predicted 1H, 13C, and 15N chemical shifts based on a protein sequence. ualberta.ca urn:lsid:biomoby.org:objectclass:ShiftYPredictionReport:2007-08-16T01-10-55Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Consensus_Sequence_Text Consensus sequences reflect the most common choice of base or amino acid at each position of a series of related DNA, RNA or protein sequences. inb.bsc.es urn:lsid:biomoby.org:objectclass:Consensus_Sequence_Text:2007-01-19T15-51-18Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GlydeII Sequence object for carbohydrates or glyco-conjugates in GlydeII encoding. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlydeII:2008-02-14T14-54-19Z r.ranzinger@dkfz.de GlycoSequence Object that can store a carbohydrate or a glyco-conjugate sequence. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycoSequence:2008-02-14T14-51-57Z r.ranzinger@dkfz.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequence ProbIDAnnotation Annotations about de novo peptide sequence inferred by ProbID www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbIDAnnotation:2007-01-15T14-56-39Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length ProbIDPeptide ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com PosteriorProb MatchedIons BayScore ZScore MGIS_ACCESSION Accessions in the MGIS database biomoby.inibap.org urn:lsid:biomoby.org:objectclass:MGIS_ACCESSION:2001-09-21T16-00-00Z m.rouard@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Biotic_stress_Yellowsig mcpd:ORIGCTY mgis:SECTION mcpd:SPECIES mcpd:COLLCODE Biotic_stress_Blacksig Biotic_stress_Fusarium Biotic_stress_pseudomonas Biotic_stress_Radopholus Biotic_stress_Pratylenchuscof Biotic_stress_Pratylenchusgood Biotic_stress_cosmopolites Abiotic_stress_Lowtemp Abiotic_stress_Drought Abiotic_stress_Flooding Abiotic_stress_Mineraldef Abiotic_stress_Winds Abiotic_stress_Soilacidity Abiotic_stress_Manganesetox Abiotic_stress_Hightemp InterProMotifAnnotation InterPro Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:InterProMotifAnnotation:2007-01-12T12-55-44Z rroyo@lsi.upc.edu ScoredMotifAnnotation Scored Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotation:2007-01-12T12-54-17Z rroyo@lsi.upc.edu MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com AC ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score DB Evidence Status DotBracketFasta DotBracketFasta is a format to cobine a sequence and its secondary structure in one string. This pair of sequence and secondary structure starts with '>' and the sequence name. The next line contains the sequence data (FASTA format). The third line represents the secondary structure and consists of . ( ) [ ] { } < > (Dot-Bracket Format). Further pairs of sequences and secondary structure are possible. >Sequence_1 UAAUCGGGUGCAACUCCCGCCCUUUUCCGAGGUCAUCGGA ....((((.......))))[[....{{{{{]]...}}}}} >Sequence_2 UAAUCGGGUGCAACUAACCGGAACCUCCGAGGUCAUCGGA ....((((..(()).))))[[....{{{{{]]...}}}}} www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:DotBracketFasta:2008-03-12T09-22-30Z web@uni-bielefeld.de FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BlocksAnnotatedAASequence BLOCKS annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:BlocksAnnotatedAASequence:2006-12-11T15-44-12Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length FamilyBLOCKAnnotation Family BLOCK Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:FamilyBLOCKAnnotation:2006-12-11T15-44-09Z rroyo@lsi.upc.edu AC Strand Combined_Evalue Num_blocks Description BLOCKAnnotation BLOCK Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:BLOCKAnnotation:2006-12-11T15-43-56Z rroyo@lsi.upc.edu AC Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Frame BLOCK_Evalue Blocks Annotations text-html HTML www.illuminae.com urn:lsid:biomoby.org:objectclass:text-html:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content WU_BLAST_Text Plaintext Blast report from WU-Blast software www.illuminae.com urn:lsid:biomoby.org:objectclass:WU_BLAST_Text:2001-09-21T16-00-00Z markw@illuminae.com BLAST-Report A parent node for all of the different types of Blast reports bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:BLAST-Report:2006-07-06T21-23-16Z markw@illuminae.com Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BriefOccurrenceRecord Brief description of a taxon returned by the GBIFGetTaxonConcepts. www.gbif.org urn:lsid:biomoby.org:objectclass:BriefOccurrenceRecord:2006-08-14T13-00-51Z fdelcastillo@gbif.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ResourceId CountryCode TaxonCanonical TaxonId SCOPDomain Domain entry from SCOP database inb.bsc.es urn:lsid:biomoby.org:objectclass:SCOPDomain:2007-05-10T12-22-41Z atorrano@bsc.es StructureDomain Information on structure domains mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureDomain:2006-10-05T09-59-53Z moby-services@mmb.pcb.ub.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name StructureBoundaries Information on structure boundaries of segments, fragments, domains, etc. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureBoundaries:2006-10-05T09-10-02Z moby-services@mmb.pcb.ub.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com End Start Chain Segments SCOPLayerNode Internal information from hierarchy at SCOP database inb.bsc.es urn:lsid:biomoby.org:objectclass:SCOPLayerNode:2007-05-10T12-22-30Z atorrano@bsc.es comentary Class GCP_Factor Factors are the independent (applied) variables to a study. GCP_Study objects dereference their factors via a MOBY:Collection of GCP_SimpleIdentifier objects that resolve to GCP_Factor objects. GCP_Factor inherits most of its functionality from GCP_Feature. The type of feature is the factor "property", the unit of the feature is the factor "scale" and the supportingEvidence documents the factor "method" (sensu ICIS DMS). GCP_Factor reports its levels as a GCP_Constraint. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Factor:2008-10-14T03-22-04Z r.bruskiewich@cgiar.org GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com constraintDefinition GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org name levels GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data constraints values MicroArrayData_Text Micro-array data in text format representing gene expression patterns. Each line must have the gene name and the expression values and the expression values for each condition. All the data items must be separated by tabulators genome.imim.es urn:lsid:biomoby.org:objectclass:MicroArrayData_Text:2006-03-27T12-19-28Z akerhornou@imim.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content TropGENE_ALLELE_FREQUENCY table of allele frequency for a pool of accessions, ordered by type of markers and locus tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:TropGENE_ALLELE_FREQUENCY:2001-09-21T16-00-00Z david.baux@cirad.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FSSP_Text FSSP plain text. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:FSSP_Text:2007-01-11T09-57-27Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GazInput Gazeteer input cipotato.org urn:lsid:biomoby.org:objectclass:GazInput:2001-09-21T16-00-00Z r.simon@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com inputString exactMatch key MSRawCdfUrlSet A set of urls (http/ftp) of raw, cdf formatted, output of a Mass Spectrometry experiment. www.ab.wur.nl urn:lsid:biomoby.org:objectclass:MSRawCdfUrlSet:2008-02-04T09-56-20Z mark.fiers@wur.nl MSRawCdfUrl the url (http/ftp) of raw, cdf formatted, output of a Mass Spectrometry experiment. www.ab.wur.nl urn:lsid:biomoby.org:objectclass:MSRawCdfUrl:2008-02-04T09-44-55Z mark.fiers@wur.nl String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Url Name SampleId ExperimentId Spectra Jackknifer Text formatted in 'jackknifer' format www.illuminae.com urn:lsid:biomoby.org:objectclass:Jackknifer:2007-02-13T17-51-31Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content genomeSNP SNP at arbitrary position in the genome www.weigelworld.org urn:lsid:biomoby.org:objectclass:genomeSNP:2006-06-26T15-41-39Z stephan.ossowski@tuebingen.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com strain Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com confidence base_var base_ref Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp end start chromosome pos SchematikonStructureAnnotation DSSP, STRIDE, and PROMOTIF annotation for a Schematikon structure segment / structure motif schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonStructureAnnotation:2001-09-21T16-00-00Z boris.steipe@utoronto.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com PROMOTIF gamma-turn PROMOTIF beta-turn DSSP STRIDE multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com value key BacMapGeneCard U of A, Genome Canada, BacMap http://wishart.biology.ualberta.ca/BacMap/ Text formatted as a Gene Card ualberta.ca urn:lsid:biomoby.org:objectclass:BacMapGeneCard:2007-08-23T23-14-09Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content TreeDet_Annotation_XML XML annotation that embedes results from Tree-Determinant methods: FASS, MB, S (Predicting Funtional Residues in Protein Sequence Alignments). cnio.es urn:lsid:biomoby.org:objectclass:TreeDet_Annotation_XML:2007-11-07T15-31-21Z jmrodriguez@cnio.es text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PlotReport A report composed only by a set of plots. inb.bsc.es urn:lsid:biomoby.org:objectclass:PlotReport:2007-01-12T14-53-55Z atorrano@lsi.upc.edu ArrayImage_Encoded An Array filled with Image_Encoded elements. inb.bsc.es urn:lsid:biomoby.org:objectclass:ArrayImage_Encoded:2007-01-12T14-52-48Z atorrano@lsi.upc.edu Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementImage_Encoded Image_Encoded belonging to an Array. inb.bsc.es urn:lsid:biomoby.org:objectclass:ElementImage_Encoded:2007-01-12T14-52-29Z atorrano@lsi.upc.edu Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com mimeType rawdata Value elements description application name text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GI_ClusterAssignment Assigns a gene symbol for a certain species to a GeneIlluminator Cluster with a certain probability. Used for gene symbol disambiguation. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GI_ClusterAssignment:2007-10-31T17-32-54Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com gene_symbol Organism An organism object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Organism:2006-03-01T18-35-20Z pieter.neerincx@gmail.com organism Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com probability gi_cluster PrimerPair A Sequence primer pair datatype. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:PrimerPair:2007-03-14T17-27-02Z ekawas@mrl.icapture.ubc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name first_primer second_primer OligoHit Biomoby object consisting of a HitPosition object and a Moby CrossReference Information Block (CRIB). The CRIB lists evidence for gene expression of the sequence in the HitPosition object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoHit:2008-04-20T13-58-31Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com HitPosition Biomoby object consisting of a MapPosition object (A position on a genetic map. Can be used to denote a sequence ID and its start and stop co-ordinates with respect to another sequence to which it is aligned), an Object object (to denote the orientation of this sequence with respect to the sequence to which it is aligned) and a String object (to denote the corresponding cigar like line of the alignment). * Cigar like line (CLL): A compact way to represent the alignment between 2 sequences. It defines the sequence of matches(M), substitutions/mismatches(S), insertions(I) or deletions(D) on the second sequence with respect to the first based on this alignment. In addition, the presence of introns(N) between High Scoring Pairs (HSPs) of a hit obtained from an alignment of the two sequences by BLAT/BLAST etc. can also be represented. For example: * 8M2S50M would be 8 matches followed by 2 substitutions (mismatches)and finally 50 matches * 30M400N30M would be two HSPs of 30 matches each seperated by an intron of length 400 bp * 2M1I25M1D6M would be 2 matches, an insertion in the hit, 25 matches, a gap in the hit and 6 matches. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:HitPosition:2008-04-20T13-58-30Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com cll MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end strand hit_position PDB-formatted-text PDB formatted text bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:PDB-formatted-text:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content RestrictReport Enzyme restriction cleavage sites reported by runEmbossRestrictFromID service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RestrictReport:2007-01-15T15-19-12Z inb@pcm.uam.es RestrictAnnotatedNASequence Nucleotidic sequence with annotations about restriction enzyme cleavage sites. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RestrictAnnotatedNASequence:2007-01-15T15-18-53Z inb@pcm.uam.es AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description RestrictAnnotation Annotations about restriction enzyme cleavage sites. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RestrictAnnotation:2007-01-15T15-05-51Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits AlignedSequences A set of sequences (AA or DNA) that have been aligned according to some method and similarity measure moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AlignedSequences:2007-07-30T22-43-30Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com CodingSNP SNPs in coding region with codons and aminoacids www.weigelworld.org urn:lsid:biomoby.org:objectclass:CodingSNP:2006-06-27T14-31-56Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome Position Strain codon_ref aa_ref codon_var aa_var aa_pos Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca aa_change iANT_entry_features-xml iANT entry features (iANT::DB::Feature) xml file. This xml format describe the list of features and patterns for one entry. iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT_entry_features-xml:2007-07-18T14-29-44Z Sebastien.Carrere@toulouse.inra.fr iANT-xml iANT xml file (entry, feature, db_entry, db_features) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT-xml:2007-07-18T12-58-41Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PubMed-MEDLINE Pubmed article in MEDLINE display format prometheus.brc.mcw.edu urn:lsid:biomoby.org:objectclass:PubMed-MEDLINE:2001-09-21T16-00-00Z vnarayan@mcw.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content OrganismsLongName Long name of organisms. test.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:OrganismsLongName:2007-10-15T13-19-18Z sebastien.letort@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content OligoTargets Biomoby object consisting of one or more Record objects with detailed information about an oligo target and a CRIB with cross references to oligos. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoTargets:2008-01-10T16-16-04Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Record A database record containing zero or more String objects. String articleName attribute = field name. String content = field data. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Record:2006-03-01T18-35-13Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com record record BLAST_XML Blast XML format. inb.bsc.es urn:lsid:biomoby.org:objectclass:BLAST_XML:2007-01-12T12-54-29Z rroyo@lsi.upc.edu text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GI_Cluster A cluster of gene symbols and their names all pointing to the same gene. Contains also terms describing the function of this gene and clades describing in which parts of the tree of life these gene symbols all point to the same gene. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GI_Cluster:2007-10-31T17-32-52Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GI_Gene A GeneIlluminater gene object. Contains a gene symbol and a gene name where the symbol is the abbreviated form of the name. Gene names and symbols can be placed in a certain namespace to denote the status of the gene and the organisation who assigned this status (Namespaces are labelled [Organisation]_[Statuslike] like for example HGNC_Approved, HGNC_Pending, HGNC_Reserved, HGNC_Withdrawn, UniProt_Name, UniProt_Synomym, UniProt_OLN, UniProt_ORF) GeneIlluminator analyses synomyms and homonyms and clusters symbols for the same gene. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GI_Gene:2007-10-31T17-32-47Z pieter.neerincx@gmail.com symbol name gi_gene GI_Function A function assigned to a gene using GeneIlluminater. Contains a String object describing the function and a Float object listing the occurence (percentage) of this function in the descriptions of this gene for different species. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GI_Function:2007-10-31T17-32-50Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com occurrence gi_function Clade A clade from the NCBI_Taxonomy. Contains a String object describing the name of the clade. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Clade:2007-10-31T17-32-51Z pieter.neerincx@gmail.com name clade text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Decypher_Text Alignment text output from Decypher hardware search accelerator coe01.ucalgary.ca urn:lsid:biomoby.org:objectclass:Decypher_Text:2001-09-21T16-00-00Z cheny@coe01.ucalgary.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DrugCard Drug Card text format used in Drug Bank, http://redpoll.pharmacy.ualberta.ca/drugbank/ ualberta.ca urn:lsid:biomoby.org:objectclass:DrugCard:2007-07-13T16-10-16Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com IMGA_Accession IMGA (http://medicago.org/genome/IMGAG.php) accession code bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:IMGA_Accession:2001-09-21T16-00-00Z Jerome.Gouzy@toulouse.inra.fr String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content text_postscript postscript text www.renci.org urn:lsid:biomoby.org:objectclass:text_postscript:2007-02-15T16-53-15Z jdr0887@renci.org text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Tropgene_accession data types containing Accession, locus and allele identifiers tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:Tropgene_accession:2001-09-21T16-00-00Z m.ruiz@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Tropgene_locus data types containing locus and allele identifiers tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:Tropgene_locus:2001-09-21T16-00-00Z m.ruiz@cirad.fr allele Tropgene_banana phylogenetic_tree phylogenetic tree www.renci.org urn:lsid:biomoby.org:objectclass:phylogenetic_tree:2007-02-15T17-07-38Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Genotype This is a genotype object cegen.upf.es urn:lsid:biomoby.org:objectclass:Genotype:2001-09-21T16-00-00Z josep.alegre@upf.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com snp sample result ProbMolWeightsAnnotatedAASequence De novo peptide sequence with annotations about mw and probability www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbMolWeightsAnnotatedAASequence:2007-01-15T14-55-25Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ProbMolWeightAnnotation Annotations about de novo peptide sequence inferred by PepNovo www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ProbMolWeightAnnotation:2007-01-15T14-54-34Z inb@pcm.uam.es MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight DeNovoPeptide Probability Annotations Amigo Objeto Pessoa www.ucb.br urn:lsid:biomoby.org:objectclass:Amigo:2001-09-21T16-00-00Z glopes@ucb.br Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Nome Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Idade mmCIF_Text PDB entry in mmCIF format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:mmCIF_Text:2007-01-12T11-09-43Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PDBLigand Information about a PDB ligand mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PDBLigand:2006-10-03T10-13-15Z adam@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com formula Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com mw Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com charge synonyms numAtoms name AnnotatedTable Tabular data described with a header and a caption moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AnnotatedTable:2007-06-26T22-05-51Z gordonp@ucalgary.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com caption tableRow A row of data for a tabular object moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:tableRow:2007-06-21T15-47-03Z gordonp@ucalgary.ca cell header table Tabular (row-based) data moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:table:2007-06-25T23-20-32Z gordonp@ucalgary.ca row Descriptor An object intended to hold the title or description of the identifier in the id field. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Descriptor:2006-08-16T00-40-37Z ekawas@mrl.ubc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description DGPI_report runDGPIGenericSequence report. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:DGPI_report:2001-09-21T16-00-00Z inb@pcm.uam.es text-html HTML www.illuminae.com urn:lsid:biomoby.org:objectclass:text-html:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Structure_Alignment_report Structure alignment report. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Structure_Alignment_report:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com text-html HTML www.illuminae.com urn:lsid:biomoby.org:objectclass:text-html:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content Report PDB-Enriched PDB structure together with a Jmol script and a html description. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:PDB-Enriched:2001-09-21T16-00-00Z inb@pcm.uam.es JmolScript Description PSea-text-formatted Text formatted by PSea bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:PSea-text-formatted:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Pair_Text Pair-wise sequence default format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Pair_Text:2001-09-21T16-00-00Z inb@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_FeatureSet A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_FeatureSet:2008-10-14T03-22-22Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type features text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BlastJob A BLAST job. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:BlastJob:2006-03-01T18-36-20Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Program A generic program object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Program:2006-03-01T18-35-17Z pieter.neerincx@gmail.com program DataBase A database object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:DataBase:2006-03-01T18-35-12Z pieter.neerincx@gmail.com database FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content fasta MolWeightsAnnotatedAASequence Molecular weights annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightsAnnotatedAASequence:2007-01-12T14-48-02Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight Annotations text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PepMWValuesTable pepcoil output www.renci.org urn:lsid:biomoby.org:objectclass:PepMWValuesTable:2008-06-04T13-33-50Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content WebFormatImage A 2D visual representation in a format whsoe rendering is supported by the major Web browsers moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:WebFormatImage:2007-04-10T23-22-43Z gordonp@ucalgary.ca Image A 2 dimensional visual element moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Image:2007-04-10T23-19-22Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GenBank_Text GenBank plain text sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:GenBank_Text:2007-01-12T10-26-14Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Charge This datatype encapsulates amino acid charge information mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Charge:2007-04-16T18-57-25Z ekawas@mrl.icapture.ubc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com position String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com residue Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com charge HMMSearch_Report Reports the results of searching a set of sequences with a HMM profile. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:HMMSearch_Report:2006-03-21T11-45-06Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Header Sequences Domains Stockholm_Text Multiple sequence alignment in Stockholm format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Stockholm_Text:2006-03-21T11-44-50Z inb@pcm.uam.es Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com content Alignments Histogram Statistics GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MatrixString MatrixString object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:MatrixString:2006-03-21T11-52-31Z inb@pcm.uam.es Matrix Matrix object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Matrix:2006-03-21T11-48-31Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ArrayString ArrayString object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayString:2006-03-21T11-52-20Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Key ElementString ElementString object for string arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementString:2006-03-21T11-52-03Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Value Element Array Program A generic program object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Program:2006-03-01T18-35-17Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com KO_Term KEGG ontology term mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:KO_Term:2008-06-13T11-25-35Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Locus A lightweight object representing a Locus. The namespace and id should indicate the specific Locus being described. The contained Allele objects may be used to indicate a series of Alleles for that locus, if appropriate. If there is no Allele information, or if specification of an Allele is not appropriate (e.g. in the case of a MappedLocus object), then a single Allele object with blank namespace, id, and description would be appropriate. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Locus:2006-06-29T16-56-19Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Allele A lightweight object representing an Allele. The namespace and id should indicate the specific Allele being described. The contained String object is a human-readable description of the Allele in whatever form is most appropriate (e.g. the phenotype). bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Allele:2006-06-29T16-47-03Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Allele ElementInteger ElementInteger object for integer arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementInteger:2006-03-21T11-51-55Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key Value InterProMotifAnnotatedAASequence InterPro motif annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:InterProMotifAnnotatedAASequence:2007-01-12T12-57-33Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length InterProMotifAnnotation InterPro Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:InterProMotifAnnotation:2007-01-12T12-55-44Z rroyo@lsi.upc.edu ScoredMotifAnnotation Scored Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotation:2007-01-12T12-54-17Z rroyo@lsi.upc.edu MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start AC ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score DB Evidence Status Annotations FastaConsensiFromGroup2 Fasta Object www.genoma.com urn:lsid:biomoby.org:objectclass:FastaConsensiFromGroup2:2001-09-21T16-00-00Z viniciusandrade@brturbo.com.br String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com autor date fasta groupCod projectName AntigenicReport Antigenic report. inb.bsc.es urn:lsid:biomoby.org:objectclass:AntigenicReport:2007-01-12T12-53-06Z rroyo@lsi.upc.edu AntigenicAnnotatedAASequence Antigenic sites annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AntigenicAnnotatedAASequence:2007-01-12T12-52-13Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length AntigenicAnnotation Annotation of antigenic sites. inb.bsc.es urn:lsid:biomoby.org:objectclass:AntigenicAnnotation:2007-01-12T12-52-11Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score Max_score_pos Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits CompartmentPrediction The results of a compartment prediction program e.g. TargetP or Predotar atidb.org urn:lsid:biomoby.org:objectclass:CompartmentPrediction:2001-09-21T16-00-00Z matthew.couchman@bbsrc.ac.uk String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com compartment Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com c_score m_score o_score s_score MappingSequence NucleotideSequence, fasta file for mapping, allowed mismatches www.weigelworld.org urn:lsid:biomoby.org:objectclass:MappingSequence:2006-06-27T13-47-15Z stephan.ossowski@tuebingen.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SeqDB Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Mismatches NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length Image_PNG A new version of container for a PNG image, base64 encoded in a string. objects.jmoby.net urn:lsid:biomoby.org:objectclass:Image_PNG:2001-09-21T16-00-00Z martin.senger@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com imagedata GCP_Protocol A GCP_Protocol documents the parameters of general experimental conditions (e.g. reagents, temperatures, etc.) of a specific laboratory manipulation, as a list of GCP_SimpleFeature annotation. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Protocol:2008-10-14T03-22-20Z r.bruskiewich@cgiar.org GCP_BiblioReference Aside from the MOBY modeling considerations noted above in the introduction, GCP_BiblioReference is generally as per the corresponding Demeter model except for the following attributes. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_BiblioReference:2008-10-14T03-22-14Z r.bruskiewich@cgiar.org GCP_SimpleCitation GCP_SimpleCitation is generally as per the Demeter model except that the date, journal source and author list attributes are modeled as simple MOBY Strings. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleCitation:2008-10-14T03-21-13Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com source date authorList GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org name valueString type format language publisher metaData authors contributors indexings content parameters SNPList New line delimited list of SNP's www.renci.org urn:lsid:biomoby.org:objectclass:SNPList:2007-01-25T16-28-06Z jdr0887@renci.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String Sputnik-Report Text formatted in 'Sputnik' format www.illuminae.com urn:lsid:biomoby.org:objectclass:Sputnik-Report:2007-02-13T16-34-51Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content protein_composition_table protein composition table www.renci.org urn:lsid:biomoby.org:objectclass:protein_composition_table:2007-02-20T06-10-50Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content nsSNP_protein Contains two string values: aa_var, aa_pos icapture.ubc.ca urn:lsid:biomoby.org:objectclass:nsSNP_protein:2006-03-31T20-49-34Z ycsong@student.cs.uwaterloo.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com aa_var aa_pos MapMan_Bin MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:MapMan_Bin:2008-06-13T11-26-56Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com iHOPsymbol It is an iHOP symbol of a gene or protein, supported by evidences cnio.es urn:lsid:biomoby.org:objectclass:iHOPsymbol:2007-04-14T12-58-00Z jmfernandez@cnio.es iHOPevidence It is an iHOP evidence of a gene or protein name cnio.es urn:lsid:biomoby.org:objectclass:iHOPevidence:2007-04-14T12-57-58Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com organism iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content homolog synonym description GOTerm A term from the Gene ontology database. inb.bsc.es urn:lsid:biomoby.org:objectclass:GOTerm:2007-01-12T14-53-05Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Accession Name Definition Comment Ontology Synonym Image A 2 dimensional visual element moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Image:2007-04-10T23-19-22Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPinteractionList-XML An iHOPinteractionList XML document from iHOP web services cnio.es urn:lsid:biomoby.org:objectclass:iHOPinteractionList-XML:2007-04-14T12-57-55Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BLOCKAnnotation BLOCK Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:BLOCKAnnotation:2006-12-11T15-43-56Z rroyo@lsi.upc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com AC Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com End Start Frame BLOCK_Evalue Transmembrane_table Table showing the predicted transmembrane spanning regions in a sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Transmembrane_table:2001-09-21T16-00-00Z inb@pcm.uam.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Start End FragmentNumber String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Subsequence Computador Descricao Computador www.genoma.com urn:lsid:biomoby.org:objectclass:Computador:2001-09-21T16-00-00Z guilhermelsfonseca@yahoo.com.br Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com qtdeProcessadores String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com modelo AlignmentML AlignmentML is a XML schema for representing multiple sequence alignments www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:AlignmentML:2008-03-04T11-58-27Z web@uni-bielefeld.de BioDom BioDOM is a JAVA library for converting native non-XML output from various bioinformatic tools to XML formats that can be validated against XMLSchemas. www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:BioDom:2008-03-04T11-47-16Z web@uni-bielefeld.de text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BasicGFF3MultiFeature An object containing all components necessary to represent a simple GFF-compliant sequence feature (the content is NOT validated against the GFF specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:BasicGFF3MultiFeature:2006-04-27T19-06-15Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com BasicGFF3SequenceFeature An object containing all components necessary to represent a simple GFF-compliant sequence feature (the content is NOT validated against the GFF specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:BasicGFF3SequenceFeature:2006-04-27T19-04-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com type source seqid Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start end Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score strand phase multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com value key column9_tag_value BasicGFF3SequenceFeature GCP_Contact A GCP_Contact is a GCP_Person with a particular affiliation to a particular GCP_Organization. Any given GCP_Person may play the role of being a specific GCP_Contact for different organizations, in distinct operational and temporal contexts of the system. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Contact:2008-10-14T03-21-58Z r.bruskiewich@cgiar.org GCP_Person A GCP_Person is a GCP_LegalEntity semantically constrained to represent a single human being in the system. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Person:2008-10-14T03-21-57Z r.bruskiewich@cgiar.org GCP_LegalEntity GCP_LegalEntity represents a general subclass for any GCP_Entity recognized in legal terms as having a legal personality (i.e. ability to have human behaviour as an individual or in aggregate, able to own property, liable for legal prosecution, etc.). This includes both person and organization. - contactingDetails. A LegalEntity obviously has details relating to its localization in the human world. For efficiency, we treat instances of another moby data type, GCP_ContactingDetails, as a subclass of GCP_Identifier, and referencing these details from GCP_LegalEntity using the pertinent GCP_SimpleIdentifier. A LegalEntity may have several such contactingDetails. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LegalEntity:2008-10-14T03-21-54Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies contactingDetails GCP_Organization A GCP_LegalEntity specific to an organization entity recognized in legal terms as having a legal personality (i.e. able to own property, liable for legal prosecution, etc.) www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Organization:2008-10-14T03-21-55Z r.bruskiewich@cgiar.org affiliation Annotated_GO_Term Provides also the description of the GO term (not the name or the ID!), an evidence code and the process (molecular function, biological process, cellular component) mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_GO_Term:2007-10-01T13-18-57Z joecker@mpiz-koeln.mpg.de GO_Term A very lightweight object holding a GO term name and its definition www.illuminae.com urn:lsid:biomoby.org:objectclass:GO_Term:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Term Definition detailed_description process evidence_code Project This object contains two defined string: * a ProjectName * a ProjectDescription www.avignon.inra.fr urn:lsid:biomoby.org:objectclass:Project:2008-06-10T14-02-39Z pierre-yves.chibon@avignon.inra.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com ProjectName ProjectDescription CATHDomain CATH domain information. inb.bsc.es urn:lsid:biomoby.org:objectclass:CATHDomain:2006-12-11T04-49-33Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com CommentedObject Description of an object identified by 'id' in 'namespace' mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:CommentedObject:2006-10-05T10-15-26Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description Class Architecture Topology Homologous_Superfamily S35 S60 S95 S100 Domain Protein_name Source Name Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Resolution AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Atom Comb StructureBoundaries Information on structure boundaries of segments, fragments, domains, etc. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureBoundaries:2006-10-05T09-10-02Z moby-services@mmb.pcb.ub.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Chain Segments SigcleaveAnnotation Annotations about protein signal cleavage sites www.pcm.uam.es urn:lsid:biomoby.org:objectclass:SigcleaveAnnotation:2007-01-15T15-23-30Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length MaturePeptide QueryString A Query object with a String containing a query. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:QueryString:2008-01-10T16-15-54Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com query Query A query object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Query:2006-03-01T18-35-19Z pieter.neerincx@gmail.com PhenotypeDescription Object containing a description of the morphological features of a species arabidopsis.info urn:lsid:biomoby.org:objectclass:PhenotypeDescription:2001-09-21T16-00-00Z beatrice@arabidopsis.info Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Phenotype ProdomMotif Prodom motif. inb.bsc.es urn:lsid:biomoby.org:objectclass:ProdomMotif:2006-07-21T13-22-30Z rroyo@lsi.upc.edu Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Alignment Radius Diameter AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ClosestSeq AC Keywords ID Consensus PatmatmotifsReport Patmatmotifs report. inb.bsc.es urn:lsid:biomoby.org:objectclass:PatmatmotifsReport:2007-01-12T12-55-19Z rroyo@lsi.upc.edu ScoredMotifAnnotatedAASequence Scored motif annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotatedAASequence:2007-01-12T12-54-19Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length ScoredMotifAnnotation Scored Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotation:2007-01-12T12-54-17Z rroyo@lsi.upc.edu MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start AC ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length TropGENE_Diversity_Matrix_Diploid tables concerning diploid accessions for diversity analysis : accessions per row, alleles in column, coded in 0/1/2 tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:TropGENE_Diversity_Matrix_Diploid:2001-09-21T16-00-00Z manuel.ruiz@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Matrix HBond_Pair Pair of residus bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:HBond_Pair:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com A H D SampleData This represents a sample. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:SampleData:2006-07-31T13-33-49Z cs01cb@csd.abdn.ac.uk MeasuredBioMaterialData This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:MeasuredBioMaterialData:2006-07-31T13-32-39Z cs01cb@csd.abdn.ac.uk Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com isPooled Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com remainingQuantity originalQuantity String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name description Chromatogram_Encoded Generic trace binary data object genome.imim.es urn:lsid:biomoby.org:objectclass:Chromatogram_Encoded:2006-05-16T14-51-50Z akerhornou@imim.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com rawdata prodom-flatfile ProDom family bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:prodom-flatfile:2006-04-03T13-12-33Z Emmanuel.Courcelle@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content iHOPabstract An iHOP analyzed abstract, where sentence fragments providing insightful information have been tagged cnio.es urn:lsid:biomoby.org:objectclass:iHOPabstract:2007-04-14T12-58-15Z jmfernandez@cnio.es iHOPsentence It is a manuscript abstract sentence, composed by iHOPTextFragments (or children of iHOPTextFragments) cnio.es urn:lsid:biomoby.org:objectclass:iHOPsentence:2007-04-14T12-58-12Z jmfernandez@cnio.es iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com sentenceNumber iHOPpmid Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com journalImpact date sentencePiece sentence title magazine date Author A manuscript author (used by iHOP services) cnio.es urn:lsid:biomoby.org:objectclass:Author:2007-04-14T12-58-10Z jmfernandez@cnio.es surname name author AlignedDNASequences DNA sequences that have been aligned according to some method and similarity measure moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AlignedDNASequences:2007-07-30T22-45-24Z gordonp@ucalgary.ca AlignedSequences A set of sequences (AA or DNA) that have been aligned according to some method and similarity measure moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AlignedSequences:2007-07-30T22-43-30Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com OMIM OMIM Record information. inb.bsc.es urn:lsid:biomoby.org:objectclass:OMIM:2007-01-23T10-31-31Z rroyo@lsi.upc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Contributor Editorhistory Journal Seealso text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com content Text Creation_date Author Number Title ClinicalSynopsis Allelicvariants Coordinates Element that allows the recording of the latitude and longitude of a recording or collecting position. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Coordinates:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com CoordinatesText LongitudeDecimal Maps to Darwin Core 2: Longitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LongitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com LongitudeDecimal LongitudeDecimal LatitudeDecimal Maps to Darwin Core 2: Latitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LatitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com LatitudeDecimal LatitudeDecimal SpatialDatum Mathematical surface on which the mapping and coordinate system used for the geocodes of the record are based www.mncn.csic.es urn:lsid:biomoby.org:objectclass:SpatialDatum:2001-09-21T16-00-00Z jatorre@gmail.com SpatialDatum SpatialDatum ExtractData This represents an extract. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:ExtractData:2006-07-31T13-34-52Z cs01cb@csd.abdn.ac.uk MeasuredBioMaterialData This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked. www.rri.sari.ac.uk urn:lsid:biomoby.org:objectclass:MeasuredBioMaterialData:2006-07-31T13-32-39Z cs01cb@csd.abdn.ac.uk Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com isPooled Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com remainingQuantity originalQuantity String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name description iHOPrelatedSymbols-XML An iHOPrelatedSymbols XML document from iHOP web services cnio.es urn:lsid:biomoby.org:objectclass:iHOPrelatedSymbols-XML:2007-04-14T12-57-53Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Strider Text formatted in 'Strider' format www.illuminae.com urn:lsid:biomoby.org:objectclass:Strider:2007-02-13T17-54-36Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content mmCIF-Text mmCIF text. inb.bsc.es urn:lsid:biomoby.org:objectclass:mmCIF-Text:2007-11-16T11-18-31Z rroyo@lsi.upc.edu text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Legoo_PrimerSearch_Report file containing Legoo primersearch results. narcisse.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:Legoo_PrimerSearch_Report:2007-11-13T10-02-23Z Sebastien.Letort@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Enzymatic_Text Enzymatic data www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Enzymatic_Text:2007-01-15T15-25-18Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Transmembrane_fragments Transmembrane spanning regions predicted by runEMBOSSTmapSingleSequence service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Transmembrane_fragments:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com From To Hitcount Transmembrane_table Table showing the predicted transmembrane spanning regions in a sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Transmembrane_table:2001-09-21T16-00-00Z inb@pcm.uam.es Start End FragmentNumber String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Subsequence GFF2_5 Generic Feature Format File type 2.5 (Gbrowse specific GFF, with special order of column 9) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF2_5:2001-09-21T16-00-00Z markw@illuminae.com GFF Generic Feature Format File (of any subtype) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content NCut_Matrix Text formatted that is returned by runNCut services and contains a matrix of homologous sequence whose values are the distance among themselves pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:NCut_Matrix:2001-09-21T16-00-00Z jmrc@cnb.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Study ICIS Germplasm List with a particular Property www.iris.irri.org urn:lsid:biomoby.org:objectclass:Study:2001-09-21T16-00-00Z mulat@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com study_name Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com study_id study_desc SchematikonVorocodeName Lightweight structural representation of Schematikon structure motif schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonVorocodeName:2001-09-21T16-00-00Z boris.steipe@utoronto.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com VorocodeName IntAct_XML This is XML based on IntAct XSD pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:IntAct_XML:2001-09-21T16-00-00Z jmfernandez@cnb.uam.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DifferentialExpressionTest Object that encapsulates the results from a differential expression test bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:DifferentialExpressionTest:2007-11-22T09-00-13Z jtarraga@cipf.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GeneExpressionTest_Text Results in text format from a differential expression test. Each line must have the gene name and the different statistics depending on the applied test bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:GeneExpressionTest_Text:2007-11-22T08-59-57Z jtarraga@cipf.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content geneexpressiontest MicroArrayData_Text Micro-array data in text format representing gene expression patterns. Each line must have the gene name and the expression values and the expression values for each condition. All the data items must be separated by tabulators genome.imim.es urn:lsid:biomoby.org:objectclass:MicroArrayData_Text:2006-03-27T12-19-28Z akerhornou@imim.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu content microarraydata Annotated_MapMan_Bin MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_MapMan_Bin:2008-06-13T11-27-33Z joecker@mpiz-koeln.mpg.de MapMan_Bin MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:MapMan_Bin:2008-06-13T11-26-56Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description RenciSequence Sequence in Renci format (FASTA format variant) workflow.renci.unc.edu urn:lsid:biomoby.org:objectclass:RenciSequence:2006-12-06T14-52-48Z nassar@renci.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com seq GeneExpressionTest_Text Results in text format from a differential expression test. Each line must have the gene name and the different statistics depending on the applied test bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:GeneExpressionTest_Text:2007-11-22T08-59-57Z jtarraga@cipf.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content XYData_Text Text in columns (used to draw plots, etc.). inb.bsc.es urn:lsid:biomoby.org:objectclass:XYData_Text:2007-01-23T10-31-30Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FeatureAnnotatedAASequence Feature annotated sequence (from Uniprot database). inb.bsc.es urn:lsid:biomoby.org:objectclass:FeatureAnnotatedAASequence:2006-12-11T04-48-37Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length FeatureAnnotation Feature Annotation (from Uniprot database). inb.bsc.es urn:lsid:biomoby.org:objectclass:FeatureAnnotation:2006-12-11T04-48-32Z rroyo@lsi.upc.edu Type Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Status Id Description Evidence Ref Annotations GCP_DetectedVariant MOBY data type for a Demeter MolecularVariant which is generally detected by a GCP_GenomicFeatureDetector but which cannot generally, without further analysis and interpretation, be unambiguously associated with a specified GenomicFeature. applied. See Demeter genotype model for further guidance. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_DetectedVariant:2008-10-14T03-22-39Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name detector GCP_MolecularVariant The GCP_MolecularVariant data type documents the (usually polymorphic) genetic content of GCP_GenomicFeature instances which is the context of the variant. Note that if the measured content (variation) is not resolved to a specified GCP_GenomicFeature detected by a GCP_GenomicFeatureDetector, then the context of the variant can simply be the GCP_GenomicFeatureDetector itself (i.e. the GCP_MolecularVariant is a detectedVariant of the GCP_GenomicFeatureDetector). GCP_MolecularVariant inherits its full documentation capacity from GCP_Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MolecularVariant:2008-10-14T03-22-38Z r.bruskiewich@cgiar.org context GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies SMILES data type for the Simplified Molecular Input Line Entry Specification, a specification for unambiguously describing the structure of chemical molecules. ualberta.ca urn:lsid:biomoby.org:objectclass:SMILES:2007-09-15T23-39-01Z biomoby@dhx.ath.cx String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com molecule Distance_matrix_text matrix of pairwise distances between all pairs of taxa, such as distances based on molecular sequence data, gene frequency genetic distances etc. bioinfo.inibap.org urn:lsid:biomoby.org:objectclass:Distance_matrix_text:2006-11-28T07-03-56Z m.rouard@cgiar.org text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content InfraspecificEpithet GBIF - The final epithet of a botanical name of infraspecific rank. AppInfo Nothing found. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:InfraspecificEpithet:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com InfraspecificEpithet OligoQualityThresholds An object containing several threshold values used to calculate whether a piece of a transcript can cause signal by binding to an oligo or not. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoQualityThresholds:2008-03-07T16-34-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com mismatches contiguous_stretch Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com free_energy percent_identity clustal-msf-formatted-text Clustalw MSF formatted text bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:clustal-msf-formatted-text:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Haplotyping_Study_obj HapMap related objects www.hapmap.org urn:lsid:biomoby.org:objectclass:Haplotyping_Study_obj:2001-09-21T16-00-00Z hapmap@hapmap.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Lutefisk_Text Lutefisk service output in flat format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Lutefisk_Text:2007-01-15T15-27-09Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Signature_cleave_motif Header and table showing the predicted cleavage sites in a sequence by means of runEMBOSSSigcleave service. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Signature_cleave_motif:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com From To Hitcount Report Signature_cleave_table Table showing the predicted cleavage sites in a sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Signature_cleave_table:2001-09-21T16-00-00Z inb@pcm.uam.es Start End Score MaturePeptide PrositeMotif Prosite motif. inb.bsc.es urn:lsid:biomoby.org:objectclass:PrositeMotif:2007-01-12T12-56-23Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com AC ID Date Description CC Pattern Pattern in prosite format. inb.bsc.es urn:lsid:biomoby.org:objectclass:Pattern:2007-01-12T12-52-18Z rroyo@lsi.upc.edu content Pattern Rules Prosite motif rules. inb.bsc.es urn:lsid:biomoby.org:objectclass:Rules:2007-01-12T12-56-07Z rroyo@lsi.upc.edu Rules Rules MotifMatrix Prosite motif matrix. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifMatrix:2007-01-12T12-56-20Z rroyo@lsi.upc.edu text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu content Matrix Doc OligoQualityRecord Biomoby OligoRecord object with additional zero or more OligoTargetSpecificity objects. The latter objects describe oligo (microarray probe) quality as a qualitative score to categorize oligos based on certain criteria. Criteria used for scoring can be described with OligoQualityThresholds objects. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoQualityRecord:2008-04-20T13-58-34Z pieter.neerincx@gmail.com OligoRecord Biomoby object containing one or more OligoHit objects and an Integer object for the length of the oligo. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoRecord:2008-04-20T13-58-32Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com length OligoHit Biomoby object consisting of a HitPosition object and a Moby CrossReference Information Block (CRIB). The CRIB lists evidence for gene expression of the sequence in the HitPosition object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoHit:2008-04-20T13-58-31Z pieter.neerincx@gmail.com HitPosition Biomoby object consisting of a MapPosition object (A position on a genetic map. Can be used to denote a sequence ID and its start and stop co-ordinates with respect to another sequence to which it is aligned), an Object object (to denote the orientation of this sequence with respect to the sequence to which it is aligned) and a String object (to denote the corresponding cigar like line of the alignment). * Cigar like line (CLL): A compact way to represent the alignment between 2 sequences. It defines the sequence of matches(M), substitutions/mismatches(S), insertions(I) or deletions(D) on the second sequence with respect to the first based on this alignment. In addition, the presence of introns(N) between High Scoring Pairs (HSPs) of a hit obtained from an alignment of the two sequences by BLAT/BLAST etc. can also be represented. For example: * 8M2S50M would be 8 matches followed by 2 substitutions (mismatches)and finally 50 matches * 30M400N30M would be two HSPs of 30 matches each seperated by an intron of length 400 bp * 2M1I25M1D6M would be 2 matches, an insertion in the hit, 25 matches, a gap in the hit and 6 matches. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:HitPosition:2008-04-20T13-58-30Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com cll MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end strand hit_position oligo_hit OligoTargetSpecificity Biomoby object consisting of two Object objects: one for transcriptome target specificity of the oligo, the other for genome target specificity. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:OligoTargetSpecificity:2008-04-20T13-58-33Z pieter.neerincx@gmail.com genome transcriptome oligo_target_specificity CodonUsageTable_Text Codon usage table. inb.bsc.es urn:lsid:biomoby.org:objectclass:CodonUsageTable_Text:2007-01-23T10-31-29Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Features Collection of name and value pairs chado.cirad.fr urn:lsid:biomoby.org:objectclass:Features:2006-05-02T14-20-54Z alexis.dereeper@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com simple_key_value_pair Basic key/value pair object for key/value pairs with a 1:1 relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:simple_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com value key feature EvocID An identifier in the Evoc Ontology eva.mpg.de urn:lsid:biomoby.org:objectclass:EvocID:2001-09-21T16-00-00Z hoehndorf@eva.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com id MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end MetaboCard MetaboCard text format used in HMDB, http://www.hmdb.ca/ ualberta.ca urn:lsid:biomoby.org:objectclass:MetaboCard:2007-09-20T20-22-33Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PDB_Enriched PDB structure together with a Jmol script and a html description. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PDB_Enriched:2006-10-04T14-28-28Z moby-services@mmb.pcb.ub.es text-html HTML www.illuminae.com urn:lsid:biomoby.org:objectclass:text-html:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Description JmolScript PDB-Text PDB format report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PDB-Text:2006-10-04T14-19-35Z moby-services@mmb.pcb.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu content iHOPsymbolInfo-XML An iHOPsymbolInfo XML document from iHOP web services cnio.es urn:lsid:biomoby.org:objectclass:iHOPsymbolInfo-XML:2007-04-14T12-57-56Z jmfernandez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Object2 hello world openinformatics.com urn:lsid:biomoby.org:objectclass:Object2:2008-02-16T00-08-35Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_orphan no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_orphan:2009-08-18T08-43-47Z julien.wollbrett@cirad.fr SO_predicted An attribute describing an unverified region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted:2009-08-18T08-40-50Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SimpleAnnotatedGIFImage Object containing a GIF image with descriptive text mips.gsf.de urn:lsid:biomoby.org:objectclass:SimpleAnnotatedGIFImage:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description b64_encoded_gif Base 64 encoded GIF-format image www.illuminae.com urn:lsid:biomoby.org:objectclass:b64_encoded_gif:2001-09-21T16-00-00Z markw@illuminae.com text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com content TransmembraneAnnotation Annotations about transmembrane fragments www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TransmembraneAnnotation:2007-01-15T14-53-36Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start TransmembraneNumber AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length TransmembraneFragment TargetP_result The results of a TargetP (http://www.cbs.dtu.dk/services/TargetP/) prediction atidb.org urn:lsid:biomoby.org:objectclass:TargetP_result:2001-09-21T16-00-00Z matthew.couchman@bbsrc.ac.uk CompartmentPrediction The results of a compartment prediction program e.g. TargetP or Predotar atidb.org urn:lsid:biomoby.org:objectclass:CompartmentPrediction:2001-09-21T16-00-00Z matthew.couchman@bbsrc.ac.uk String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com compartment Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com c_score m_score o_score s_score Edge unstable; under development; subject to redefinition or deregistration without notice; please do not use llama.med.harvard.edu urn:lsid:biomoby.org:objectclass:Edge:2001-09-21T16-00-00Z gberriz@hms.harvard.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com partner Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com direction FASTA_AA AA sequence in FASTA format bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:FASTA_AA:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com From To Hitcount MSRawCdfUrl the url (http/ftp) of raw, cdf formatted, output of a Mass Spectrometry experiment. www.ab.wur.nl urn:lsid:biomoby.org:objectclass:MSRawCdfUrl:2008-02-04T09-44-55Z mark.fiers@wur.nl String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Url Name SampleId ExperimentId LutefiskAnnotatedAASequence De novo peptide sequence with Lutefisk annotations www.pcm.uam.es urn:lsid:biomoby.org:objectclass:LutefiskAnnotatedAASequence:2007-01-15T15-02-45Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length LutefiskAnnotation Annotations about de novo peptide sequence inferred by Lutefisk www.pcm.uam.es urn:lsid:biomoby.org:objectclass:LutefiskAnnotation:2007-01-15T15-02-17Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start LutefiskPeptide Rank Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Prc PevzScr Quality IntScr X-corr Annotations RNACard RNACard text format used in the CCRNA database for describing RNA molecules found in E.coli, http://redpoll.pharmacy.ualberta.ca/CCDB/ ualberta.ca urn:lsid:biomoby.org:objectclass:RNACard:2007-09-21T21-21-56Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ScoredMotifAnnotation Scored Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:ScoredMotifAnnotation:2007-01-12T12-54-17Z rroyo@lsi.upc.edu MotifAnnotation Motif Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MotifAnnotation:2007-01-12T12-53-04Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com AC ID Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score PESTMotif This datatype encapsulates a PEST motif. PEST motifs were defined as hydrophilic stretches of at least 12 amino acids length with a high local concentration of critical amino acids. Remarkably, negatively charged amino acids are clustered within these motifs while positively charged amino acids, arginine (R), histidine (H) and lysine (K) are generally forbidden. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:PESTMotif:2007-04-16T19-51-29Z ekawas@mrl.icapture.ubc.ca Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com stop start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com hydrophobicity_index score DEPST_percentage String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com motif DescribedLink A URL with a textual description of the data at that address moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:DescribedLink:2007-04-06T15-40-35Z gordonp@ucalgary.ca Link contains a string representing a URL (e.g. http://www.eu-plant-genome.net) mips.gsf.de urn:lsid:biomoby.org:objectclass:Link:2006-05-17T13-26-22Z Octave.Noubibou@gsf.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com url description GCP_AdministrativeDivision A GCP_AdministrativeDivision is a kind of GCP_SimpleLocation that corresponds to regional political division of land, such as a country or subnational region (state/province, city, etc.) See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_AdministrativeDivision:2008-10-14T03-23-28Z r.bruskiewich@cgiar.org GCP_SimpleLocation A GCP_SimpleLocation is a kind of GCP_MapFeature that answers a lightweight version of the question "where?" as it relates to a specified geographical (cartographic) context. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleLocation:2008-10-14T03-21-47Z r.bruskiewich@cgiar.org GCP_MapFeature A GCP_MapFeature models a kind of GCP_Feature that has a coordinate position on a coordinate-dimensioned space called a map, which is identified by a GCP_SimpleIdentifier (see GCP_Map below). The MapFeature class is subclassed into domain specific map feature concepts such as biological GenomicFeature and geographical Location classes. By definition, a MapFeature belongs to only one map; however, the point, interval or space located by the map feature may be mapped onto more than one map, and may have many associated characteristics, which are generally retrievable by suitable web services using the MOBY namespace and identifier associated with the GCP_MapFeature. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapFeature:2008-10-14T03-21-39Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name map GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values geoReference enclosingAdministrativeDivision country GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type iHOPMeSHevidence A MeSH term used by iHOP services to label text fragments cnio.es urn:lsid:biomoby.org:objectclass:iHOPMeSHevidence:2007-04-14T12-58-08Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com meshId iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es content List_Text List of values in text format where each line has one value genome.imim.es urn:lsid:biomoby.org:objectclass:List_Text:2006-07-06T15-35-53Z akerhornou@imim.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com PDGJOB This object represents a job id, with the answering MOBY method, killcode, and a timeout pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:PDGJOB:2001-09-21T16-00-00Z jmfernandez@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com answerService authURI DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com timeout killcode killService allele_freq Allele Frequencey www.hapmap.org urn:lsid:biomoby.org:objectclass:allele_freq:2001-09-21T16-00-00Z hapmap@hapmap.edu snp_allele Snp Allele www.hapmap.org urn:lsid:biomoby.org:objectclass:snp_allele:2001-09-21T16-00-00Z hapmap@hapmap.edu DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length frequency panel_lsid snp_lsid CommentedRNASequence Represents a RNA Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedRNASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description RNASequence Lightweight representation an RNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:RNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length TaxonName GBIF - Concatenated scientific name, preferrably formed in accordance with a Code of Nomenclature, i. e. a monomial, bionomial, or trinomial plus author(s) or author team(s) and - where relevant - year, or the name of a cultivar or cultivar group, or a hybrid formula, as fully as possible. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:TaxonName:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com TaxonName FirstEpithet GBIF - The first epithet in a botanical name combination (species epithet or the epithet of the subdivision of a genus. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:FirstEpithet:2001-09-21T16-00-00Z jatorre@gmail.com FirstEpithet FirstEpithet Genus GBIF test - Genus www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Genus:2001-09-21T16-00-00Z jatorre@gmail.com Genus InfraspecificEpithet GBIF - The final epithet of a botanical name of infraspecific rank. AppInfo Nothing found. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:InfraspecificEpithet:2001-09-21T16-00-00Z jatorre@gmail.com InfraspecificEpithet InfraspecificEpithet GCP_LocusSequence Sequence of a locus for GCP tropgenedb.cirad.fr urn:lsid:biomoby.org:objectclass:GCP_LocusSequence:2006-05-24T09-51-47Z alexis.dereeper@cirad.fr NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length TransmembraneAnnotatedAASequence Aminoacid sequence with annotations about transmembrane regions www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TransmembraneAnnotatedAASequence:2007-01-15T15-10-30Z inb@pcm.uam.es AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length TransmembraneAnnotation Annotations about transmembrane fragments www.pcm.uam.es urn:lsid:biomoby.org:objectclass:TransmembraneAnnotation:2007-01-15T14-53-36Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start TransmembraneNumber TransmembraneFragment Annotations GI_Function A function assigned to a gene using GeneIlluminater. Contains a String object describing the function and a Float object listing the occurence (percentage) of this function in the descriptions of this gene for different species. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GI_Function:2007-10-31T17-32-50Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com occurrence NCBI_Blast_XML_Gif_Map XML formatted NCBI Blast report with a clickable graphical display of the hits mips.gsf.de urn:lsid:biomoby.org:objectclass:NCBI_Blast_XML_Gif_Map:2001-09-21T16-00-00Z D.Haase@gsf.de text-html HTML www.illuminae.com urn:lsid:biomoby.org:objectclass:text-html:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content areaMap NCBI_Blast_XML_Gif XML formatted NCBI Blast report with a graphical display of the hits mips.gsf.de urn:lsid:biomoby.org:objectclass:NCBI_Blast_XML_Gif:2001-09-21T16-00-00Z D.Haase@gsf.de b64_encoded_gif Base 64 encoded GIF-format image www.illuminae.com urn:lsid:biomoby.org:objectclass:b64_encoded_gif:2001-09-21T16-00-00Z markw@illuminae.com text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com hitGraph NCBI_Blast_XML XML formatted NCBI Blast report www.illuminae.com urn:lsid:biomoby.org:objectclass:NCBI_Blast_XML:2001-09-21T16-00-00Z markw@illuminae.com text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com Interaction An interaction object, in native BioMOBY format. It has one or more interactors, a method and a result pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:Interaction:2001-09-21T16-00-00Z jmfernandez@cnb.uam.es Interactor An interactor is a reference to an object, with a role pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:Interactor:2001-09-21T16-00-00Z jmfernandez@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com role participant result resultUnits Typed_Image An image encoded with a legend mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Typed_Image:2006-10-05T11-03-27Z moby-services@mmb.pcb.ub.es Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com mimeType rawdata legend NCut_Clusters Clusters of homologous sequence whose values are the distance among themselves in text format cnio.es urn:lsid:biomoby.org:objectclass:NCut_Clusters:2007-07-03T17-28-08Z jmrodriguez@cnio.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content NamedSpliceVariant A splicevariant with a name and an ID (in TAIR's case a TAIR_Accession) arabidopsis.org urn:lsid:biomoby.org:objectclass:NamedSpliceVariant:2007-06-21T01-59-44Z cwilks@stanford.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name SCOPLayerNode Internal information from hierarchy at SCOP database inb.bsc.es urn:lsid:biomoby.org:objectclass:SCOPLayerNode:2007-05-10T12-22-30Z atorrano@bsc.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com comentary StructureDomain Information on structure domains mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureDomain:2006-10-05T09-59-53Z moby-services@mmb.pcb.ub.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name StructureBoundaries Information on structure boundaries of segments, fragments, domains, etc. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureBoundaries:2006-10-05T09-10-02Z moby-services@mmb.pcb.ub.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com End Start Chain Segments Genus GBIF test - Genus www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Genus:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description Organism_Name Object representing the binomial convention of naming organisms: genus name followed by the species name. ualberta.ca urn:lsid:biomoby.org:objectclass:Organism_Name:2007-09-04T07-49-39Z biomoby@dhx.ath.cx Organism An organism object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Organism:2006-03-01T18-35-20Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Genus Species ShowORF-Text a nucleic acid sequence with its protein translation in a style suitable for publication obtained from showorf. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:ShowORF-Text:2007-03-15T19-39-24Z ekawas@mrl.icapture.ubc.ca text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MatrixInteger MatrixInteger object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:MatrixInteger:2006-03-21T11-52-43Z inb@pcm.uam.es Matrix Matrix object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Matrix:2006-03-21T11-48-31Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ArrayInteger ArrayInteger object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayInteger:2006-03-21T11-52-11Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Key ElementInteger ElementInteger object for integer arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementInteger:2006-03-21T11-51-55Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Value Element Array GeneticMap A genetic map contains mapped loci. The length component should indicate the length of the map in map units, but does NOT have to be zero-based; i.e. the length is simply the distance from the most proximal to the most distal marker on the map, regardless of whether or not the proximal marker is at position '0' on the map. It is likely that, in many cases, the namespace and id of this GeneticMap will be identical to the namespace and id of the 'chromosome' component of the MappedLoci's MapPosition, but this isn't required if the various Loci are more sensibly associated with another map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:GeneticMap:2006-07-31T17-47-08Z markw@illuminae.com MappedLocus A locus that is mapped to a genetic map. the Locus component should hold a Locus (with the associated namespace and id as appropriate), while the MapPosition component should hold the chromosome, start, and end position for that Locus. Start and end may be the same to indicate point maps rather than range maps. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MappedLocus:2006-07-31T17-41-15Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Locus A lightweight object representing a Locus. The namespace and id should indicate the specific Locus being described. The contained Allele objects may be used to indicate a series of Alleles for that locus, if appropriate. If there is no Allele information, or if specification of an Allele is not appropriate (e.g. in the case of a MappedLocus object), then a single Allele object with blank namespace, id, and description would be appropriate. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Locus:2006-06-29T16-56-19Z markw@illuminae.com Allele A lightweight object representing an Allele. The namespace and id should indicate the specific Allele being described. The contained String object is a human-readable description of the Allele in whatever form is most appropriate (e.g. the phenotype). bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Allele:2006-06-29T16-47-03Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Allele Locus MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end MapPosition MappedLocus length SchematikonMotifID Schematikon protein structure motif ID schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonMotifID:2001-09-21T16-00-00Z boris.steipe@utoronto.ca SchematikonSegmentID Schematikon protein structure segment ID schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonSegmentID:2001-09-21T16-00-00Z boris.steipe@utoronto.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ID b64_encoded_gif Base 64 encoded GIF-format image www.illuminae.com urn:lsid:biomoby.org:objectclass:b64_encoded_gif:2001-09-21T16-00-00Z markw@illuminae.com text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Molecule Concept of a chemical molecule, such a metabolite. The molecule is represented in Chemical Markup Language. org.openscience.cdk urn:lsid:biomoby.org:objectclass:Molecule:2007-09-21T16-43-52Z egonw@users.sf.net Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com StructureBoundaries Information on structure boundaries of segments, fragments, domains, etc. mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:StructureBoundaries:2006-10-05T09-10-02Z moby-services@mmb.pcb.ub.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Chain phylogenetic_distance_matrix phylogenetic tree www.renci.org urn:lsid:biomoby.org:objectclass:phylogenetic_distance_matrix:2007-02-15T17-09-49Z jdr0887@renci.org text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ProbeExpressionData Expression data on a probe derived from microarray experiment. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:ProbeExpressionData:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp TargetCondition Experimental result under treatment type or growth conditions for microarray experiment. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:TargetCondition:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ratio condition ProbeId Material placed on a spot on microarray to represent a biological sequence. The ProbeID comes from KOME database, e,g, AU088561, 002-168-D12. typeOfMicroArray is e.g. cDNA, oligo. www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:ProbeId:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp probeid EMBL_Text EMBL plain text sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:EMBL_Text:2007-01-12T10-58-40Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_ManagementNeighbourhood Most germplasm neighbourhoods are defined by biological relationships, but a specific kind of GCP_ManagementNeighbourhood serves to conserve biodiversity of a given set of germplasm called its "founding germplasm" for some organizational purpose (e.g. ex situ conservation as an genetic resource accession). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_ManagementNeighbourhood:2008-10-14T03-23-09Z r.bruskiewich@cgiar.org GCP_MaintenanceNeighbourhood A GCP_MaintenanceNeighbourhood is a GCP_GermplasmNeighbourhood striving to conserve biological diversity in a set of Germplasm. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MaintenanceNeighbourhood:2008-10-14T03-22-03Z r.bruskiewich@cgiar.org GCP_GermplasmNeighbourhood GCP_GermplasmNeighbourhood is a kind of GCP_GermplasmSet which has a formal biological or management role (see GCP domain model descriptions). Such a set is formally established by source_germplasm (modeled as a set of GCP_SimpleIdentifiers identifying GCP_Germplasm objects) and (generally) belongs to a specified germplasm_collection (also specified by a GCP_SimpleIdentifiers). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmNeighbourhood:2008-10-14T03-22-01Z r.bruskiewich@cgiar.org GCP_GermplasmSet GCP_GermplasmSet is simply any collection of germplasm objects of a specified type (inferred by the namespace of its primary identifier, since it indirectly inherits from GCP_SimpleIdentifier via GCP_Entity). The list of germplasm is identified indirectly by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmSet:2008-10-14T03-22-00Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies germplasm germplasmCollection sourceGermplasm foundingGermplasm GeneSwingerObject An object containing NASCArrays URL to various experiments (http://affy.arabidopsis.info), experiment name, coefficient of variance, a mean signal value for the selected gene in that experiment, the standard deviation of the signal for the selected gene in that experiment and the number of slides in that experiment. arabidopsis.info urn:lsid:biomoby.org:objectclass:GeneSwingerObject:2007-11-15T12-07-06Z beatrice@arabidopsis.info String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com NASCsubmitter Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com StandardDeviation NASCArraysExperimentName MeanSignal Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com SlideNumber COV URL An Universal Resource Locater (URL). www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:URL:2006-03-01T18-35-11Z pieter.neerincx@gmail.com NASCArraysWebURL Matrix_row an item in a row of a matrix, where the key is the position of the item in the row and the value is the value of the item in the matrix at that particular position mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Matrix_row:2007-04-24T21-21-57Z ekawas@mrl.icapture.ubc.ca simple_key_value_pair Basic key/value pair object for key/value pairs with a 1:1 relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:simple_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com value key item Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com row_position ProteinChargeTable Two column table representing the ionic charge of a protein at each residue moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:ProteinChargeTable:2007-06-26T22-10-38Z gordonp@ucalgary.ca AnnotatedTable Tabular data described with a header and a caption moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:AnnotatedTable:2007-06-26T22-05-51Z gordonp@ucalgary.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com caption tableRow A row of data for a tabular object moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:tableRow:2007-06-21T15-47-03Z gordonp@ucalgary.ca cell header table Tabular (row-based) data moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:table:2007-06-25T23-20-32Z gordonp@ucalgary.ca row clustal-aln-formatted-text Clustalw aln format bioserv.rpbs.jussieu.fr urn:lsid:biomoby.org:objectclass:clustal-aln-formatted-text:2001-09-21T16-00-00Z rpbs-feedback@ebgm.jussieu.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_SimpleFeatureWithSearchOperator Extension of the SimpleFeature that can be used as an input to various searches, where the "valueString" will be compared using a new article name "operator". The "operator" values are: Operators applicable for all value types: EQ: Strict equality. GT: Greater than. GTE: Greater than or equal. LT: Less than. LTE: Less than or equal. Operators applicable for strings only: LIKE: Case and accent insensitive equality (look at the SQL operator) allowing the value character "*" in the string. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeatureWithSearchOperator:2008-10-14T03-21-16Z m.skofic@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type operator myTree Phylogenetic tree www.phytome.org urn:lsid:biomoby.org:objectclass:myTree:2001-09-21T16-00-00Z dlu@email.unc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DiseaseModel Single disease locus www.renci.org urn:lsid:biomoby.org:objectclass:DiseaseModel:2007-01-25T16-25-47Z jdr0887@renci.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com String alignment_in_fasta_format Datatype to store also the probability, that this GO Term ist right or wrong mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:alignment_in_fasta_format:2007-11-14T15-27-07Z joecker@mpiz-koeln.mpg.de Alignment Sequence alignment genopole.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:Alignment:2001-09-21T16-00-00Z carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content nsSNP Contains string values, which represents alleles, strand positions, codon positions, amino acid variants and positions for specific SNP icapture.ubc.ca urn:lsid:biomoby.org:objectclass:nsSNP:2006-04-02T17-05-52Z ycsong@student.cs.uwaterloo.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com codon_pos allele strand aa_var aa_pos Rules Prosite motif rules. inb.bsc.es urn:lsid:biomoby.org:objectclass:Rules:2007-01-12T12-56-07Z rroyo@lsi.upc.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Rules iHOPLabelledTextFragment It is a text fragment which has been labelled/tagged with one or more objects cnio.es urn:lsid:biomoby.org:objectclass:iHOPLabelledTextFragment:2007-04-14T12-58-04Z jmfernandez@cnio.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com tag iHOPTextFragment It is basically a text fragment object used by iHOP services cnio.es urn:lsid:biomoby.org:objectclass:iHOPTextFragment:2007-04-14T12-57-57Z jmfernandez@cnio.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content Chart2D Provides data for plotting a two dimensional graph. Contains one or more GraphSeries2D objects as well as a chart title, chart description and labels for the axis. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Chart2D:2008-05-11T12-21-50Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com title description dimension1_axis_label dimension2_axis_label GraphSeries2D Contains one or more GraphPoint2D objects to plot a two dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeries2D:2008-05-11T12-21-46Z pieter.neerincx@gmail.com GraphPoint2D GraphPoint1D with an additional Float object for the second dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint2D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com dimension2 dimension1 GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com GeneExpressionAnnotation Annotations about gene expression www.cnb.uam.es urn:lsid:biomoby.org:objectclass:GeneExpressionAnnotation:2008-04-07T13-53-07Z natalia@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GeneSymbol Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es mimeType rawdata GeneName Component Description ExpressionPattern ExpressionLevel ExpressionNotes Collector An specimen collector. Usually the name of the person who collected an specimen. biocase.org urn:lsid:biomoby.org:objectclass:Collector:2006-07-31T02-08-09Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MEME_Text MEME text output www.sdsc.edu urn:lsid:biomoby.org:objectclass:MEME_Text:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content interaction_partner unstable; under development; subject to redefinition or deregistration without notice; please do not use llama.med.harvard.edu urn:lsid:biomoby.org:objectclass:interaction_partner:2001-09-21T16-00-00Z gberriz@hms.harvard.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com direction String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com partner MSXcmsTestOutput Output of an xcms run - TEST: this is not in production stage - yet. www.ab.wur.nl urn:lsid:biomoby.org:objectclass:MSXcmsTestOutput:2008-02-05T13-35-31Z mark.fiers@wur.nl MSEicPdfUrl Link to a PDFed image of an EIC (Extracted Ion Chromatogram) of an alignment, possible generated by XCMS. www.ab.wur.nl urn:lsid:biomoby.org:objectclass:MSEicPdfUrl:2008-02-05T13-31-09Z mark.fiers@wur.nl Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name ExperimentId Url MSEicPdfUrl XcmsTopDiffTsvUrl Uuid Name ArrayImage_Encoded An Array filled with Image_Encoded elements. inb.bsc.es urn:lsid:biomoby.org:objectclass:ArrayImage_Encoded:2007-01-12T14-52-48Z atorrano@lsi.upc.edu Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementImage_Encoded Image_Encoded belonging to an Array. inb.bsc.es urn:lsid:biomoby.org:objectclass:ElementImage_Encoded:2007-01-12T14-52-29Z atorrano@lsi.upc.edu Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com mimeType rawdata Value elements EC_Number EC number mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:EC_Number:2008-06-13T11-23-05Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MappedLocus A locus that is mapped to a genetic map. the Locus component should hold a Locus (with the associated namespace and id as appropriate), while the MapPosition component should hold the chromosome, start, and end position for that Locus. Start and end may be the same to indicate point maps rather than range maps. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MappedLocus:2006-07-31T17-41-15Z markw@illuminae.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Locus A lightweight object representing a Locus. The namespace and id should indicate the specific Locus being described. The contained Allele objects may be used to indicate a series of Alleles for that locus, if appropriate. If there is no Allele information, or if specification of an Allele is not appropriate (e.g. in the case of a MappedLocus object), then a single Allele object with blank namespace, id, and description would be appropriate. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Locus:2006-06-29T16-56-19Z markw@illuminae.com Allele A lightweight object representing an Allele. The namespace and id should indicate the specific Allele being described. The contained String object is a human-readable description of the Allele in whatever form is most appropriate (e.g. the phenotype). bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Allele:2006-06-29T16-47-03Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Allele Locus MapPosition A position on a genetic map. bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:MapPosition:2006-07-31T17-38-07Z markw@illuminae.com chromosome Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com start end MapPosition MolWeightsArray Molecular weights. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightsArray:2006-08-09T11-03-28Z rroyo@lsi.upc.edu ArrayFloat ArrayFloat object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ArrayFloat:2006-03-21T11-50-38Z inb@pcm.uam.es Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementFloat ElementFloat object for float arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:ElementFloat:2006-03-21T11-50-31Z inb@pcm.uam.es Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Value Element ByoDynInput Input values for a simulation of the program ByoDyn (http://cbbl.imim.es:8080/ByoDyn) cbbl.imim.es urn:lsid:biomoby.org:objectclass:ByoDynInput:2008-06-12T14-18-24Z jflo@imim.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content modelFormat integrationMethod Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com time timestep runningType GCP_ValueSet A GCP_ValueSet is explicitly modeled here as MOBY data types (rather than a vanilla MOBY:Collection) because they are used in contexts (e.g. a GCP_Study) where their management as a complex unit (e.g. the Study observationUnit is an important kind of ValueSet). That said, a GCP_ValueSet contains values that are a MOBY:Collection of GCP_Value objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_ValueSet:2008-10-14T03-22-29Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values SchematikonSegmentAttributes PDB ID, chain ID, starting amino acid position (chain position) in the PDB file, insert code, and length for a Schematikon structure segment -- attributes from a PDB file that uniquely identify a structure segment in the Schematikon database schematikon.org urn:lsid:biomoby.org:objectclass:SchematikonSegmentAttributes:2001-09-21T16-00-00Z boris.steipe@utoronto.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Insert code Starting amino acid position Chain ID PDB ID RNAML Syntax for exchanging RNA information. This syntax was designed to easily express data on RNA sequence and structure, and to allow the transmission of information among the RNA community. bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:RNAML:2006-02-09T09-24-45Z Celine.Noirot@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content RNAStructAlignmentML RNAStructAlignmentML is a XML schema for representing multiple RNA secondary structure alignments www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:RNAStructAlignmentML:2008-03-12T09-13-36Z web@uni-bielefeld.de BioDom BioDOM is a JAVA library for converting native non-XML output from various bioinformatic tools to XML formats that can be validated against XMLSchemas. www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:BioDom:2008-03-04T11-47-16Z web@uni-bielefeld.de text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GeneAccessionList List of gene accessions bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:GeneAccessionList:2001-09-21T16-00-00Z Sebastien.Carrere@toulouse.inra.fr text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Clustering Object that encapsulates micro array data clustering bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:Clustering:2007-11-22T09-00-22Z jtarraga@cipf.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Newick_Text phylogenetic tree in Newick format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Newick_Text:2001-09-21T16-00-00Z inb@pcm.uam.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content newick MicroArrayData_Text Micro-array data in text format representing gene expression patterns. Each line must have the gene name and the expression values and the expression values for each condition. All the data items must be separated by tabulators genome.imim.es urn:lsid:biomoby.org:objectclass:MicroArrayData_Text:2006-03-27T12-19-28Z akerhornou@imim.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu content microarraydata PNGFormatImage An image in Portable Network Graphics format moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:PNGFormatImage:2007-04-10T23-25-15Z gordonp@ucalgary.ca WebFormatImage A 2D visual representation in a format whsoe rendering is supported by the major Web browsers moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:WebFormatImage:2007-04-10T23-22-43Z gordonp@ucalgary.ca Image A 2 dimensional visual element moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Image:2007-04-10T23-19-22Z gordonp@ucalgary.ca text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content CGView-xml CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file (http://wishart.biology.ualberta.ca/cgview/xml_overview.html) bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:CGView-xml:2007-06-19T10-27-14Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FooBar This is a classic foobar datatype. Fill it in as you see fit! www.foobar.com urn:lsid:biomoby.org:objectclass:FooBar:2007-11-30T14-46-03Z foo@bar.com BasicGFFSequenceFeature An object containing all components necessary to represent a simple GFF-compliant sequence feature (the content is NOT validated against the GFF specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:BasicGFFSequenceFeature:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com reference source method Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start stop Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score strand frame phase multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com value key column9_tag_value AntigenicAnnotatedAASequence Antigenic sites annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AntigenicAnnotatedAASequence:2007-01-12T12-52-13Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length AntigenicAnnotation Annotation of antigenic sites. inb.bsc.es urn:lsid:biomoby.org:objectclass:AntigenicAnnotation:2007-01-12T12-52-11Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score Max_score_pos Annotations GOGraph Gene Ontology graph (xml format). inb.bsc.es urn:lsid:biomoby.org:objectclass:GOGraph:2007-01-12T14-53-24Z rroyo@lsi.upc.edu text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BlatJob A BLAT job. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:BlatJob:2006-03-01T18-36-39Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com content fasta DataBase A database object. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:DataBase:2006-03-01T18-35-12Z pieter.neerincx@gmail.com database MetwareExperimentId A LSID pointing out a metware experiment ab.wur.nl urn:lsid:biomoby.org:objectclass:MetwareExperimentId:2008-05-29T09-45-00Z mark.fiers@wur.nl String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ExperimentId multi_slide_expression_values Name: multi_slide_gene_expression_values Auth: ssg.uab.edu Desc: Intent of datatype is to model MxN matrix of gene expression data. Data is primarily expression intensity values and columns are modelled as the following: 1) First column => models probeset names [OR] any identifier. 2) Columns [2.... N] models models SlideNames [OR] any identifier. ---------------------------------------------------------------------------------------------------- Probeset | Slide1 | Slide2 | Slide3 |SlideN | ---------------------------------------------------------------------------------------------------- 1234_at | 3.6 | 6.7 | 9.8 | 10.45 | ---------------------------------------------------------------------------------------------------- A collection of this object can be created to model the following: ---------------------------------------------------------------------------------------------------- Probeset | Slide1 | Slide2 | Slide3 |SlideN | ---------------------------------------------------------------------------------------------------- 1234_at | 3.6 | 6.7 | 9.8 | 10.45 | ---------------------------------------------------------------------------------------------------- 7895_at | | 1.6 | 8.7 | 9.8 | 0.45 | ---------------------------------------------------------------------------------------------------- 5389_at | | 1 1.6 | 98.7 | 29.8 | 5.45 | ---------------------------------------------------------------------------------------------------- ssg.uab.edu urn:lsid:biomoby.org:objectclass:multi_slide_expression_values:2007-09-22T22-55-28Z vinodh@uab.edu Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com expression_intensity_value DigestReport Digest report. inb.bsc.es urn:lsid:biomoby.org:objectclass:DigestReport:2007-01-12T14-49-12Z rroyo@lsi.upc.edu MolWeightsAnnotatedAASequence Molecular weights annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightsAnnotatedAASequence:2007-01-12T14-48-02Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight Annotations AnnotationHits Annotation hits for AnnotatedAASequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:AnnotationHits:2007-01-12T12-52-16Z rroyo@lsi.upc.edu From To Hitcount AnnotationHits Matrix Matrix object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Matrix:2006-03-21T11-48-31Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com RestrictAnnotatedNASequence Nucleotidic sequence with annotations about restriction enzyme cleavage sites. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RestrictAnnotatedNASequence:2007-01-15T15-18-53Z inb@pcm.uam.es AnnotatedNASequence AnnotatedNASequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:AnnotatedNASequence:2007-01-15T15-07-52Z inb@pcm.uam.es CommentedNASequence Commented nucleic acid sequence. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:CommentedNASequence:2001-09-21T16-00-00Z inb@pcm.uam.es NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Description RestrictAnnotation Annotations about restriction enzyme cleavage sites. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:RestrictAnnotation:2007-01-15T15-05-51Z inb@pcm.uam.es Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev Annotations BoundingBox Longitud/latitude bounding box delimited by: Left Right Upper Lower www.gbif.org urn:lsid:biomoby.org:objectclass:BoundingBox:2006-08-16T14-24-17Z fdcastillo@gbif.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com LongitudeDecimal Maps to Darwin Core 2: Longitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LongitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com LongitudeDecimal Left Right LatitudeDecimal Maps to Darwin Core 2: Latitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LatitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com LatitudeDecimal Upper Lower DTA_Text DTA MS/MS peak list format. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:DTA_Text:2007-01-12T13-55-57Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ElementContainer Element data type contains evidences and subelements. itag.sol urn:lsid:biomoby.org:objectclass:ElementContainer:2008-03-12T16-21-30Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Evidence Evidence data type that can hold different kind of score objects. itag.sol urn:lsid:biomoby.org:objectclass:Evidence:2008-03-12T16-03-48Z joecker@mpiz-koeln.mpg.de Evidence SubElement SubElement data type that can hold different kind of information about certain regions, like exons. itag.sol urn:lsid:biomoby.org:objectclass:SubElement:2008-03-12T16-11-00Z joecker@mpiz-koeln.mpg.de Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start stop strand Evidence SubElement text-uuencoded uuencoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-uuencoded:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content LatitudeDecimal Maps to Darwin Core 2: Latitude. Express in decimal degrees www.mncn.csic.es urn:lsid:biomoby.org:objectclass:LatitudeDecimal:2001-09-21T16-00-00Z jatorre@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com LatitudeDecimal IRFGCDemo_PIDList Phenotype IDs and corresponding GID list (IRFGC Demo) www.iris.irri.org urn:lsid:biomoby.org:objectclass:IRFGCDemo_PIDList:2001-09-21T16-00-00Z m.anacleto@cgiar.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GIDs CodonAdaptationIndex Codon Adaptation Index is a simple, effective measure of synonymous codon usage bias. The CAI index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene sequence is calculated from the frequency of use of all codons in that gene sequence. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression. mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:CodonAdaptationIndex:2007-03-14T17-45-04Z ekawas@mrl.icapture.ubc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com cai sequence_name GCP_Germplasm GCP_Germplasm inherits alot of its basic functionality from GCP_Entity. Every germplasm sample requires a unique identifier. This model facility for achieving this comes by inheritance of the Germplasm model from the Entity model, which itself, inherits from Identifier.(Germplasm-to-germplasm relationships are modeled as GCP_EntityRelationship instances of type specified by the GCP GermplasmRelationship ontology) In the GCP domain model, Germplasm refers to living plant material carrying genetic information that may be propagated naturally or artificially, either by sexual reproduction or clonally. The Germplasm domain model describes such instances of seed or clonal stocks of a specified and distinct genetic composition. A germplasm sample or instance can be thought of as a packet of seeds (or other propagating material) that is managed separately from other packets of seeds in a collection in a sense that germplasm specialists would not want to mix them. - type: an ontology term that describes the germplasm (e.g. seed/whole plant, tissue culture, cell culture, clone) - taxon: holds classification information (e.g. genus, species) for the germplasm www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Germplasm:2008-10-14T03-22-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name storageLocations acquisitionSource taxon DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com acquisitionDate type GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies cropName intellectualPropertyPortfolio biologicalStatus Interactor An interactor is a reference to an object, with a role pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:Interactor:2001-09-21T16-00-00Z jmfernandez@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com role NCBI_BLAST_Text Plaintext Blast report from NCBI Blast software www.illuminae.com urn:lsid:biomoby.org:objectclass:NCBI_BLAST_Text:2001-09-21T16-00-00Z markw@illuminae.com BLAST-Report A parent node for all of the different types of Blast reports bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:BLAST-Report:2006-07-06T21-23-16Z markw@illuminae.com Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com GenePosition position of a gene on a single strand ualberta.ca urn:lsid:biomoby.org:objectclass:GenePosition:2007-07-31T21-57-11Z biomoby@dhx.ath.cx Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com start end Link contains a string representing a URL (e.g. http://www.eu-plant-genome.net) mips.gsf.de urn:lsid:biomoby.org:objectclass:Link:2006-05-17T13-26-22Z Octave.Noubibou@gsf.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com url PotentialTaxon a potential taxon is a scientific name plus the taxonomic reference where this name has been described. biocase.org urn:lsid:biomoby.org:objectclass:PotentialTaxon:2006-09-19T16-13-01Z jatorre@gmail.com TaxonScientificName Full taxon name. skofic.net urn:lsid:biomoby.org:objectclass:TaxonScientificName:2001-09-21T16-00-00Z info@skofic.net Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name Reference GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome Position Strain xdom-flatfile ProDom decomposition of a protein bioinfo.genopole-toulouse.prd.fr urn:lsid:biomoby.org:objectclass:xdom-flatfile:2006-04-03T13-12-39Z Emmanuel.Courcelle@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Locality Original locality data as appearing on a label or in an original entry. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Locality:2001-09-21T16-00-00Z jatorre@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com LocalityText BL2GAnnotation Annotation of blast2gene. inb.bsc.es urn:lsid:biomoby.org:objectclass:BL2GAnnotation:2007-10-17T14-53-35Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Strand Type AntigenicAnnotation Annotation of antigenic sites. inb.bsc.es urn:lsid:biomoby.org:objectclass:AntigenicAnnotation:2007-01-12T12-52-11Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Score Max_score_pos DnaSequenceHolder holds 3 dnasequences www.mobycentral.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:DnaSequenceHolder:2001-09-21T16-00-00Z ed.kawas@gmail.com DNASequence Lightweight representation a DNA sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:DNASequence:2001-09-21T16-00-00Z markw@illuminae.com NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length Sequence3 Sequence1 Sequence2 genbank-flatfile a formatted plaintext genbank flatfile www.illuminae.com urn:lsid:biomoby.org:objectclass:genbank-flatfile:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com End Start ChinookServiceObject A chinook bioinformatics service that is runnable for the given Moby Data Input smweb.bcgsc.bc.ca urn:lsid:biomoby.org:objectclass:ChinookServiceObject:2001-09-21T16-00-00Z smontgom@bcgsc.bc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com MobyXMLData-input name type location version GO_Term A very lightweight object holding a GO term name and its definition www.illuminae.com urn:lsid:biomoby.org:objectclass:GO_Term:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Term Definition InvertedRepeat inverted repeats in a nucleotide sequence. The 'a' sequence runs 5' to 3' while the 'b' sequence runs 3' to 5' The start of the sequence refers to the 5' start of sequence 'a' and the 3' start of sequence 'b' The end of the sequence refers to the 3' end of sequence 'a' and the 5' end of sequence 'b' mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:InvertedRepeat:2007-04-24T19-58-44Z ekawas@mrl.icapture.ubc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com a_start a_end b_start b_end NucleotideSequence Lightweight representation of any type of nucleotide sequence (DNA, RNA, etc) www.illuminae.com urn:lsid:biomoby.org:objectclass:NucleotideSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Length a_seq b_seq SequenceComplexity The linguistic complexity of a sequence mrl.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:SequenceComplexity:2007-03-14T18-19-59Z ekawas@mrl.icapture.ubc.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com sequenceName Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com length Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com complexity NCBI_Blast_Database a description of a sequence or protein database for use with NCBI BLAST sgn.cornell.edu urn:lsid:biomoby.org:objectclass:NCBI_Blast_Database:2001-09-21T16-00-00Z rmb32@cornell.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com title Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com idNumber proteinOrNucleotide fileBasename numSequences unixTimestamp comment CODATA Text formatted in 'CODATA' format www.illuminae.com urn:lsid:biomoby.org:objectclass:CODATA:2007-02-13T17-49-56Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name object type annotation FunCUT_Annotation_XML Annotations of homologous sequences from FunCUT services in xml format pdg.cnb.uam.es urn:lsid:biomoby.org:objectclass:FunCUT_Annotation_XML:2007-03-07T15-41-32Z jmrc@cnb.uam.es text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content ISS_Annotation_XML Annotations of homologous sequences from ISS services in xml format cnio.es urn:lsid:biomoby.org:objectclass:ISS_Annotation_XML:2007-03-26T16-20-11Z jmrodriguez@cnio.es text_xml text in xml. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:text_xml:2007-01-12T11-31-56Z inb@pcm.uam.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PDB-Enriched PDB structure together with a Jmol script and a html description. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:PDB-Enriched:2001-09-21T16-00-00Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com JmolScript text-html HTML www.illuminae.com urn:lsid:biomoby.org:objectclass:text-html:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com content Description AttributableObject An object whose data is attributed to a source/author metnetdb.org urn:lsid:biomoby.org:objectclass:AttributableObject:2007-05-25T13-36-52Z rannic@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com source GraphPoint3D GraphPoint2D with an additional Float object for the third dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint3D:2008-05-11T12-21-44Z pieter.neerincx@gmail.com GraphPoint2D GraphPoint1D with an additional Float object for the second dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint2D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com dimension2 dimension3 FASTA_Base_Quality Sequence base quality data in FASTA format genome.imim.es urn:lsid:biomoby.org:objectclass:FASTA_Base_Quality:2006-05-03T09-02-34Z akerhornou@imim.es FASTA FASTA formatted sequence www.sdsc.edu urn:lsid:biomoby.org:objectclass:FASTA:2001-09-21T16-00-00Z steube@sdsc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GFF1 Generic Feature Format File type 1 (original Sanger specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF1:2001-09-21T16-00-00Z markw@illuminae.com GFF Generic Feature Format File (of any subtype) www.illuminae.com urn:lsid:biomoby.org:objectclass:GFF:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content Evidence Evidence data type that can hold different kind of score objects. itag.sol urn:lsid:biomoby.org:objectclass:Evidence:2008-03-12T16-03-48Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com DSSP_Text DSSP plain text. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:DSSP_Text:2007-01-11T09-54-03Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MMP_Locus Maize Mapping Project Locus Id www.maizemap.org urn:lsid:biomoby.org:objectclass:MMP_Locus:2001-09-21T16-00-00Z coee@missouri.edu Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EvocDIGDescription A DIGDescription using only terms from the Evoc Ontology eva.mpg.de urn:lsid:biomoby.org:objectclass:EvocDIGDescription:2001-09-21T16-00-00Z hoehndorf@eva.mpg.de DIGDescription A concept description in DIG format eva.mpg.de urn:lsid:biomoby.org:objectclass:DIGDescription:2001-09-21T16-00-00Z hoehndorf@eva.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com description ProcheckReport Set of textual and image-plot reports produced by PROCHECK. inb.bsc.es urn:lsid:biomoby.org:objectclass:ProcheckReport:2007-01-12T15-10-50Z atorrano@lsi.upc.edu PDB-Text PDB format report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:PDB-Text:2006-10-04T14-19-35Z moby-services@mmb.pcb.ub.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content new secstr nb anglen stereochemical_parameters PlotReport A report composed only by a set of plots. inb.bsc.es urn:lsid:biomoby.org:objectclass:PlotReport:2007-01-12T14-53-55Z atorrano@lsi.upc.edu ArrayImage_Encoded An Array filled with Image_Encoded elements. inb.bsc.es urn:lsid:biomoby.org:objectclass:ArrayImage_Encoded:2007-01-12T14-52-48Z atorrano@lsi.upc.edu Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Key ElementImage_Encoded Image_Encoded belonging to an Array. inb.bsc.es urn:lsid:biomoby.org:objectclass:ElementImage_Encoded:2007-01-12T14-52-29Z atorrano@lsi.upc.edu Element Element object for arrays and matrixes. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Element:2006-03-21T11-50-25Z inb@pcm.uam.es Key Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es mimeType rawdata Value elements description application name Ramachandran Gly_and_Pro_Ramachandran Chi1-Chi2 Main-chain_parameters Side-chain_parameters Residue_properties Main-chain_bond_length_distributions Main-chain_bond_angle_distributions RMS_distances_from_planarity Distorted_geometry_plots GraphSeries2D Contains one or more GraphPoint2D objects to plot a two dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeries2D:2008-05-11T12-21-46Z pieter.neerincx@gmail.com GraphPoint2D GraphPoint1D with an additional Float object for the second dimension. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint2D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com GraphPoint1D Base GraphPoint object. Contains a value for a data point in a one dimensional graph. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphPoint1D:2008-05-11T12-21-43Z pieter.neerincx@gmail.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com dimension2 dimension1 GraphSeriesBase Base object for data series to plot graphs. Specifies a color for each series. Namespace must be either RGB, RGB-hex or CMYK. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:GraphSeriesBase:2008-03-07T16-27-10Z pieter.neerincx@gmail.com Color Simple object to list a color value. Notation of color values depends on the namespace. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Color:2008-03-07T16-27-08Z pieter.neerincx@gmail.com BasicGFFSequenceFeature An object containing all components necessary to represent a simple GFF-compliant sequence feature (the content is NOT validated against the GFF specification) www.illuminae.com urn:lsid:biomoby.org:objectclass:BasicGFFSequenceFeature:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com reference source method Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com start stop Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score strand frame phase multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com value key column9_tag_value Record A database record containing zero or more String objects. String articleName attribute = field name. String content = field data. www.bioinformatics.nl urn:lsid:biomoby.org:objectclass:Record:2006-03-01T18-35-13Z pieter.neerincx@gmail.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com record M_GIS GIS elements in the MGIS database composed of latitude, logitude and altitude bioinfo.inibap.org urn:lsid:biomoby.org:objectclass:M_GIS:2001-09-21T16-00-00Z m.rouard@cgiar.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com longitude latitude altitude EmowseAnnotatedAASequence Molecular weights annotated sequence with Emowse report information. inb.bsc.es urn:lsid:biomoby.org:objectclass:EmowseAnnotatedAASequence:2007-01-12T14-48-08Z rroyo@lsi.upc.edu MolWeightsAnnotatedAASequence Molecular weights annotated sequence. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightsAnnotatedAASequence:2007-01-12T14-48-02Z rroyo@lsi.upc.edu AnnotatedAASequence Annotated aminoacid sequence mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:AnnotatedAASequence:2006-10-05T14-55-58Z moby-services@mmb.pcb.ub.es CommentedAASequence Represents a Amino Acid Sequence including a String (Description). mips.gsf.de urn:lsid:biomoby.org:objectclass:CommentedAASequence:2001-09-21T16-00-00Z Rebecca.Ernst@gsf.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Description AminoAcidSequence Lightweight representation an amino acid sequence www.illuminae.com urn:lsid:biomoby.org:objectclass:AminoAcidSequence:2001-09-21T16-00-00Z markw@illuminae.com GenericSequence Represents any molecule that can be described as a 'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any other molecule with a sequence. This is most useful for cases where it is not known what specific type of molecule will be represented in the object. www.illuminae.com urn:lsid:biomoby.org:objectclass:GenericSequence:2001-09-21T16-00-00Z markw@illuminae.com SequenceString VirtualSequence This root of the Sequence object hierarchy carries only the length of the sequence. Can be used, for example, to pre-screen results based on sequence size before retrieving a more heavyweight sequence object www.illuminae.com urn:lsid:biomoby.org:objectclass:VirtualSequence:2001-09-21T16-00-00Z markw@illuminae.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Length MolWeightAnnotation Molecular weight Annotation. inb.bsc.es urn:lsid:biomoby.org:objectclass:MolWeightAnnotation:2007-01-12T14-47-58Z rroyo@lsi.upc.edu Annotation Sequence Annotation mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Annotation:2006-10-05T09-07-44Z moby-services@mmb.pcb.ub.es End Start Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com MolWeight Annotations Score Hit Accuracy_ratio Name AlignedDotBracketFasta AlignedDotBracketFasta is a format to cobine multiple sequences with secondary structures in one string. It contains at least two pairs of sequence and secondary structure. A sequence starts with '>' and the sequence name. The next line contains the sequence data (FASTA format). The third line represents the secondary structure and consists of - . ( ) [ ] { } < > (Dot-Bracket Format). Further pairs of sequences and secondary structure are possible. >Sequence_1 AAA-CGG-ACGTA (..(-..)(-).) >Sequence_2 ATTGC-A-TTAAC ..((..-..).-) bibiserv.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:AlignedDotBracketFasta:2008-01-14T15-18-35Z webmaster@uni-bielefeld.de Sequence_alignment_report Sequence alginment reports. org.inab.upc urn:lsid:biomoby.org:objectclass:Sequence_alignment_report:2006-02-28T12-11-26Z rroyo@lsi.upc.edu text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FASTA-Report An FASTA alignment Report bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:FASTA-Report:2006-07-06T22-09-38Z markw@illuminae.com FASTA-Report EmageAnnotation Annotations about gene expression from EMAGE database mapped on the image www.cnb.uam.es urn:lsid:biomoby.org:objectclass:EmageAnnotation:2007-11-19T12-06-12Z natalia@cnb.uam.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com ExpressionLevel ExpressionPattern Description Component Image_Encoded An image encoded in Base-64 mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:Image_Encoded:2006-10-05T11-02-08Z moby-services@mmb.pcb.ub.es mimeType rawdata GeneSymbol GeneName ExpressionNotes Pepcoil_Text runEmbossPepcoil output. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Pepcoil_Text:2007-01-15T15-26-39Z inb@pcm.uam.es text_formatted Fractional solvation report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:text_formatted:2006-03-15T17-37-53Z ivanp@mmb.pcb.ub.es text_plain testo plain www.tttd.edu urn:lsid:biomoby.org:objectclass:text_plain:2001-09-21T16-00-00Z tttd@sdsc.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BacMapSpeciesCard U of A, Genome Canada, BacMap http://wishart.biology.ualberta.ca/BacMap/ Text formatted as a Species Card ualberta.ca urn:lsid:biomoby.org:objectclass:BacMapSpeciesCard:2007-08-23T23-15-15Z biomoby@dhx.ath.cx text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name Annotated_GO_Term_With_Probability Datatype to store also the probability, that this GO Term ist right or wrong mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_GO_Term_With_Probability:2007-11-14T15-30-15Z joecker@mpiz-koeln.mpg.de Annotated_GO_Term Provides also the description of the GO term (not the name or the ID!), an evidence code and the process (molecular function, biological process, cellular component) mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_GO_Term:2007-10-01T13-18-57Z joecker@mpiz-koeln.mpg.de GO_Term A very lightweight object holding a GO term name and its definition www.illuminae.com urn:lsid:biomoby.org:objectclass:GO_Term:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Term Definition detailed_description process evidence_code Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Probability BriefTaxonConcept Brief description of a taxon returned by the GBIFGetTaxonConcepts. www.gbif.org urn:lsid:biomoby.org:objectclass:BriefTaxonConcept:2006-08-08T09-24-41Z fdelcastillo@gbif.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Key CanonicalName Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Accepted PublicationKey b64_encoded_svgz Base 64 encoded svgz image (a base64 encoded, gezipped svg vector graphics) mapman.mpimp-golm.mpg.de urn:lsid:biomoby.org:objectclass:b64_encoded_svgz:2006-05-28T16-08-33Z usadel@mpimp-golm.mpg.de text-base64 base64-encoded data www.illuminae.com urn:lsid:biomoby.org:objectclass:text-base64:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content amirna_gi an object cshl.edu urn:lsid:biomoby.org:objectclass:amirna_gi:2007-06-14T21-11-55Z leotta@cshl.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com status multi_key_value_pair key/value pair object for key/value pairs with a 1:many relationship www.illuminae.com urn:lsid:biomoby.org:objectclass:multi_key_value_pair:2001-09-21T16-00-00Z markw@illuminae.com value key multi_key_value_pair target_seq mirna_pattern mirna_long Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com energy amirna_id loop_144 optimal_energy Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com mutations score SequenceML SequenceML is a XML schema for representing multiple sequences with some meta information (FASTA replacement) For example: <?xml version="1.0" encoding="UTF-8"?> <ns3:sequenceML xmlns="http://hobit.sourceforge.net/xsds/20060102/sequenceML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns3="http://hobit.sourceforge.net/xsds/20060102/sequenceML" version="0.1" xsi:schemaLocation="http://hobit.sourceforge.net/xsds/20060102/sequenceML http://hobit.sourceforge.net/xsds/20060102/sequenceML.xsd"> <sequence seqID="Sequence_1"> <description>Comment</description> <freeSequence>ABCAHCANCNCNAHCHACHAHCNBN</freeSequence> </sequence> <sequence seqID="Sequence_2"> <description>Comment2</description> <freeSequence>BDABCBACBABBCKLAKLCKLABKN</freeSequence> </sequence> </ns3:sequenceML> www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:SequenceML:2008-03-04T11-52-55Z web@uni-bielefeld.de BioDom BioDOM is a JAVA library for converting native non-XML output from various bioinformatic tools to XML formats that can be validated against XMLSchemas. www.techfak.uni-bielefeld.de urn:lsid:biomoby.org:objectclass:BioDom:2008-03-04T11-47-16Z web@uni-bielefeld.de text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SO_RNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA:2009-08-18T08-41-51Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA:2009-08-18T08-41-15Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_GenomicFeatureAssay Associates GCP_GenomicFeatureDetector in a many-to-many relationship to GCP_GenomicFeatureDetectionProtocol instances, for genotyping experimental assays. This allows reuse of protocols for different detectors (and several protocols being applied to one specified detector). See Demeter genotype model for further guidance. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenomicFeatureAssay:2008-10-14T03-22-25Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies detector protocol GCP_BiblioReference Aside from the MOBY modeling considerations noted above in the introduction, GCP_BiblioReference is generally as per the corresponding Demeter model except for the following attributes. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_BiblioReference:2008-10-14T03-22-14Z r.bruskiewich@cgiar.org GCP_SimpleCitation GCP_SimpleCitation is generally as per the Demeter model except that the date, journal source and author list attributes are modeled as simple MOBY Strings. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleCitation:2008-10-14T03-21-13Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com source date authorList GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org name valueString type format language publisher metaData authors contributors indexings content GCP_MapPoint A GCP_MapPoint is a point coordinate defining a GCP_MapPosition. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPoint:2008-10-14T03-23-06Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints GCP_Person A GCP_Person is a GCP_LegalEntity semantically constrained to represent a single human being in the system. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Person:2008-10-14T03-21-57Z r.bruskiewich@cgiar.org GCP_LegalEntity GCP_LegalEntity represents a general subclass for any GCP_Entity recognized in legal terms as having a legal personality (i.e. ability to have human behaviour as an individual or in aggregate, able to own property, liable for legal prosecution, etc.). This includes both person and organization. - contactingDetails. A LegalEntity obviously has details relating to its localization in the human world. For efficiency, we treat instances of another moby data type, GCP_ContactingDetails, as a subclass of GCP_Identifier, and referencing these details from GCP_LegalEntity using the pertinent GCP_SimpleIdentifier. A LegalEntity may have several such contactingDetails. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LegalEntity:2008-10-14T03-21-54Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies contactingDetails GCP_Study GCP_Study, inherits from GCP_Entity and records general meta-data (but not the data contents) of a study. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Study:2008-10-14T03-21-28Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies project investigators factors variates effects SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_repeat_unit The simplest repeated component of a repeat region. A single repeat. cirad.fr urn:lsid:biomoby.org:objectclass:SO_repeat_unit:2009-08-18T08-42-10Z julien.wollbrett@cirad.fr SO_topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_topologically_defined_region:2009-08-18T08-39-42Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com OSE_object Is an object for the OSE project, it contains an Id a Name and a Description avilin05.avignon.inra.fr urn:lsid:biomoby.org:objectclass:OSE_object:2008-08-20T15-19-49Z pierre-yves.chibon@avignon.inra.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Id String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Name Description SO_encodes_disjoint_polypeptides A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_disjoint_polypeptides:2009-08-18T08-44-58Z julien.wollbrett@cirad.fr SO_encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_greater_than_1_polypeptide:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_cryptic no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_cryptic:2009-08-18T08-42-27Z julien.wollbrett@cirad.fr SO_edited An attribute describing a sequence that is modified by editing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_edited:2009-08-18T08-40-48Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_antisense A region sequence that is complementary to a sequence of messenger RNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_antisense:2009-08-18T08-44-42Z julien.wollbrett@cirad.fr SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values CodingSNP_Extended An extended version of the former CodingSNP, featuring the additional fields: reference_allele, genotype_allele husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Extended:2010-11-24T14-13-31Z genome@dkfz.de CodingSNP SNPs in coding region with codons and aminoacids www.weigelworld.org urn:lsid:biomoby.org:objectclass:CodingSNP:2006-06-27T14-31-56Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com end start String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com chromosome Position Strain codon_ref aa_ref codon_var aa_var aa_pos Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca aa_change reference_allele genotype_allele CodingSNP_Consequences_NMD Changes in Non Mediated Decay produced by SNP changes. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Consequences_NMD:2010-12-23T08-52-17Z genome@dkfz.de Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com nmd_change AnnotatedCodingSNP SNP in the context of its location in a protein including annotations. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedCodingSNP:2010-12-01T11-49-27Z genome@dkfz.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com wt_aa_seq CodingSNP_Extended An extended version of the former CodingSNP, featuring the additional fields: reference_allele, genotype_allele husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Extended:2010-11-24T14-13-31Z genome@dkfz.de CodingSNP SNPs in coding region with codons and aminoacids www.weigelworld.org urn:lsid:biomoby.org:objectclass:CodingSNP:2006-06-27T14-31-56Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com end start chromosome Position Strain codon_ref aa_ref codon_var aa_var aa_pos aa_change reference_allele genotype_allele mut_aa_seq ext_database_refs AnnotatedSNPAndTranscriptLocation annotated SNP including its location in a transcript husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedSNPAndTranscriptLocation:2010-11-09T15-25-18Z genome@dkfz.de NGS_SNP An annotated SNP derived from Next Generation Sequencing data. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:NGS_SNP:2010-04-29T06-36-18Z genome@dkfz.de Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com coverage_all coverage_new_allele AnnotatedSNP A SNP descibed by its location on the reference genome and quality of the assay. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedSNP:2010-04-29T06-31-15Z genome@dkfz.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com genetype_allele GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp end start chromosome Position Strain reference_allele confidence SNPTranscript transcript in context of a SNP husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:SNPTranscript:2010-11-09T15-20-27Z genome@dkfz.de snp_type AnnotatedTranscript Annotated transcript husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedTranscript:2010-11-09T15-18-45Z genome@dkfz.de database_references GeneticElement GeneticElement including name, type, start, stop, strand (0 for forward, 1 for reverse), and description; use name for element identifier (like 'exon_1'), type for the element class (like 'exon') mips.gsf.de urn:lsid:biomoby.org:objectclass:GeneticElement:2006-06-14T11-45-25Z Octave.Noubibou@gsf.de strand description name type stop start snp_transcripts Sifter_Function_Terms Provides from Sifter predicted lists of members from Annotated_GO_Term, Annotated_KO_Term, Annotated_EC_Number and Annotated_MapMan_Bin. mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Sifter_Function_Terms:2010-08-25T16-44-40Z klee@mpipz.mpg.de Annotated_MapMan_Bin MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_MapMan_Bin:2008-06-13T11-27-33Z joecker@mpiz-koeln.mpg.de MapMan_Bin MapMan bin mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:MapMan_Bin:2008-06-13T11-26-56Z joecker@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description Annotated_MapMan_Bin Annotated_EC_Number EC number mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_EC_Number:2008-06-13T11-24-52Z joecker@mpiz-koeln.mpg.de EC_Number EC number mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:EC_Number:2008-06-13T11-23-05Z joecker@mpiz-koeln.mpg.de description Annotated_EC_Number Annotated_KO_Term KEGG ontology term mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_KO_Term:2008-06-13T11-26-24Z joecker@mpiz-koeln.mpg.de description KO_Term KEGG ontology term mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:KO_Term:2008-06-13T11-25-35Z joecker@mpiz-koeln.mpg.de Annotated_KO_Term Annotated_GO_Term Provides also the description of the GO term (not the name or the ID!), an evidence code and the process (molecular function, biological process, cellular component) mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_GO_Term:2007-10-01T13-18-57Z joecker@mpiz-koeln.mpg.de GO_Term A very lightweight object holding a GO term name and its definition www.illuminae.com urn:lsid:biomoby.org:objectclass:GO_Term:2001-09-21T16-00-00Z markw@illuminae.com Term Definition detailed_description process evidence_code Annotated_GO_Term BioObjectOrthologues Object containing information about a orthologous genes in GabiPD. Orthologues were identified with InParanoid v4 or higher. Only orthologues with confidence score higher than 0.7 and bootstrap support higher than 0.9 will be retrieved by this service. www.gabipd.org urn:lsid:biomoby.org:objectclass:BioObjectOrthologues:2010-07-14T06-56-56Z gabipd@mpimp-golm.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com BioObjectSourceDescription BioObject Object containing information about a bioobject www.gabipd.org urn:lsid:biomoby.org:objectclass:BioObject:2010-06-16T06-59-28Z gabipd@mpimp-golm.mpg.de Name Type Description Genotype Strain TaxonName GBIF - Concatenated scientific name, preferrably formed in accordance with a Code of Nomenclature, i. e. a monomial, bionomial, or trinomial plus author(s) or author team(s) and - where relevant - year, or the name of a cultivar or cultivar group, or a hybrid formula, as fully as possible. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:TaxonName:2001-09-21T16-00-00Z jatorre@gmail.com TaxonName FirstEpithet GBIF - The first epithet in a botanical name combination (species epithet or the epithet of the subdivision of a genus. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:FirstEpithet:2001-09-21T16-00-00Z jatorre@gmail.com FirstEpithet FirstEpithet Genus GBIF test - Genus www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Genus:2001-09-21T16-00-00Z jatorre@gmail.com Genus InfraspecificEpithet GBIF - The final epithet of a botanical name of infraspecific rank. AppInfo Nothing found. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:InfraspecificEpithet:2001-09-21T16-00-00Z jatorre@gmail.com InfraspecificEpithet InfraspecificEpithet Species AccessPageUrl BioObjectSource BioObjectTargetDescription BioObjectTarget AnnotatedCodingSNP SNP in the context of its location in a protein including annotations. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedCodingSNP:2010-12-01T11-49-27Z genome@dkfz.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com wt_aa_seq CodingSNP_Extended An extended version of the former CodingSNP, featuring the additional fields: reference_allele, genotype_allele husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Extended:2010-11-24T14-13-31Z genome@dkfz.de CodingSNP SNPs in coding region with codons and aminoacids www.weigelworld.org urn:lsid:biomoby.org:objectclass:CodingSNP:2006-06-27T14-31-56Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com end start chromosome Position Strain codon_ref aa_ref codon_var aa_var aa_pos Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca aa_change reference_allele genotype_allele mut_aa_seq ext_database_refs SNPTranscript transcript in context of a SNP husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:SNPTranscript:2010-11-09T15-20-27Z genome@dkfz.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com snp_type AnnotatedTranscript Annotated transcript husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedTranscript:2010-11-09T15-18-45Z genome@dkfz.de database_references GeneticElement GeneticElement including name, type, start, stop, strand (0 for forward, 1 for reverse), and description; use name for element identifier (like 'exon_1'), type for the element class (like 'exon') mips.gsf.de urn:lsid:biomoby.org:objectclass:GeneticElement:2006-06-14T11-45-25Z Octave.Noubibou@gsf.de Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com strand description name type stop start Pizza_Country A class that is equivalent to the set of individuals that are described in the enumeration - ie Countries can only be either America, England, France, Germany or Italy and nothing else. Note that these individuals have been asserted to be allDifferent from each other. c.fr urn:lsid:biomoby.org:objectclass:Pizza_Country:2011-10-14T15-17-00Z j@c.fr Pizza_DomainConcept no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DomainConcept:2011-10-14T15-16-56Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com component Component that descibes a part of a composition. Containing the name of a residue and a minimum and maximum value. rings.t.soka.ac.jp urn:lsid:biomoby.org:objectclass:component:2010-08-26T11-36-22Z kkiyoko@soka.ac.jp GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com minValue maxValue String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com carbbank_name AnnotatedTranscript Annotated transcript husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedTranscript:2010-11-09T15-18-45Z genome@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com database_references GeneticElement GeneticElement including name, type, start, stop, strand (0 for forward, 1 for reverse), and description; use name for element identifier (like 'exon_1'), type for the element class (like 'exon') mips.gsf.de urn:lsid:biomoby.org:objectclass:GeneticElement:2006-06-14T11-45-25Z Octave.Noubibou@gsf.de Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com strand String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com description name type stop start Annotated_MapMan_Reaction Biochemical reaction as a string. Additional fields store the RHEA ID, EC code and subcellular localization, if known. mpimp-golm.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_MapMan_Reaction:2011-05-23T13-52-00Z lohse@mpimp-golm.mpg.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com rhea_id reaction subcellular_loc ec_code Motif_Changes Includes changes in motifs from a protein sequence caused by SNPs. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:Motif_Changes:2010-12-20T09-04-37Z genome@dkfz.de Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com score String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com motif_mutant consequence method snp_inside motif_ref MSPeak datatype for representing a single peak from mass spectrometry data peak has a float value representing m/z, another one representing corresponding intensity value and a third one representing retention time of peak ipb-halle.de urn:lsid:biomoby.org:objectclass:MSPeak:2008-07-12T15-45-51Z mgerlich@ipb-halle.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com intensity mz retentiontime MSPeakList datatype for representing a complete peaklist from mass spectrometry data each peak from that list is represented using data type MSPeak which provides mz, intensity and retention time values for each single peak ipb-halle.de urn:lsid:biomoby.org:objectclass:MSPeakList:2008-07-12T15-48-41Z mgerlich@ipb-halle.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MSPeak datatype for representing a single peak from mass spectrometry data peak has a float value representing m/z, another one representing corresponding intensity value and a third one representing retention time of peak ipb-halle.de urn:lsid:biomoby.org:objectclass:MSPeak:2008-07-12T15-45-51Z mgerlich@ipb-halle.de Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com intensity mz retentiontime MSPeak SO_sequence_difference A region where the sequence differs from that of a specified sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_difference:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SIAM_Annotation_XML Gene Ontology terms from SIAM service in xml format cnio.es urn:lsid:biomoby.org:objectclass:SIAM_Annotation_XML:2008-06-26T16-19-58Z jmrodriguez@cnio.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content BlastXP-Text Output of the BlastXP service cgl.imim.es urn:lsid:biomoby.org:objectclass:BlastXP-Text:2008-07-08T14-52-20Z jflo@imim.es BLAST-Text PSIBLAST report mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:BLAST-Text:2001-09-21T16-00-00Z gelpi@bq.ub.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content FatiGO-XML FatiGO results in XML format bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:FatiGO-XML:2008-07-11T06-55-57Z jtarraga@cipf.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MicroArrayData-Text Micro-array data in text format representing gene expression patterns. Each line must have the gene name and the expression values and the expression values for each condition. All the data items must be separated by tabulators bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:MicroArrayData-Text:2008-07-11T06-55-10Z jtarraga@cipf.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content List-Text A list where each line is an elemenent in the list bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:List-Text:2008-07-11T06-56-52Z jtarraga@cipf.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content DifferentialExpressionTest-Text Results in text format from a differential expression test. Each line must have the gene name and the different statistics depending on the applied test bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:DifferentialExpressionTest-Text:2008-07-11T06-57-43Z jtarraga@cipf.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content WeightedList-Text A weighted list. Each line must have two values separated by tabulator. The first value is the name (ex. a gene name) and the second value is the weight (ex. a p-value for that gene) bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:WeightedList-Text:2008-07-11T06-58-26Z jtarraga@cipf.es text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content PredictionModel-XML XML object for a prediction model of gene expression data that includes a graphical representation of the model, the confussion matrix, the classification and the own model. bioinfo.cipf.es urn:lsid:biomoby.org:objectclass:PredictionModel-XML:2008-07-11T08-15-48Z jtarraga@cipf.es text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MSPeakRel datatype representing a single mass spectrometry peak with m/z value (float) and relative intensity (integer, range 0-999) ipb-halle.de urn:lsid:biomoby.org:objectclass:MSPeakRel:2008-08-10T09-58-58Z mgerlich@ipb-halle.de Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com mz Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com relInt AglycaResidue Stores a aglycon residue of a carbohydrate. The information consist of the name of the residue the carbohydrate is attachted to and if this aglcon is at the reducing end or not. www.glycome-db.org urn:lsid:biomoby.org:objectclass:AglycaResidue:2008-08-10T16-47-11Z rene.ranzinger@gmx.de GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca reducing Annotated_Interaction An interaction of two interactors. It stores additionally the detection methods and interactiontypes. mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_Interaction:2008-08-12T06-20-08Z groscurt@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Annotated_Interactor An interactor which is part of an interaction. It stores additional crossreferences to other databases. mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_Interactor:2008-08-12T06-19-48Z groscurt@mpiz-koeln.mpg.de crossreferences interactorA interactorB detectedMethods interactionTypes Annotated_Interactor An interactor which is part of an interaction. It stores additional crossreferences to other databases. mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Annotated_Interactor:2008-08-12T06-19-48Z groscurt@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com crossreferences CommentedWeightedObject A commented Object (Object with Description) with an Integer cgl.imim.es urn:lsid:biomoby.org:objectclass:CommentedWeightedObject:2008-08-29T09-46-47Z jflo@imim.es Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Weight CommentedObject Description of an object identified by 'id' in 'namespace' mmb.pcb.ub.es urn:lsid:biomoby.org:objectclass:CommentedObject:2006-10-05T10-15-26Z moby-services@mmb.pcb.ub.es String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Description ExpiredEntry Stores a ID and the name of an expired entry in a database. In addition a timestamp is given. www.glycome-db.org urn:lsid:biomoby.org:objectclass:ExpiredEntry:2008-08-31T12-55-11Z rene.ranzinger@gmx.de DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com timestamp GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_supported_by_sequence_similarity An attribute to describe a feature that has been predicted using sequence similarity techniques. cirad.fr urn:lsid:biomoby.org:objectclass:SO_supported_by_sequence_similarity:2009-08-18T08-42-28Z julien.wollbrett@cirad.fr SO_predicted An attribute describing an unverified region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted:2009-08-18T08-40-50Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_cryptic_splice_donor_activation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_cryptic_splice_donor_activation:2009-08-18T08-41-31Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_cryptic_splice_activator A sequence variant causing a new (functional) splice site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_cryptic_splice_activator:2009-08-18T08-40-12Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_splice_acceptor A sequence_variant_effect that changes the splice acceptor sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splice_acceptor:2009-08-18T08-40-38Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_natural An attribute describing a feature that occurs in nature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_natural:2009-08-18T08-40-20Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_RNA_motif A motif that is active in RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_motif:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_ds_oligo A double stranded oligonucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ds_oligo:2009-08-18T08-44-18Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_four_demethylwyosine 4_demethylwyosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_four_demethylwyosine:2009-08-18T08-47-45Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sarcin_like_RNA_motif A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sarcin_like_RNA_motif:2009-08-18T08-45-53Z julien.wollbrett@cirad.fr SO_asymmetric_RNA_internal_loop An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. cirad.fr urn:lsid:biomoby.org:objectclass:SO_asymmetric_RNA_internal_loop:2009-08-18T08-45-22Z julien.wollbrett@cirad.fr SO_RNA_internal_loop A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_internal_loop:2009-08-18T08-44-06Z julien.wollbrett@cirad.fr SO_RNA_motif A motif that is active in RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_motif:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_two_prime_O_dimethylcytidine 5,2'-O-dimethylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_two_prime_O_dimethylcytidine:2009-08-18T08-47-50Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_prime_five_prime_overlap An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_prime_five_prime_overlap:2009-08-18T08-44-56Z julien.wollbrett@cirad.fr SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_VD_gene Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205). cirad.fr urn:lsid:biomoby.org:objectclass:SO_VD_gene:2009-08-18T08-46-29Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment:2009-08-18T08-46-10Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_OntologyTerm A fully documented GCP_OntologyTerm object is a simply specialised kind of GCP_Entity documenting an abstract concept, belonging to a GCP hosted ontology (itself identified by a GCP_SimpleIdentifier). The name, description and namespace attributes of the superclass GCP_SimpleIdentifier and GCP_Identifier serve as the concept name, definition and parent ontology, respectively. The GCP_Entity synonyms covers all concept alias names and database cross references. Of course, since GCP_OntologyTerm is a kind of GCP_Entity, it may also have a primary_citation supporting its definition, plus other pertinent annotation. *Note: Generally speaking, MOBY services only need to to use GCP_SimpleIdentifier references to GCP_OntologyTerm instances, not the full GCP_OntologyTerm, except when the full ontology term definition (GCP_OntologyTerm) is requested by the end user for display in their application. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_OntologyTerm:2008-10-14T03-22-44Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies GCP_ContactingDetail GCP_ContactingDetail describes where and how system users may communicate to a specified GCP_LegalEntity located at a particular site (e.g. home, office, etc.). Reflecting the Demeter model, a GCP_ContactingDetail is modeled as a kind of GCP_SimpleFeature which has some additional locational descriptive attributes. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_ContactingDetail:2008-10-14T03-21-42Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type administrativeDivisions postalCode GCP_CommunicationDetail A GCP_CommunicationDetail is a GCP_SimpleFeature which documents a mode of communication the type - phone, fax, email, etc. - of which is indicated by a GCP_SimpleIdentifier resolving to a GCP_OntologyTerm, and the communication information itself documented by the valueString. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CommunicationDetail:2008-10-14T03-21-10Z r.bruskiewich@cgiar.org communicationModes streetAddress GCP_GenomicMapStudy GCP_GenotypeMapStudy is a kind of GCP_GenotypeStudy conducted against mappedGermplasm (which is a GCP_GermplasmSet retrieved by a GCP_SimpleIdentifier) that generates a set of linkageMaps (identified by GCP_SimpleIdentifiers but whose details are fully recorded in GCP_LinkageMap objects). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenomicMapStudy:2008-10-14T03-21-51Z r.bruskiewich@cgiar.org GCP_GenotypeStudy A GCP_GenotypeStudy is a kind of LaboratoryStudy that applies a set of markers (which is a GCP_MolecularVariantSet identified by a GCP_SimpleIdentifier) to analyze a set of samples (which is a GCP_GermplasmSet of GCP_BiologicalSamples). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenotypeStudy:2008-10-14T03-21-49Z r.bruskiewich@cgiar.org GCP_LaboratoryGermplasmStudy A GCP_LaboratoryGermplasmStudy captures laboratory experimental data about its samples (which are GCP_BiologicalSample objects managed in a GCP_GermplasmSet which is dereferenced using a GCP_SimpleIdentifier). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LaboratoryGermplasmStudy:2008-10-14T03-21-35Z r.bruskiewich@cgiar.org GCP_GermplasmStudy GCP_GermplasmStudy is a kind of Study that characterises a GCP_GermplasmSet of germplasm (identified for retrieval by a GCP_SimpleIdentifier) and documenting growthConditions and treatments as MOBY:Collections of GCP_SimpleFeature objects (with feature types defined by a suitable ontology). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmStudy:2008-10-14T03-21-32Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name treatments GCP_Study GCP_Study, inherits from GCP_Entity and records general meta-data (but not the data contents) of a study. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Study:2008-10-14T03-21-28Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies project investigators factors variates effects germplasm growthConditions samples markers mappedGermplasm linkageMaps GCP_BiologicalSample A GCP_BiologicalSample is a modeled as a kind of Germplasm to which transformations may be applied. It is typically obtained from an organismPart at a specified developmentStage (both annotation specified as a controlled vocabulary identified by GCP_SimpleIdentifier). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_BiologicalSample:2008-10-14T03-22-53Z r.bruskiewich@cgiar.org GCP_Germplasm GCP_Germplasm inherits alot of its basic functionality from GCP_Entity. Every germplasm sample requires a unique identifier. This model facility for achieving this comes by inheritance of the Germplasm model from the Entity model, which itself, inherits from Identifier.(Germplasm-to-germplasm relationships are modeled as GCP_EntityRelationship instances of type specified by the GCP GermplasmRelationship ontology) In the GCP domain model, Germplasm refers to living plant material carrying genetic information that may be propagated naturally or artificially, either by sexual reproduction or clonally. The Germplasm domain model describes such instances of seed or clonal stocks of a specified and distinct genetic composition. A germplasm sample or instance can be thought of as a packet of seeds (or other propagating material) that is managed separately from other packets of seeds in a collection in a sense that germplasm specialists would not want to mix them. - type: an ontology term that describes the germplasm (e.g. seed/whole plant, tissue culture, cell culture, clone) - taxon: holds classification information (e.g. genus, species) for the germplasm www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Germplasm:2008-10-14T03-22-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name storageLocations acquisitionSource taxon DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com acquisitionDate type GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies cropName intellectualPropertyPortfolio biologicalStatus organismPart developmentalStage GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies GCP_RelativeMapPosition The GCP domain model concept of RelativeMapPosition can be modelled as a kind of GCP_MapPosition with a relationship defined by a GCP_SimpleIdentifier specifying a term in a relationship ontology. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_RelativeMapPosition:2008-10-14T03-22-49Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints relationship mapPosition GCP_GermplasmNeighbourhood GCP_GermplasmNeighbourhood is a kind of GCP_GermplasmSet which has a formal biological or management role (see GCP domain model descriptions). Such a set is formally established by source_germplasm (modeled as a set of GCP_SimpleIdentifiers identifying GCP_Germplasm objects) and (generally) belongs to a specified germplasm_collection (also specified by a GCP_SimpleIdentifiers). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmNeighbourhood:2008-10-14T03-22-01Z r.bruskiewich@cgiar.org GCP_GermplasmSet GCP_GermplasmSet is simply any collection of germplasm objects of a specified type (inferred by the namespace of its primary identifier, since it indirectly inherits from GCP_SimpleIdentifier via GCP_Entity). The list of germplasm is identified indirectly by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmSet:2008-10-14T03-22-00Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies germplasm germplasmCollection sourceGermplasm GCP_GenotypeStudy A GCP_GenotypeStudy is a kind of LaboratoryStudy that applies a set of markers (which is a GCP_MolecularVariantSet identified by a GCP_SimpleIdentifier) to analyze a set of samples (which is a GCP_GermplasmSet of GCP_BiologicalSamples). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenotypeStudy:2008-10-14T03-21-49Z r.bruskiewich@cgiar.org GCP_LaboratoryGermplasmStudy A GCP_LaboratoryGermplasmStudy captures laboratory experimental data about its samples (which are GCP_BiologicalSample objects managed in a GCP_GermplasmSet which is dereferenced using a GCP_SimpleIdentifier). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LaboratoryGermplasmStudy:2008-10-14T03-21-35Z r.bruskiewich@cgiar.org GCP_GermplasmStudy GCP_GermplasmStudy is a kind of Study that characterises a GCP_GermplasmSet of germplasm (identified for retrieval by a GCP_SimpleIdentifier) and documenting growthConditions and treatments as MOBY:Collections of GCP_SimpleFeature objects (with feature types defined by a suitable ontology). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmStudy:2008-10-14T03-21-32Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name treatments GCP_Study GCP_Study, inherits from GCP_Entity and records general meta-data (but not the data contents) of a study. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Study:2008-10-14T03-21-28Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies project investigators factors variates effects germplasm growthConditions samples markers GCP_SimpleLocation A GCP_SimpleLocation is a kind of GCP_MapFeature that answers a lightweight version of the question "where?" as it relates to a specified geographical (cartographic) context. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleLocation:2008-10-14T03-21-47Z r.bruskiewich@cgiar.org GCP_MapFeature A GCP_MapFeature models a kind of GCP_Feature that has a coordinate position on a coordinate-dimensioned space called a map, which is identified by a GCP_SimpleIdentifier (see GCP_Map below). The MapFeature class is subclassed into domain specific map feature concepts such as biological GenomicFeature and geographical Location classes. By definition, a MapFeature belongs to only one map; however, the point, interval or space located by the map feature may be mapped onto more than one map, and may have many associated characteristics, which are generally retrievable by suitable web services using the MOBY namespace and identifier associated with the GCP_MapFeature. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapFeature:2008-10-14T03-21-39Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name map GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values geoReference enclosingAdministrativeDivision GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints GCP_LaboratoryGermplasmStudy A GCP_LaboratoryGermplasmStudy captures laboratory experimental data about its samples (which are GCP_BiologicalSample objects managed in a GCP_GermplasmSet which is dereferenced using a GCP_SimpleIdentifier). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LaboratoryGermplasmStudy:2008-10-14T03-21-35Z r.bruskiewich@cgiar.org GCP_GermplasmStudy GCP_GermplasmStudy is a kind of Study that characterises a GCP_GermplasmSet of germplasm (identified for retrieval by a GCP_SimpleIdentifier) and documenting growthConditions and treatments as MOBY:Collections of GCP_SimpleFeature objects (with feature types defined by a suitable ontology). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmStudy:2008-10-14T03-21-32Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name treatments GCP_Study GCP_Study, inherits from GCP_Entity and records general meta-data (but not the data contents) of a study. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Study:2008-10-14T03-21-28Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies project investigators factors variates effects germplasm growthConditions samples GCP_Effect GCP_Effect indexes the observation_units of of the study by the levels of specified factors, both of which are modeled as a MOBY:Collection of GCP_SimpleIdentifier objects that should resolve, respectively, to GCP_Factor descriptions, and GCP_ValueSet objects containing references to GCP_Value objects, the latter each of which whose index value should point to the GCP_Factor or GCP_Variate objects which document them. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Effect:2008-10-14T03-20-57Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name observationUnits factors GCP_MultipleSequenceAlignment A GCP_MultipleSequenceAlignment inherits from GCP_CorrelatedLinkageMapSet to align several sequences to one another using bioinformatics analysis (e.g. ClustalW). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MultipleSequenceAlignment:2008-10-14T03-23-15Z r.bruskiewich@cgiar.org GCP_CorrelatedLinkageMapSet A GCP_CorrelatedLinkageMapSet is a kind of GCP_CorrelatedMapSet composed of GCP_LinkageMap objects. The set may specify a consensusMap which is the integration of all maps in the set into one GCP_LinkageMap (identified by GCP_SimpleIdentifier). An example of this is a contig map of physical or sequence clones. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CorrelatedLinkageMapSet:2008-10-14T03-22-42Z r.bruskiewich@cgiar.org GCP_CorrelatedMapSet Used for comparative mapping, a CorrelatedMapSet aggregates a set of Map objects that can be related to one another by a common set of MapFeatures, that are themselves documented in a CorrelatedMapFeatureSet. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CorrelatedMapSet:2008-10-14T03-21-25Z r.bruskiewich@cgiar.org GCP_Map A GCP_Map is a collection of map_features instances are just represented as GCP_SimpleIdentifier which identify corresponding GCP_MapFeature objects (usually retrievable using a separate web service). This class can manage either genetic or geographic map features, depending on the context specified by map_type. GCP_Map also may have a specified units for the map (e.g. centiMorgan, degrees). Both map_type and units are specified by ontology terms identified by GCP_SimpleIdentifier. Although the GCP model specifies that maps are a kind of map feature, GCP_Map are modeled separately from GCP_MapFeature for simplicity. GCP_Map inherits from GCP_SimpleIdentifier. If it is feasible and desirable to embed maps into maps (e.g. see map layers below), it is assumed that one could use the GCP_Map as a source of GCP_SimpleIdentifier for a context requiring specification of a GCP_MapFeature identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Map:2008-10-14T03-21-23Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies units mapFeature correlatedMaps correlatedMapFeatures consensusMap sequences GCP_CommunicationDetail A GCP_CommunicationDetail is a GCP_SimpleFeature which documents a mode of communication the type - phone, fax, email, etc. - of which is indicated by a GCP_SimpleIdentifier resolving to a GCP_OntologyTerm, and the communication information itself documented by the valueString. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CommunicationDetail:2008-10-14T03-21-10Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type SO_single_stranded_cDNA no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_single_stranded_cDNA:2009-08-18T08-44-48Z julien.wollbrett@cirad.fr SO_cDNA DNA synthesized by reverse transcriptase using RNA as a template. cirad.fr urn:lsid:biomoby.org:objectclass:SO_cDNA:2009-08-18T08-42-23Z julien.wollbrett@cirad.fr SO_DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA:2009-08-18T08-41-15Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_subarray_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_subarray_member:2009-08-18T08-43-57Z julien.wollbrett@cirad.fr SO_gene_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array_member:2009-08-18T08-41-24Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_cap A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_cap:2009-08-18T08-41-09Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_GenomicFeatureDetectionProtocol Documents the general (non-DNA specific) characteristics of genotyping experiments. See Demeter genotype model for further guidance. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenomicFeatureDetectionProtocol:2008-10-14T03-22-41Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name assays GCP_Protocol A GCP_Protocol documents the parameters of general experimental conditions (e.g. reagents, temperatures, etc.) of a specific laboratory manipulation, as a list of GCP_SimpleFeature annotation. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Protocol:2008-10-14T03-22-20Z r.bruskiewich@cgiar.org GCP_BiblioReference Aside from the MOBY modeling considerations noted above in the introduction, GCP_BiblioReference is generally as per the corresponding Demeter model except for the following attributes. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_BiblioReference:2008-10-14T03-22-14Z r.bruskiewich@cgiar.org GCP_SimpleCitation GCP_SimpleCitation is generally as per the Demeter model except that the date, journal source and author list attributes are modeled as simple MOBY Strings. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleCitation:2008-10-14T03-21-13Z r.bruskiewich@cgiar.org source date authorList GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type format language publisher metaData authors contributors indexings content parameters GCP_LegalEntity GCP_LegalEntity represents a general subclass for any GCP_Entity recognized in legal terms as having a legal personality (i.e. ability to have human behaviour as an individual or in aggregate, able to own property, liable for legal prosecution, etc.). This includes both person and organization. - contactingDetails. A LegalEntity obviously has details relating to its localization in the human world. For efficiency, we treat instances of another moby data type, GCP_ContactingDetails, as a subclass of GCP_Identifier, and referencing these details from GCP_LegalEntity using the pertinent GCP_SimpleIdentifier. A LegalEntity may have several such contactingDetails. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_LegalEntity:2008-10-14T03-21-54Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies contactingDetails SO_N4_acetylcytidine N4-acetylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N4_acetylcytidine:2009-08-18T08-47-20Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of GCP_SimpleSequence A GCP_SimpleSequence is a kind of GCP_SimpleFeature with a specified type defined by GCP_SimpleIdentifier identifying a GCP_OntologyTerm and a valueString corresponding to the content of a biological sequence, which should be a string of letters encoding for nucleotide base pairs or amino acid residues, in accordance with IUPAC conventions. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleSequence:2008-10-14T03-21-09Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type GCP_GeoPoint A GeoPoint is a GeoPosition that has singular latitude, longitude and elevation point coordinates. It may belong to a GCP_LinearFeature object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPoint:2008-10-14T03-22-34Z r.bruskiewich@cgiar.org GCP_GeoPosition Constrains GCP_MapPosition to be more GIS like. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints geographicalProjection geographicalDatum linearFeature latitude longitude elevation GCP_Taxon A GCP_Taxon inherits from GCP_Clade to document the full hierarchical biological classification of organisms (e.g. Species of germplasm). A GCP_Taxon has an attribute taxonRank which is documented by a GCP_SimpleIdentifier which identifies to a GCP_OntologyTerm definition that classifies the level of the taxon instance in the taxonomic hierarchy (e.g. "Genus", "Species", etc.). generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Taxon:2008-10-14T03-22-12Z r.bruskiewich@cgiar.org GCP_Clade Taxonomy trees centre around the concept of a clade or rooted node of a subtree. The clade data type is semantically constrained as a special kind of GCP_Entity so that it can be treated as a fully documented artifact, including relationships between clade instances modeled using the GCP_EntityRelationship data type in GCP_Entity. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Clade:2008-10-14T03-22-11Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies taxonRank SO_primer A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. cirad.fr urn:lsid:biomoby.org:objectclass:SO_primer:2009-08-18T08-45-16Z julien.wollbrett@cirad.fr SO_ss_oligo A single stranded oligonucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ss_oligo:2009-08-18T08-44-58Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N4_2_prime_O_dimethylcytidine N4,2'-O-dimethylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N4_2_prime_O_dimethylcytidine:2009-08-18T08-48-14Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_inside_intron An attribute to describe a gene when it is located within the intron of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inside_intron:2009-08-18T08-44-05Z julien.wollbrett@cirad.fr SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com glycoJPG Image of a carbohydrates or glyco-conjugates in PNG format. The binary data of the LPG is BASE64 encoded. www.glycome-db.org urn:lsid:biomoby.org:objectclass:glycoJPG:2010-08-26T11-29-11Z r.ranzinger@dkfz.de glycoImage Any of several image types that illustrate glycan structures ccrc.uga.edu urn:lsid:biomoby.org:objectclass:glycoImage:2008-02-15T02-39-46Z will@ccrc.uga.edu String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com imageData GlycomicsObject Main object for the (semantic) glyco-bio-informatics object tree. Parent object for all objects that are used in glyco-informatics web applications. www.glycome-db.org urn:lsid:biomoby.org:objectclass:GlycomicsObject:2008-02-14T14-46-20Z r.ranzinger@dkfz.de GCP_MolecularPhylogeny A GCP_MolecularPhylogeny inherits from GCP_Entity to track molecular clades. This data type has sequence and a multiple sequence alignment attributes, both identified by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MolecularPhylogeny:2008-10-14T03-23-18Z r.bruskiewich@cgiar.org GCP_Clade Taxonomy trees centre around the concept of a clade or rooted node of a subtree. The clade data type is semantically constrained as a special kind of GCP_Entity so that it can be treated as a fully documented artifact, including relationships between clade instances modeled using the GCP_EntityRelationship data type in GCP_Entity. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Clade:2008-10-14T03-22-11Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies alignment sequence SO_RNA_replication_mode no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_replication_mode:2009-08-18T08-39-39Z julien.wollbrett@cirad.fr SO_sequence_replication_mode no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_replication_mode:2009-08-18T08-39-13Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N2_N2_2_prime_O_trimethylguanosine N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N2_N2_2_prime_O_trimethylguanosine:2009-08-18T08-48-10Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_methyluridine 5_methyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_methyluridine:2009-08-18T08-48-18Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of GCP_GenomicFeatureVariant MOBY data type for a GCP_DetectedVariant that can be unambiguously associated with a specified GCP_GenomicFeature. See Demeter genotype model for further guidance. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GenomicFeatureVariant:2008-10-14T03-22-59Z r.bruskiewich@cgiar.org GCP_DetectedVariant MOBY data type for a Demeter MolecularVariant which is generally detected by a GCP_GenomicFeatureDetector but which cannot generally, without further analysis and interpretation, be unambiguously associated with a specified GenomicFeature. applied. See Demeter genotype model for further guidance. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_DetectedVariant:2008-10-14T03-22-39Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name detector GCP_MolecularVariant The GCP_MolecularVariant data type documents the (usually polymorphic) genetic content of GCP_GenomicFeature instances which is the context of the variant. Note that if the measured content (variation) is not resolved to a specified GCP_GenomicFeature detected by a GCP_GenomicFeatureDetector, then the context of the variant can simply be the GCP_GenomicFeatureDetector itself (i.e. the GCP_MolecularVariant is a detectedVariant of the GCP_GenomicFeatureDetector). GCP_MolecularVariant inherits its full documentation capacity from GCP_Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MolecularVariant:2008-10-14T03-22-38Z r.bruskiewich@cgiar.org context GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies genomicFeature GCP_GeoLinearFeature A GeoLinearFeature is a set of line segments defined by two or more GeoPoints. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoLinearFeature:2008-10-14T03-23-03Z r.bruskiewich@cgiar.org GCP_GeoPosition Constrains GCP_MapPosition to be more GIS like. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints geographicalProjection geographicalDatum GCP_GeoPoint A GeoPoint is a GeoPosition that has singular latitude, longitude and elevation point coordinates. It may belong to a GCP_LinearFeature object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPoint:2008-10-14T03-22-34Z r.bruskiewich@cgiar.org linearFeature latitude longitude elevation vertices SO_hyperploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. cirad.fr urn:lsid:biomoby.org:objectclass:SO_hyperploid:2009-08-18T08-41-57Z julien.wollbrett@cirad.fr SO_aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid:2009-08-18T08-39-41Z julien.wollbrett@cirad.fr SO_chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_number_variation:2009-08-18T08-39-29Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_syntenic Attribute describing sequence regions occurring in same order on chromosome of different species. cirad.fr urn:lsid:biomoby.org:objectclass:SO_syntenic:2009-08-18T08-41-51Z julien.wollbrett@cirad.fr SO_conserved no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved:2009-08-18T08-40-08Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_i_motif A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH. cirad.fr urn:lsid:biomoby.org:objectclass:SO_i_motif:2009-08-18T08-44-11Z julien.wollbrett@cirad.fr SO_DNA_sequence_secondary_structure A folded DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_sequence_secondary_structure:2009-08-18T08-42-40Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_Authority GCP_Authority extends GCP_NameSpace to assert a "namespace of namespaces" that are specified and managed by a given authority, usually defined in terms of a URL and owner. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Authority:2008-10-14T03-23-07Z r.bruskiewich@cgiar.org GCP_NameSpace GCP_NameSpace extends GCP_Identifier (so it can itself be identified) but forms an aggregation of related components which are related instances of GCP_Identifier. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_NameSpace:2008-10-14T03-23-02Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description components owner URL GCP_Accession An Accession is modeled as a special type of GCP_ManagementNeighbourhood. A GCP_Accession has passport data which is not explicitly connected to the object but rather, obtained using a suitable web service call. The identification of the GCP_Accession is a globally distinct identifier whose MOBY namespace specifies the genetic resources collection ("genebank") which manages it. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Accession:2008-10-14T03-23-11Z r.bruskiewich@cgiar.org GCP_ManagementNeighbourhood Most germplasm neighbourhoods are defined by biological relationships, but a specific kind of GCP_ManagementNeighbourhood serves to conserve biodiversity of a given set of germplasm called its "founding germplasm" for some organizational purpose (e.g. ex situ conservation as an genetic resource accession). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_ManagementNeighbourhood:2008-10-14T03-23-09Z r.bruskiewich@cgiar.org GCP_MaintenanceNeighbourhood A GCP_MaintenanceNeighbourhood is a GCP_GermplasmNeighbourhood striving to conserve biological diversity in a set of Germplasm. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MaintenanceNeighbourhood:2008-10-14T03-22-03Z r.bruskiewich@cgiar.org GCP_GermplasmNeighbourhood GCP_GermplasmNeighbourhood is a kind of GCP_GermplasmSet which has a formal biological or management role (see GCP domain model descriptions). Such a set is formally established by source_germplasm (modeled as a set of GCP_SimpleIdentifiers identifying GCP_Germplasm objects) and (generally) belongs to a specified germplasm_collection (also specified by a GCP_SimpleIdentifiers). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmNeighbourhood:2008-10-14T03-22-01Z r.bruskiewich@cgiar.org GCP_GermplasmSet GCP_GermplasmSet is simply any collection of germplasm objects of a specified type (inferred by the namespace of its primary identifier, since it indirectly inherits from GCP_SimpleIdentifier via GCP_Entity). The list of germplasm is identified indirectly by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmSet:2008-10-14T03-22-00Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies germplasm germplasmCollection sourceGermplasm foundingGermplasm passport Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca isPartOfHolderCoreCollection relatedAccessions GCP_MapInterval A GCP_MapInterval is a segment pair of coordinates defining a GCP_MapPosition. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapInterval:2008-10-14T03-22-51Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints startPosition endPosition GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints GCP_MapDistribution See Demeter MapDistribution model narratives for guidance. The MOBY specification of this model uses GCP_SimpleFeature objects to specify the map position. The name attribute can be used as the key, the valueString as the value of the data map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapDistribution:2008-10-14T03-23-20Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints distribution SO_N6_glycinylcarbamoyladenosine N6_glycinylcarbamoyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_glycinylcarbamoyladenosine:2009-08-18T08-47-13Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_inactive_ligand_binding_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_inactive_ligand_binding_site:2009-08-18T08-43-34Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_loss_of_function_of_polypeptide no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_loss_of_function_of_polypeptide:2009-08-18T08-41-47Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_G_to_T_transversion A transversion from guanine to thymine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_G_to_T_transversion:2009-08-18T08-49-11Z julien.wollbrett@cirad.fr SO_purine_to_pyrimidine_transversion Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. cirad.fr urn:lsid:biomoby.org:objectclass:SO_purine_to_pyrimidine_transversion:2009-08-18T08-49-07Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_sequence_variant_decreasing_rate_of_transcription A sequence variation that decreases the rate a which transcription of the sequence occurs. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_decreasing_rate_of_transcription:2009-08-18T08-43-43Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_rate_of_transcription A mutation that alters the rate a which transcription of the sequence occurs. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_rate_of_transcription:2009-08-18T08-41-27Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_transcription Mutation affects the process of transcription, its initiation, progression or termination. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcription:2009-08-18T08-40-04Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_non_terminal_residue The residue at an extremity of the sequence is not the terminal residue. cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_terminal_residue:2009-08-18T08-44-35Z julien.wollbrett@cirad.fr SO_polypeptide_sequencing_information Incompatibility in the sequence due to some experimental problem. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polypeptide_sequencing_information:2009-08-18T08-42-31Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N6_cis_hydroxyisopentenyl_adenosine N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_cis_hydroxyisopentenyl_adenosine:2009-08-18T08-48-23Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_recombinationally_rearranged no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombinationally_rearranged:2009-08-18T08-39-55Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_homo_compound_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_homo_compound_chromosome:2009-08-18T08-41-14Z julien.wollbrett@cirad.fr SO_compound_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_compound_chromosome:2009-08-18T08-40-05Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_golden_path A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_golden_path:2009-08-18T08-44-23Z julien.wollbrett@cirad.fr SO_sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_assembly:2009-08-18T08-42-37Z julien.wollbrett@cirad.fr SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nuclease_sensitive_site A region of nucleotide sequence targeted by a nuclease enzyme. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_sensitive_site:2009-08-18T08-45-13Z julien.wollbrett@cirad.fr SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com MSPeakRelList array of MSPeakRel used to describe a peaklist with each peak defined by mz (float) and relative intensity (integer, 0-999) ipb-halle.de urn:lsid:biomoby.org:objectclass:MSPeakRelList:2009-02-19T09-08-24Z mgerlich@ipb-halle.de MSPeakRel datatype representing a single mass spectrometry peak with m/z value (float) and relative intensity (integer, range 0-999) ipb-halle.de urn:lsid:biomoby.org:objectclass:MSPeakRel:2008-08-10T09-58-58Z mgerlich@ipb-halle.de Array Array object. www.pcm.uam.es urn:lsid:biomoby.org:objectclass:Array:2006-03-21T11-48-57Z inb@pcm.uam.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com mz Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com relInt MSPeakRel SO_sequence_variant_causing_complex_change_of_translational_product Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_complex_change_of_translational_product:2009-08-18T08-39-58Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_MolecularVariant The GCP_MolecularVariant data type documents the (usually polymorphic) genetic content of GCP_GenomicFeature instances which is the context of the variant. Note that if the measured content (variation) is not resolved to a specified GCP_GenomicFeature detected by a GCP_GenomicFeatureDetector, then the context of the variant can simply be the GCP_GenomicFeatureDetector itself (i.e. the GCP_MolecularVariant is a detectedVariant of the GCP_GenomicFeatureDetector). GCP_MolecularVariant inherits its full documentation capacity from GCP_Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MolecularVariant:2008-10-14T03-22-38Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name context GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies GCP_Map A GCP_Map is a collection of map_features instances are just represented as GCP_SimpleIdentifier which identify corresponding GCP_MapFeature objects (usually retrievable using a separate web service). This class can manage either genetic or geographic map features, depending on the context specified by map_type. GCP_Map also may have a specified units for the map (e.g. centiMorgan, degrees). Both map_type and units are specified by ontology terms identified by GCP_SimpleIdentifier. Although the GCP model specifies that maps are a kind of map feature, GCP_Map are modeled separately from GCP_MapFeature for simplicity. GCP_Map inherits from GCP_SimpleIdentifier. If it is feasible and desirable to embed maps into maps (e.g. see map layers below), it is assumed that one could use the GCP_Map as a source of GCP_SimpleIdentifier for a context requiring specification of a GCP_MapFeature identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Map:2008-10-14T03-21-23Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies units mapFeature GCP_Location A GCP_Location is a fully-documented kind of GCP_Map Additional details associated with the location (i.e. synonyms, environmental conditions, etc.) would be retrievable through suitable web services. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Location:2008-10-14T03-23-25Z r.bruskiewich@cgiar.org GCP_Map A GCP_Map is a collection of map_features instances are just represented as GCP_SimpleIdentifier which identify corresponding GCP_MapFeature objects (usually retrievable using a separate web service). This class can manage either genetic or geographic map features, depending on the context specified by map_type. GCP_Map also may have a specified units for the map (e.g. centiMorgan, degrees). Both map_type and units are specified by ontology terms identified by GCP_SimpleIdentifier. Although the GCP model specifies that maps are a kind of map feature, GCP_Map are modeled separately from GCP_MapFeature for simplicity. GCP_Map inherits from GCP_SimpleIdentifier. If it is feasible and desirable to embed maps into maps (e.g. see map layers below), it is assumed that one could use the GCP_Map as a source of GCP_SimpleIdentifier for a context requiring specification of a GCP_MapFeature identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Map:2008-10-14T03-21-23Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies units mapFeature GCP_SimpleLocation A GCP_SimpleLocation is a kind of GCP_MapFeature that answers a lightweight version of the question "where?" as it relates to a specified geographical (cartographic) context. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleLocation:2008-10-14T03-21-47Z r.bruskiewich@cgiar.org GCP_MapFeature A GCP_MapFeature models a kind of GCP_Feature that has a coordinate position on a coordinate-dimensioned space called a map, which is identified by a GCP_SimpleIdentifier (see GCP_Map below). The MapFeature class is subclassed into domain specific map feature concepts such as biological GenomicFeature and geographical Location classes. By definition, a MapFeature belongs to only one map; however, the point, interval or space located by the map feature may be mapped onto more than one map, and may have many associated characteristics, which are generally retrievable by suitable web services using the MOBY namespace and identifier associated with the GCP_MapFeature. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapFeature:2008-10-14T03-21-39Z r.bruskiewich@cgiar.org map GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values geoReference enclosingAdministrativeDivision simpleLocation DateTime a date or time in ISO-8601 format openinformatics.com urn:lsid:biomoby.org:objectclass:DateTime:2001-09-21T16-00-00Z jason@openinformatics.com creationTime destructionTime GCP_Clade Taxonomy trees centre around the concept of a clade or rooted node of a subtree. The clade data type is semantically constrained as a special kind of GCP_Entity so that it can be treated as a fully documented artifact, including relationships between clade instances modeled using the GCP_EntityRelationship data type in GCP_Entity. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Clade:2008-10-14T03-22-11Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies GCP_CorrelatedMapFeatureSet Used for comparative mapping, a CorrelatedMapSet aggregates a set of Map objects that can be related to one another by a common set of MapFeatures, that are themselves documented in a CorrelatedMapFeatureSet. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CorrelatedMapFeatureSet:2008-10-14T03-20-55Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name mapFeatures correlatedMap GCP_MapFeature A GCP_MapFeature models a kind of GCP_Feature that has a coordinate position on a coordinate-dimensioned space called a map, which is identified by a GCP_SimpleIdentifier (see GCP_Map below). The MapFeature class is subclassed into domain specific map feature concepts such as biological GenomicFeature and geographical Location classes. By definition, a MapFeature belongs to only one map; however, the point, interval or space located by the map feature may be mapped onto more than one map, and may have many associated characteristics, which are generally retrievable by suitable web services using the MOBY namespace and identifier associated with the GCP_MapFeature. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapFeature:2008-10-14T03-21-39Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name map GCP_Feature A GCP_FeatureSet inherits most of its article names (attributes) from GCP_SimpleFeature but also includes a MOBY:Collection under the article name features which is itself, a set of GCP_SimpleFeature objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Feature:2008-10-14T03-21-36Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org valueString type unit supportingEvidence GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints values GCP_CorrelatedMapSet Used for comparative mapping, a CorrelatedMapSet aggregates a set of Map objects that can be related to one another by a common set of MapFeatures, that are themselves documented in a CorrelatedMapFeatureSet. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CorrelatedMapSet:2008-10-14T03-21-25Z r.bruskiewich@cgiar.org GCP_Map A GCP_Map is a collection of map_features instances are just represented as GCP_SimpleIdentifier which identify corresponding GCP_MapFeature objects (usually retrievable using a separate web service). This class can manage either genetic or geographic map features, depending on the context specified by map_type. GCP_Map also may have a specified units for the map (e.g. centiMorgan, degrees). Both map_type and units are specified by ontology terms identified by GCP_SimpleIdentifier. Although the GCP model specifies that maps are a kind of map feature, GCP_Map are modeled separately from GCP_MapFeature for simplicity. GCP_Map inherits from GCP_SimpleIdentifier. If it is feasible and desirable to embed maps into maps (e.g. see map layers below), it is assumed that one could use the GCP_Map as a source of GCP_SimpleIdentifier for a context requiring specification of a GCP_MapFeature identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Map:2008-10-14T03-21-23Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies units mapFeature correlatedMaps correlatedMapFeatures GCP_Protein A GCP_Protein is a GCP_GeneProduct composed of a functional aggregation of GCP_PeptideSequence objects, which are identified by a set of GCP_SimpleIdentifier objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Protein:2008-10-14T03-23-00Z r.bruskiewich@cgiar.org GCP_GeneProduct A GCP_GeneProduct is a wrapper defining molecular biological products in living cells, whose function can be characterized using GCP_OntologyTerms specifying Gene Ontology (GO) terms. These are partitioned in this data type as molecularFunctions, biologicalProcesses and cellularCompartments attributes identified by the corresponding sets of GCP_SimpleIdentifier objects. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeneProduct:2008-10-14T03-22-45Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name molecularFunctions cellularCompartments biologicalProcesses GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies peptideSequences GCP_GeoPosition Constrains GCP_MapPosition to be more GIS like. See Demeter GeoPosition model for details. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GeoPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_MapPosition A GCP_MapPosition is a kind of GCP_Value pertaining to a position on a Map. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MapPosition:2008-10-14T03-22-31Z r.bruskiewich@cgiar.org GCP_Value A GCP_Value inherits directly from MOBY:Object and is a generic container for the Demeter Value model. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Value:2008-10-14T03-21-11Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type index data GCP_Constraint GCP_Constraint is a kind of GCP_SimpleIdentifier. This data type specifies ways to limit or validate one or more GCP Value instances. - constraintDefinition. Provides additional information about the specific interpretation of the constraint. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Constraint:2008-10-14T03-20-53Z r.bruskiewich@cgiar.org constraintDefinition constraints geographicalProjection geographicalDatum GCP_MolecularVariantSet MolecularVariantSet is any ad hoc Set of MolecularVariant instances. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MolecularVariantSet:2008-10-14T03-21-07Z r.bruskiewich@cgiar.org GCP_SimpleFeature In MOBY, features are modeled at the most basic level as a GCP_SimpleFeature (equivalent to the Demeter SimpleFeature). A GCP_SimpleFeature inherits from GCP_SimpleIdentifier its capacity to be uniquely identified (by MOBY Object namespace and id) and to be given a human readable characteristic name label. In addition to identification, a GCP_SimpleFeature has a type which is specified as a GCP_SimpleIdentifier that is expected to resolve to a GCP_OntologyTerm (i.e. is in effect a SimpleOntologyTerm identifier in disguise). A GCP_SimpleFeature only represents any associated feature value as a valueString which is a MOBY:String object. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleFeature:2008-10-14T03-21-05Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name valueString type molecularVariants GCP_Indexing Aside from the MOBY modeling considerations noted above in the introduction, GCP_Indexing is generally as per the Demeter model except that it inherits its object status directly from MOBY:Object and models classificationCodes as GCP_SimpleIdentifier objects that identify classification code ontology terms. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Indexing:2008-10-14T03-21-01Z r.bruskiewich@cgiar.org Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com name librarian authority subjectHeadingOntology subjectHeadings classificationCodes keywords Interaction_With_Evidence An interaction between a query identifier and the id of this interaction object. The evidence is the three letter code used by GO to determine the source of the interaction. mpiz-koeln.mpg.de urn:lsid:biomoby.org:objectclass:Interaction_With_Evidence:2008-12-15T08-44-22Z groscurt@mpiz-koeln.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com evidence Publication Contains four string values, each representing the author, title of the article, the journal and the abstract of the publication bioinfo.icapture.ubc.ca urn:lsid:biomoby.org:objectclass:Publication:2009-02-06T18-23-32Z ekawas@mrl.ubc.ca String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Year Abstract Title Journal Author SO_uncharacterised_chromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_uncharacterised_chromosomal_mutation:2009-08-18T08-40-16Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com GCP_CorrelatedLinkageMapSet A GCP_CorrelatedLinkageMapSet is a kind of GCP_CorrelatedMapSet composed of GCP_LinkageMap objects. The set may specify a consensusMap which is the integration of all maps in the set into one GCP_LinkageMap (identified by GCP_SimpleIdentifier). An example of this is a contig map of physical or sequence clones. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CorrelatedLinkageMapSet:2008-10-14T03-22-42Z r.bruskiewich@cgiar.org GCP_CorrelatedMapSet Used for comparative mapping, a CorrelatedMapSet aggregates a set of Map objects that can be related to one another by a common set of MapFeatures, that are themselves documented in a CorrelatedMapFeatureSet. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_CorrelatedMapSet:2008-10-14T03-21-25Z r.bruskiewich@cgiar.org GCP_Map A GCP_Map is a collection of map_features instances are just represented as GCP_SimpleIdentifier which identify corresponding GCP_MapFeature objects (usually retrievable using a separate web service). This class can manage either genetic or geographic map features, depending on the context specified by map_type. GCP_Map also may have a specified units for the map (e.g. centiMorgan, degrees). Both map_type and units are specified by ontology terms identified by GCP_SimpleIdentifier. Although the GCP model specifies that maps are a kind of map feature, GCP_Map are modeled separately from GCP_MapFeature for simplicity. GCP_Map inherits from GCP_SimpleIdentifier. If it is feasible and desirable to embed maps into maps (e.g. see map layers below), it is assumed that one could use the GCP_Map as a source of GCP_SimpleIdentifier for a context requiring specification of a GCP_MapFeature identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Map:2008-10-14T03-21-23Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies units mapFeature correlatedMaps correlatedMapFeatures consensusMap GCP_MaintenanceNeighbourhood A GCP_MaintenanceNeighbourhood is a GCP_GermplasmNeighbourhood striving to conserve biological diversity in a set of Germplasm. generationcp.org urn:lsid:biomoby.org:objectclass:GCP_MaintenanceNeighbourhood:2008-10-14T03-22-03Z r.bruskiewich@cgiar.org GCP_GermplasmNeighbourhood GCP_GermplasmNeighbourhood is a kind of GCP_GermplasmSet which has a formal biological or management role (see GCP domain model descriptions). Such a set is formally established by source_germplasm (modeled as a set of GCP_SimpleIdentifiers identifying GCP_Germplasm objects) and (generally) belongs to a specified germplasm_collection (also specified by a GCP_SimpleIdentifiers). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmNeighbourhood:2008-10-14T03-22-01Z r.bruskiewich@cgiar.org GCP_GermplasmSet GCP_GermplasmSet is simply any collection of germplasm objects of a specified type (inferred by the namespace of its primary identifier, since it indirectly inherits from GCP_SimpleIdentifier via GCP_Entity). The list of germplasm is identified indirectly by GCP_SimpleIdentifiers. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_GermplasmSet:2008-10-14T03-22-00Z r.bruskiewich@cgiar.org GCP_Entity A GCP_Entity is a generic MOBY data type for encapsulating the generic properties of GCP scientific objects("Entity") like identification (synonyms), documentation (primary citation) and general feature annotation. Since GCP_Entity inherit from GCP_Identifier, they are uniquely identifiable objects(and from there it has a link to a NameSpace and Authority to which this Entity belongs). - primaryCitation: This is a source that cites or makes mention of the GCP_Entity. More specifically, it points to a GCP_SimpleIdentifier that resolves to a GCP_BiblioReference. - annotation: This is a description of the GCP Entity. More specifically, this points to GCP_SimpleIdentifiers that resolve to GCP_Feature objects. - synonyms: This is documented by a list of GCP_Identifier instances that provide alternate names for a GCP Entity. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Entity:2008-10-14T03-21-19Z r.bruskiewich@cgiar.org GCP_Identifier A more heavily annotated identifier intended to capture the additional semantics of the Generation CP Identifier object. - description. A free text describing the purpose of this Identifier. - version. Part of an identifier can be a version. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_Identifier:2008-10-14T03-21-08Z r.bruskiewich@cgiar.org GCP_SimpleIdentifier A light weight data type, providing a wrapper for the global identifier (encoded in the namespace and id attributes) plus a human readable name, for all objects that are constrained semantically to be a Generation CP MOBY data object. The semantics of LSID's are assumed here, in which the MOBY namespace combines the LSID "Authority_NameSpace" and the LSID object identifier (and possibly, the version) is encoded in the MOBY object identifier. www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_SimpleIdentifier:2006-11-28T07-43-56Z r.bruskiewich@cgiar.org String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com name version description primaryCitation type GCP_EntityRelationship GCP_EntityRelationship represent the relationships from a subject Entity to target object Entities. A GCP Entity can have a relationship with other GCP Entities, such as containment or derivation. Such relationship instances can document giving rise to a richly connected graph of general associations between all kinds of entities. For example, an instance of Germplasm (which is also an Entity) can point to another Germplasm (an Entity) using a relationship named derivedFrom, or sourceOf. - type. A GCP_SimpleIdentifier which identifies a GCP_OntologyTerm defining the relationship type. This is specified by an ontology term (terms from controlled vocabularies). - object. The target object instances of the relationship. These are GCP_SimpleIdentifiers that identify other GCP_Entities. - annotation. Semantically related sets of features recorded by GCP_SimpleIdentifiers. Note: more specific features of a given subclass of domain object (i.e. like GCP_Germplasm) may provide GCP_Features that are more precisely labeled by MOBY articleNames. Such annotation can, for instance, document additional details of how the subject Entity is transformed into the object Entity. For example, if the subject is a whole plant (Germplasm) from a field experiment, the object could be a BiologicalSample derived from a part of the plant by some experimental protocol (which could be attached to the EntityRelationship association). www.generationcp.org urn:lsid:biomoby.org:objectclass:GCP_EntityRelationship:2006-11-28T08-19-09Z r.bruskiewich@cgiar.org object type annotation relationships synonyms annotations citations studies germplasm germplasmCollection sourceGermplasm SO_rescue An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. cirad.fr urn:lsid:biomoby.org:objectclass:SO_rescue:2009-08-18T08-40-35Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_copy_number_variation A variation that increases or decreases the copy number of a given region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_copy_number_variation:2009-08-18T08-39-28Z julien.wollbrett@cirad.fr SO_sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant:2009-08-18T08-39-14Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_WC_base_pair The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_WC_base_pair:2009-08-18T08-44-49Z julien.wollbrett@cirad.fr SO_base_pair no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_base_pair:2009-08-18T08-42-42Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_linear A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue. cirad.fr urn:lsid:biomoby.org:objectclass:SO_linear:2009-08-18T08-41-16Z julien.wollbrett@cirad.fr SO_topology_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_topology_attribute:2009-08-18T08-40-06Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transposable_element_flanking_region The region of sequence surrounding a transposible element. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transposable_element_flanking_region:2009-08-18T08-43-18Z julien.wollbrett@cirad.fr SO_flanking_region The sequences extending on either side of a specific region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanking_region:2009-08-18T08-41-40Z julien.wollbrett@cirad.fr SO_topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_topologically_defined_region:2009-08-18T08-39-42Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_transcription Mutation affects the process of transcription, its initiation, progression or termination. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcription:2009-08-18T08-40-04Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nucleotide_deletion One or more continuous nucleotides are excised from the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_deletion:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_indel A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified. cirad.fr urn:lsid:biomoby.org:objectclass:SO_indel:2009-08-18T08-39-57Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_polyadenylated A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polyadenylated:2009-08-18T08-42-46Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_prime_O_methyluridine 2prime_O_methyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_prime_O_methyluridine:2009-08-18T08-47-29Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_dif_site A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase. cirad.fr urn:lsid:biomoby.org:objectclass:SO_dif_site:2009-08-18T08-46-13Z julien.wollbrett@cirad.fr SO_resolution_site A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. cirad.fr urn:lsid:biomoby.org:objectclass:SO_resolution_site:2009-08-18T08-45-45Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_vertebrate_immunoglobulin_T_cell_receptor_gene_cluster no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_gene_cluster:2009-08-18T08-46-01Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nc_conserved_region Non-coding region of sequence similarity by descent from a common ancestor. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nc_conserved_region:2009-08-18T08-43-41Z julien.wollbrett@cirad.fr SO_conserved_region Region of sequence similarity by descent from a common ancestor. cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved_region:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_nonconservative_amino_acid_substitution no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_nonconservative_amino_acid_substitution:2009-08-18T08-43-53Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_amino_acid_substitution The replacement of a single amino acid by another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_amino_acid_substitution:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_partially_characterised_change_in_transcript The nature of the mutation event is only partially characterised. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_partially_characterised_change_in_transcript:2009-08-18T08-41-29Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_uncharacterised_change_in_transcript The nature of the mutation event is either uncharacterised or only partially characterised. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_uncharacterised_change_in_transcript:2009-08-18T08-40-15Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_decreasing_level_of_transcript A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_decreasing_level_of_transcript:2009-08-18T08-41-46Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_level_of_transcript A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_level_of_transcript:2009-08-18T08-39-43Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_theta_replication no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_theta_replication:2009-08-18T08-39-44Z julien.wollbrett@cirad.fr SO_DNA_replication_mode no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_replication_mode:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_replication_mode no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_replication_mode:2009-08-18T08-39-13Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_EST_match A match against an EST sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_EST_match:2009-08-18T08-45-19Z julien.wollbrett@cirad.fr SO_expressed_sequence_match A match to an EST or cDNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_expressed_sequence_match:2009-08-18T08-44-24Z julien.wollbrett@cirad.fr SO_nucleotide_match A match against a nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_match:2009-08-18T08-42-36Z julien.wollbrett@cirad.fr SO_match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. cirad.fr urn:lsid:biomoby.org:objectclass:SO_match:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_delete_U An edit to delete a uridine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_delete_U:2009-08-18T08-40-11Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_synonymous_codon_change_in_transcript The changed codon has the same translation product as the original codon. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_synonymous_codon_change_in_transcript:2009-08-18T08-44-28Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_amino_acid_coding_codon_change_in_transcript The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_amino_acid_coding_codon_change_in_transcript:2009-08-18T08-43-07Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_carboxymethylaminomethyluridine 5_carboxymethylaminomethyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carboxymethylaminomethyluridine:2009-08-18T08-47-06Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_predicted_by_ab_initio_computation An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted_by_ab_initio_computation:2009-08-18T08-42-37Z julien.wollbrett@cirad.fr SO_predicted An attribute describing an unverified region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted:2009-08-18T08-40-50Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array_member:2009-08-18T08-41-24Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_resolution_site A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. cirad.fr urn:lsid:biomoby.org:objectclass:SO_resolution_site:2009-08-18T08-45-45Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_cDNA DNA synthesized by reverse transcriptase using RNA as a template. cirad.fr urn:lsid:biomoby.org:objectclass:SO_cDNA:2009-08-18T08-42-23Z julien.wollbrett@cirad.fr SO_DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA:2009-08-18T08-41-15Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_increasing_level_of_translation_product no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_increasing_level_of_translation_product:2009-08-18T08-41-55Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_level_of_translational_product no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_level_of_translational_product:2009-08-18T08-40-02Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_invalidated_by_genomic_polyA_primed_cDNA An attribute to describe a feature that is invalidated due to polyA priming. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated_by_genomic_polyA_primed_cDNA:2009-08-18T08-43-33Z julien.wollbrett@cirad.fr SO_invalidated An attribute describing a feature that is invalidated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated:2009-08-18T08-41-06Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_D_gene Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_D_gene:2009-08-18T08-46-36Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_segment:2009-08-18T08-46-04Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_pseudouridine A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pseudouridine:2009-08-18T08-48-16Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_polycistronic An attribute describing a sequence that contains the code for more than one gene product. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polycistronic:2009-08-18T08-41-56Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_one_methyl_three_three_amino_three_carboxypropyl_pseudouridine 1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_one_methyl_three_three_amino_three_carboxypropyl_pseudouridine:2009-08-18T08-47-11Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_pseudoknot A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pseudoknot:2009-08-18T08-42-55Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_V_gene_recombination_feature Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_V_gene_recombination_feature:2009-08-18T08-46-25Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_signal_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_signal_feature:2009-08-18T08-46-07Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insert_U An edit to insert a U. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_U:2009-08-18T08-40-37Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transcribed_fragment An experimental region, defined by a tiling array experiment to be transcribed at some level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcribed_fragment:2009-08-18T08-41-34Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_splice_donor A sequence_variant_effect that changes the splice donor sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splice_donor:2009-08-18T08-40-24Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_affecting_reading_frame An umbrella term for terms describing an effect of a sequence variation on the frame of translation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_reading_frame:2009-08-18T08-42-51Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insert_dinucleotide An edit to insert a dinucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_dinucleotide:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_minicircle A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs. cirad.fr urn:lsid:biomoby.org:objectclass:SO_minicircle:2009-08-18T08-48-37Z julien.wollbrett@cirad.fr SO_replicon A region containing at least one unique origin of replication and a unique termination site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_replicon:2009-08-18T08-40-49Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_kinetoplast A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. cirad.fr urn:lsid:biomoby.org:objectclass:SO_kinetoplast:2009-08-18T08-39-34Z julien.wollbrett@cirad.fr SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr part_of SO_LNA An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link. cirad.fr urn:lsid:biomoby.org:objectclass:SO_LNA:2009-08-18T08-41-39Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_complex_chromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_complex_chromosomal_mutation:2009-08-18T08-40-27Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_conserved no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved:2009-08-18T08-40-08Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_silenced_by_histone_methylation An attribute describing an epigenetic process where a gene is inactivated by histone methylation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_histone_methylation:2009-08-18T08-46-22Z julien.wollbrett@cirad.fr SO_silenced_by_histone_modification An attribute describing an epigenetic process where a gene is inactivated by histone modification. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_histone_modification:2009-08-18T08-45-47Z julien.wollbrett@cirad.fr SO_silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_coding_conserved_region Coding region of sequence similarity by descent from a common ancestor. cirad.fr urn:lsid:biomoby.org:objectclass:SO_coding_conserved_region:2009-08-18T08-43-47Z julien.wollbrett@cirad.fr SO_conserved_region Region of sequence similarity by descent from a common ancestor. cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved_region:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_aptamer DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. cirad.fr urn:lsid:biomoby.org:objectclass:SO_aptamer:2009-08-18T08-44-23Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_G_to_C_transversion A transversion from guanine to cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_G_to_C_transversion:2009-08-18T08-49-18Z julien.wollbrett@cirad.fr SO_purine_to_pyrimidine_transversion Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. cirad.fr urn:lsid:biomoby.org:objectclass:SO_purine_to_pyrimidine_transversion:2009-08-18T08-49-07Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_polypeptide_sequencing_information Incompatibility in the sequence due to some experimental problem. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polypeptide_sequencing_information:2009-08-18T08-42-31Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_methyl_2_thiouridine 5_methyl_2_thiouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_methyl_2_thiouridine:2009-08-18T08-47-16Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_N2_7_2prirme_O_trimethylguanosine N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N2_7_2prirme_O_trimethylguanosine:2009-08-18T08-47-40Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_post_translationally_regulated_by_protein_stability An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_post_translationally_regulated_by_protein_stability:2009-08-18T08-44-31Z julien.wollbrett@cirad.fr SO_post_translationally_regulated An attribute describing a gene that is regulated after it has been translated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_post_translationally_regulated:2009-08-18T08-43-11Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insert_GC An edit to insert a GC dinucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_GC:2009-08-18T08-41-17Z julien.wollbrett@cirad.fr SO_insert_dinucleotide An edit to insert a dinucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_dinucleotide:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_methoxyuridine 5_methoxyuridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_methoxyuridine:2009-08-18T08-47-49Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_affecting_3D_structure_of_polypeptide A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_3D_structure_of_polypeptide:2009-08-18T08-39-40Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_partially_characterised_change_in_DNA_sequence The nature of the mutation event is only partially characterised. cirad.fr urn:lsid:biomoby.org:objectclass:SO_partially_characterised_change_in_DNA_sequence:2009-08-18T08-40-43Z julien.wollbrett@cirad.fr SO_uncharacterised_change_in_nucleotide_sequence The nature of the mutation event is either uncharacterised or only partially characterised. cirad.fr urn:lsid:biomoby.org:objectclass:SO_uncharacterised_change_in_nucleotide_sequence:2009-08-18T08-39-45Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster:2009-08-18T08-46-05Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_one_two_prime_O_dimethyladenosine 1,2'-O-dimethyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_one_two_prime_O_dimethyladenosine:2009-08-18T08-46-58Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_formylcytidine 5-formylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_formylcytidine:2009-08-18T08-47-14Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_seven_methylguanosine 7_methylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_methylguanosine:2009-08-18T08-47-57Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_reverse_Hoogsteen_base_pair A type of non-canonical base-pairing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reverse_Hoogsteen_base_pair:2009-08-18T08-44-59Z julien.wollbrett@cirad.fr SO_base_pair no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_base_pair:2009-08-18T08-42-42Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mutation_causing_inframe_polypeptide_N_terminal_elongation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_inframe_polypeptide_N_terminal_elongation:2009-08-18T08-45-08Z julien.wollbrett@cirad.fr SO_mutation_causing_polypeptide_N_terminal_elongation . cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_polypeptide_N_terminal_elongation:2009-08-18T08-43-09Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_polypeptide_elongation The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_elongation:2009-08-18T08-41-37Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N4_N4_2_prime_O_trimethylcytidine N4_N4_2_prime_O_trimethylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N4_N4_2_prime_O_trimethylcytidine:2009-08-18T08-47-12Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_random_sequence A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components. cirad.fr urn:lsid:biomoby.org:objectclass:SO_random_sequence:2009-08-18T08-41-53Z julien.wollbrett@cirad.fr SO_synthetic_sequence An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_synthetic_sequence:2009-08-18T08-40-21Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mini_gene By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL))nand MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mini_gene:2009-08-18T08-44-17Z julien.wollbrett@cirad.fr SO_ORF The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ORF:2009-08-18T08-42-52Z julien.wollbrett@cirad.fr SO_reading_frame A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reading_frame:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_polyploid A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polyploid:2009-08-18T08-40-13Z julien.wollbrett@cirad.fr SO_chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_number_variation:2009-08-18T08-39-29Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_T_to_A_transversion A transversion from T to A. cirad.fr urn:lsid:biomoby.org:objectclass:SO_T_to_A_transversion:2009-08-18T08-49-12Z julien.wollbrett@cirad.fr SO_pyrimidine_to_purine_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_to_purine_transversion:2009-08-18T08-49-05Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_RNA_junction_loop no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_junction_loop:2009-08-18T08-44-29Z julien.wollbrett@cirad.fr SO_RNA_motif A motif that is active in RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_motif:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_SAGE_tag A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. cirad.fr urn:lsid:biomoby.org:objectclass:SO_SAGE_tag:2009-08-18T08-45-29Z julien.wollbrett@cirad.fr SO_tag A nucleotide sequence that may be used to identify a larger sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_tag:2009-08-18T08-44-26Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_leucoplast_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_leucoplast_sequence:2009-08-18T08-43-06Z julien.wollbrett@cirad.fr SO_plastid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_plastid_sequence:2009-08-18T08-40-59Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_partial_loss_of_function_of_polypeptide no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_partial_loss_of_function_of_polypeptide:2009-08-18T08-43-46Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_loss_of_function_of_polypeptide no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_loss_of_function_of_polypeptide:2009-08-18T08-41-47Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_one_methylpseudouridine 1_methylpseudouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_one_methylpseudouridine:2009-08-18T08-47-10Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N6_N6_2_prime_O_trimethyladenosine N6_N6_2prime_O_trimethyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_N6_2_prime_O_trimethyladenosine:2009-08-18T08-47-56Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_insertional_duplication A chromosome duplication involving the insertion of a duplicated region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insertional_duplication:2009-08-18T08-42-24Z julien.wollbrett@cirad.fr SO_chromosomal_duplication An extra chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_duplication:2009-08-18T08-40-52Z julien.wollbrett@cirad.fr SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_attB_site An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_attB_site:2009-08-18T08-46-16Z julien.wollbrett@cirad.fr SO_integration_excision_site A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integration_excision_site:2009-08-18T08-45-41Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_assortment_derived_deficiency_plus_duplication A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assortment_derived_deficiency_plus_duplication:2009-08-18T08-39-37Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_allopolyploid A polyploid where the multiple chromosome set was derived from a different organism. cirad.fr urn:lsid:biomoby.org:objectclass:SO_allopolyploid:2009-08-18T08-41-25Z julien.wollbrett@cirad.fr SO_polyploid A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polyploid:2009-08-18T08-40-13Z julien.wollbrett@cirad.fr SO_chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_number_variation:2009-08-18T08-39-29Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_amino_acid_substitution The replacement of a single amino acid by another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_amino_acid_substitution:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_silenced_by_DNA_methylation An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_DNA_methylation:2009-08-18T08-46-17Z julien.wollbrett@cirad.fr SO_silenced_by_DNA_modification An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_DNA_modification:2009-08-18T08-45-43Z julien.wollbrett@cirad.fr SO_silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_hydroxymethylcytidine 5-hydroxymethylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_hydroxymethylcytidine:2009-08-18T08-47-21Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_maxicircle A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. cirad.fr urn:lsid:biomoby.org:objectclass:SO_maxicircle:2009-08-18T08-48-36Z julien.wollbrett@cirad.fr SO_replicon A region containing at least one unique origin of replication and a unique termination site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_replicon:2009-08-18T08-40-49Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_kinetoplast A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. cirad.fr urn:lsid:biomoby.org:objectclass:SO_kinetoplast:2009-08-18T08-39-34Z julien.wollbrett@cirad.fr SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr part_of SO_chromosome Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome:2009-08-18T08-42-38Z julien.wollbrett@cirad.fr SO_replicon A region containing at least one unique origin of replication and a unique termination site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_replicon:2009-08-18T08-40-49Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_expressed_sequence_assembly A sequence assembly derived from expressed sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_expressed_sequence_assembly:2009-08-18T08-44-52Z julien.wollbrett@cirad.fr SO_sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_assembly:2009-08-18T08-42-37Z julien.wollbrett@cirad.fr SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_prime_O_methylinosine 2'-O-methylinosine is a modified inosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_prime_O_methylinosine:2009-08-18T08-48-26Z julien.wollbrett@cirad.fr SO_modified_inosine A modified inosine is an inosine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_inosine:2009-08-18T08-47-09Z julien.wollbrett@cirad.fr SO_inosine A modified RNA base in which hypoxanthine is bound to the ribose ring. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inosine:2009-08-18T08-46-49Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_recombination_hotspot A region in a genome which promotes recombination. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_hotspot:2009-08-18T08-42-43Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNA_binding_site A region of a molecule that binds to DNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_binding_site:2009-08-18T08-42-35Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_seven_cyano_seven_deazaguanosine 7_cyano_7_deazaguanosine is a modified 7-deazoguanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_cyano_seven_deazaguanosine:2009-08-18T08-48-30Z julien.wollbrett@cirad.fr SO_seven_deazaguanosine 7-deazaguanosine is a moddified guanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_deazaguanosine:2009-08-18T08-46-56Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_Hoogsteen_base_pair A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. cirad.fr urn:lsid:biomoby.org:objectclass:SO_Hoogsteen_base_pair:2009-08-18T08-45-07Z julien.wollbrett@cirad.fr SO_base_pair no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_base_pair:2009-08-18T08-42-42Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_foreign An attribute to describe a region from another species. cirad.fr urn:lsid:biomoby.org:objectclass:SO_foreign:2009-08-18T08-40-34Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_MNP A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. cirad.fr urn:lsid:biomoby.org:objectclass:SO_MNP:2009-08-18T08-49-04Z julien.wollbrett@cirad.fr SO_complex_substitution When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_complex_substitution:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_purine_transition A substitution of a purine, A or G, for another purine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_purine_transition:2009-08-18T08-49-06Z julien.wollbrett@cirad.fr SO_transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transition:2009-08-18T08-49-03Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant:2009-08-18T08-39-14Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_three_prime_D_recombination_signal_sequence Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_three_prime_D_recombination_signal_sequence:2009-08-18T08-46-37Z julien.wollbrett@cirad.fr SO_D_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_D_gene_recombination_feature:2009-08-18T08-46-24Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_signal_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_signal_feature:2009-08-18T08-46-07Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transition:2009-08-18T08-49-03Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_possible_assembly_error A region of sequence where there may have been an error in the assembly. cirad.fr urn:lsid:biomoby.org:objectclass:SO_possible_assembly_error:2009-08-18T08-44-07Z julien.wollbrett@cirad.fr SO_sequence_difference A region where the sequence differs from that of a specified sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_difference:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_operon_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_operon_member:2009-08-18T08-43-55Z julien.wollbrett@cirad.fr SO_gene_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array_member:2009-08-18T08-41-24Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_inside_intron_parallel An attribute to describe a gene when it is located within the intron of another gene and on the same strand. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inside_intron_parallel:2009-08-18T08-45-27Z julien.wollbrett@cirad.fr SO_inside_intron An attribute to describe a gene when it is located within the intron of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inside_intron:2009-08-18T08-44-05Z julien.wollbrett@cirad.fr SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_QTL A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. cirad.fr urn:lsid:biomoby.org:objectclass:SO_QTL:2009-08-18T08-41-58Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_restriction_fragment A region of polynucleotide sequence produced by digestion with a restriction endonuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_restriction_fragment:2009-08-18T08-43-02Z julien.wollbrett@cirad.fr SO_assembly_component A region of known length which may be used to manufacture a longer region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly_component:2009-08-18T08-40-54Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_invert To invert a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invert:2009-08-18T08-39-28Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_minus_2_frameshift A frameshift caused by deleting two bases. cirad.fr urn:lsid:biomoby.org:objectclass:SO_minus_2_frameshift:2009-08-18T08-45-09Z julien.wollbrett@cirad.fr SO_frameshift An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift:2009-08-18T08-42-50Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_minus_1_translationally_frameshifted An attribute describing a translational frameshift of -1. cirad.fr urn:lsid:biomoby.org:objectclass:SO_minus_1_translationally_frameshifted:2009-08-18T08-45-28Z julien.wollbrett@cirad.fr SO_translationally_frameshifted Recoding by frameshifting a particular site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translationally_frameshifted:2009-08-18T08-44-14Z julien.wollbrett@cirad.fr SO_recoded An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recoded:2009-08-18T08-42-34Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_carbamoylmethyluridine 5_carbamoylmethyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carbamoylmethyluridine:2009-08-18T08-47-25Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_prime_three_prime_overlap An attribute to describe a gene when the five prime region overlaps with another gene's 3' region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_prime_three_prime_overlap:2009-08-18T08-44-33Z julien.wollbrett@cirad.fr SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_purine_to_pyrimidine_transversion Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. cirad.fr urn:lsid:biomoby.org:objectclass:SO_purine_to_pyrimidine_transversion:2009-08-18T08-49-07Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_prophage A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island". cirad.fr urn:lsid:biomoby.org:objectclass:SO_prophage:2009-08-18T08-49-37Z julien.wollbrett@cirad.fr SO_proviral_region A viral sequence which has integrated into a host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_proviral_region:2009-08-18T08-49-34Z julien.wollbrett@cirad.fr SO_integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integrated_mobile_genetic_element:2009-08-18T08-49-32Z julien.wollbrett@cirad.fr SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_pericentric_inversion no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_pericentric_inversion:2009-08-18T08-43-39Z julien.wollbrett@cirad.fr SO_chromosomal_inversion no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_inversion:2009-08-18T08-40-45Z julien.wollbrett@cirad.fr SO_intrachromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_intrachromosomal_mutation:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_interchromosomal_duplication A chromosome duplication involving an insertion from another chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_interchromosomal_duplication:2009-08-18T08-43-27Z julien.wollbrett@cirad.fr SO_chromosomal_duplication An extra chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_duplication:2009-08-18T08-40-52Z julien.wollbrett@cirad.fr SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_pseudogenic_tRNA A non functional descendent of a tRNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pseudogenic_tRNA:2009-08-18T08-43-39Z julien.wollbrett@cirad.fr SO_pseudogenic_region A non-functional descendent of a functional entity. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pseudogenic_region:2009-08-18T08-40-53Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_deletion_junction The space between two bases in a sequence which marks the position where a deletion has occurred. cirad.fr urn:lsid:biomoby.org:objectclass:SO_deletion_junction:2009-08-18T08-48-34Z julien.wollbrett@cirad.fr SO_junction A sequence_feature with an extent of zero. cirad.fr urn:lsid:biomoby.org:objectclass:SO_junction:2009-08-18T08-39-22Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_delete To remove a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_delete:2009-08-18T08-39-31Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr position_of SO_sequence_variant_causing_polypeptide_truncation The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062). cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_truncation:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nuclease_hypersensitive_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_hypersensitive_site:2009-08-18T08-45-56Z julien.wollbrett@cirad.fr SO_nuclease_sensitive_site A region of nucleotide sequence targeted by a nuclease enzyme. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_sensitive_site:2009-08-18T08-45-13Z julien.wollbrett@cirad.fr SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_wobble_base_pair A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C. cirad.fr urn:lsid:biomoby.org:objectclass:SO_wobble_base_pair:2009-08-18T08-44-28Z julien.wollbrett@cirad.fr SO_base_pair no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_base_pair:2009-08-18T08-42-42Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_homing_endonuclease_binding_site The binding site (recognition site) of a homing endonuclease. The binding site is typically large. cirad.fr urn:lsid:biomoby.org:objectclass:SO_homing_endonuclease_binding_site:2009-08-18T08-45-34Z julien.wollbrett@cirad.fr SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_predicted An attribute describing an unverified region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted:2009-08-18T08-40-50Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_endogenous_retroviral_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_endogenous_retroviral_sequence:2009-08-18T08-42-03Z julien.wollbrett@cirad.fr SO_proviral_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_proviral_location:2009-08-18T08-40-31Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_flanking_region The sequences extending on either side of a specific region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanking_region:2009-08-18T08-41-40Z julien.wollbrett@cirad.fr SO_topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_topologically_defined_region:2009-08-18T08-39-42Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_encodes_overlapping_peptides_different_start A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_overlapping_peptides_different_start:2009-08-18T08-45-24Z julien.wollbrett@cirad.fr SO_encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_overlapping_peptides:2009-08-18T08-44-25Z julien.wollbrett@cirad.fr SO_encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_greater_than_1_polypeptide:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_no_output An experimental region wherean analysis has been run and not produced any annotation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_no_output:2009-08-18T08-45-06Z julien.wollbrett@cirad.fr SO_experimental_result_region A region of sequence implicated in an experimental result. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_result_region:2009-08-18T08-43-30Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_genotype A genotype is a variant genome, complete or incomplete. cirad.fr urn:lsid:biomoby.org:objectclass:SO_genotype:2009-08-18T08-48-39Z julien.wollbrett@cirad.fr SO_sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant:2009-08-18T08-39-14Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_genome A genome is the sum of genetic material within a cell or virion. cirad.fr urn:lsid:biomoby.org:objectclass:SO_genome:2009-08-18T08-39-34Z julien.wollbrett@cirad.fr SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr variant_of SO_wild_type An attribute describing sequence with the genotype found in nature and/or standard laboratory stock. cirad.fr urn:lsid:biomoby.org:objectclass:SO_wild_type:2009-08-18T08-40-39Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N2_2_prime_O_dimethylguanosine N2_2prime_O_dimethylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N2_2_prime_O_dimethylguanosine:2009-08-18T08-47-32Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_silenced_by_RNA_interference An attribute describing an epigenetic process where a gene is inactivated by RNA interference. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_RNA_interference:2009-08-18T08-45-55Z julien.wollbrett@cirad.fr SO_silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_J_gene_recombination_feature Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_J_gene_recombination_feature:2009-08-18T08-46-33Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_signal_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_signal_feature:2009-08-18T08-46-07Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_paralogous An attribute describing a kind of homology where divergence occurred after a duplication event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_paralogous:2009-08-18T08-43-32Z julien.wollbrett@cirad.fr SO_homologous Similarity due to common ancestry. cirad.fr urn:lsid:biomoby.org:objectclass:SO_homologous:2009-08-18T08-41-05Z julien.wollbrett@cirad.fr SO_conserved no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved:2009-08-18T08-40-08Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_invalidated_by_chimeric_cDNA A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated_by_chimeric_cDNA:2009-08-18T08-43-25Z julien.wollbrett@cirad.fr SO_invalidated An attribute describing a feature that is invalidated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated:2009-08-18T08-41-06Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_tiling_path A set of regions which overlap with minimal polymorphism to form a linear sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_tiling_path:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_assembly:2009-08-18T08-42-37Z julien.wollbrett@cirad.fr SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_integron A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integron:2009-08-18T08-49-36Z julien.wollbrett@cirad.fr SO_integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integrated_mobile_genetic_element:2009-08-18T08-49-32Z julien.wollbrett@cirad.fr SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_five_carboxymethyluridine 5_carboxymethyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carboxymethyluridine:2009-08-18T08-47-55Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_no_change_of_translational_product The sequence variant at RNA level does not lead to any change in polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_no_change_of_translational_product:2009-08-18T08-40-39Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_expressed_sequence_match A match to an EST or cDNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_expressed_sequence_match:2009-08-18T08-44-24Z julien.wollbrett@cirad.fr SO_nucleotide_match A match against a nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_match:2009-08-18T08-42-36Z julien.wollbrett@cirad.fr SO_match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. cirad.fr urn:lsid:biomoby.org:objectclass:SO_match:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_V_gene Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. cirad.fr urn:lsid:biomoby.org:objectclass:SO_V_gene:2009-08-18T08-46-35Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_segment:2009-08-18T08-46-04Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_genomic_island A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_genomic_island:2009-08-18T08-49-33Z julien.wollbrett@cirad.fr SO_integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integrated_mobile_genetic_element:2009-08-18T08-49-32Z julien.wollbrett@cirad.fr SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_N6_acetyladenosine N6_acetyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_acetyladenosine:2009-08-18T08-48-19Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_mutation_causing_out_of_frame_polypeptide_N_terminal_elongation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_out_of_frame_polypeptide_N_terminal_elongation:2009-08-18T08-44-30Z julien.wollbrett@cirad.fr SO_mutation_causing_polypeptide_N_terminal_elongation . cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_polypeptide_N_terminal_elongation:2009-08-18T08-43-09Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_polypeptide_elongation The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_elongation:2009-08-18T08-41-37Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_interchromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_interchromosomal_mutation:2009-08-18T08-40-33Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_editing Sequence variant affects the editing of the transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_editing:2009-08-18T08-43-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_transcript_processing Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_processing:2009-08-18T08-41-41Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_uncharacterised_change_in_transcript The nature of the mutation event is either uncharacterised or only partially characterised. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_uncharacterised_change_in_transcript:2009-08-18T08-40-15Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insert_C An edit to insert a cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_C:2009-08-18T08-39-56Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_kinetoplast A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. cirad.fr urn:lsid:biomoby.org:objectclass:SO_kinetoplast:2009-08-18T08-39-34Z julien.wollbrett@cirad.fr SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_affecting_complex_change_in_transcript no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_complex_change_in_transcript:2009-08-18T08-40-23Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_decreasing_transcript_stability Sequence variant decreases the stability (half-life) of the transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_decreasing_transcript_stability:2009-08-18T08-43-37Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_transcript_stability Sequence variant affects the stability of the transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_stability:2009-08-18T08-41-14Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_wyosine Wyosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_wyosine:2009-08-18T08-46-55Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_plus_1_translationally_frameshifted An attribute describing a translational frameshift of +1. cirad.fr urn:lsid:biomoby.org:objectclass:SO_plus_1_translationally_frameshifted:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_translationally_frameshifted Recoding by frameshifting a particular site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translationally_frameshifted:2009-08-18T08-44-14Z julien.wollbrett@cirad.fr SO_recoded An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recoded:2009-08-18T08-42-34Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_T_to_G_transversion A transversion from T to G. cirad.fr urn:lsid:biomoby.org:objectclass:SO_T_to_G_transversion:2009-08-18T08-49-17Z julien.wollbrett@cirad.fr SO_pyrimidine_to_purine_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_to_purine_transversion:2009-08-18T08-49-05Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_ribozymic An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ribozymic:2009-08-18T08-41-50Z julien.wollbrett@cirad.fr SO_enzymatic An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_enzymatic:2009-08-18T08-39-58Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_assortment_derived_deficiency A multi-chromosome deficiency aberration generated by reassortment of other aberration components. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assortment_derived_deficiency:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_chromosome_fission no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_fission:2009-08-18T08-40-58Z julien.wollbrett@cirad.fr SO_intrachromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_intrachromosomal_mutation:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causes_intron_gain A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072). cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causes_intron_gain:2009-08-18T08-40-09Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_thiouridine 2_thiouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_thiouridine:2009-08-18T08-47-01Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_nucleotide_insertion One or more nucleotides are added between two adjacent nucleotides in the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_insertion:2009-08-18T08-41-33Z julien.wollbrett@cirad.fr SO_indel A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified. cirad.fr urn:lsid:biomoby.org:objectclass:SO_indel:2009-08-18T08-39-57Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_thio_two_prime_O_methyluridine 2_thio_2prime_O_methyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_thio_two_prime_O_methyluridine:2009-08-18T08-48-00Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_regulon A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulon:2009-08-18T08-43-14Z julien.wollbrett@cirad.fr SO_gene_group A collection of related genes. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_group:2009-08-18T08-40-42Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_allelically_excluded Allelic exclusion is a process occuring in diploid organisms, where a gene is inactivated and not expressed in that cell. cirad.fr urn:lsid:biomoby.org:objectclass:SO_allelically_excluded:2009-08-18T08-42-42Z julien.wollbrett@cirad.fr SO_epigenetically_modified This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. cirad.fr urn:lsid:biomoby.org:objectclass:SO_epigenetically_modified:2009-08-18T08-40-53Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_ORF The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ORF:2009-08-18T08-42-52Z julien.wollbrett@cirad.fr SO_reading_frame A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reading_frame:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_methylated_C A methylated deoxy-cytosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylated_C:2009-08-18T08-48-04Z julien.wollbrett@cirad.fr SO_methylated_base_feature A nucleotide modified by methylation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylated_base_feature:2009-08-18T08-46-48Z julien.wollbrett@cirad.fr SO_modified_base_site A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_base_site:2009-08-18T08-46-39Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integrated_mobile_genetic_element:2009-08-18T08-49-32Z julien.wollbrett@cirad.fr SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_epitope A region of a macromolecule that is recognized by the immune system. cirad.fr urn:lsid:biomoby.org:objectclass:SO_epitope:2009-08-18T08-43-45Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_minus_1_frameshift A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_minus_1_frameshift:2009-08-18T08-45-38Z julien.wollbrett@cirad.fr SO_frameshift_sequence_variation A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift_sequence_variation:2009-08-18T08-44-16Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_reading_frame An umbrella term for terms describing an effect of a sequence variation on the frame of translation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_reading_frame:2009-08-18T08-42-51Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_inversion A continuous nucleotide sequence is inverted in the same position. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inversion:2009-08-18T08-48-52Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_invert To invert a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invert:2009-08-18T08-39-28Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_translocation A region of nucleotide sequence that has translocated to a new position. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translocation:2009-08-18T08-48-41Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_translocate To translocate a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translocate:2009-08-18T08-39-36Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_C_to_G_transversion no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_C_to_G_transversion:2009-08-18T08-49-20Z julien.wollbrett@cirad.fr SO_pyrimidine_to_purine_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_to_purine_transversion:2009-08-18T08-49-05Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_edited An attribute describing a sequence that is modified by editing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_edited:2009-08-18T08-40-48Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_C_D_box_snoRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_C_D_box_snoRNA_encoding:2009-08-18T08-45-05Z julien.wollbrett@cirad.fr SO_snoRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_snoRNA_encoding:2009-08-18T08-43-53Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_STS Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. cirad.fr urn:lsid:biomoby.org:objectclass:SO_STS:2009-08-18T08-45-21Z julien.wollbrett@cirad.fr SO_tag A nucleotide sequence that may be used to identify a larger sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_tag:2009-08-18T08-44-26Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_C_to_A_transversion A transversion from cytidine to adenine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_C_to_A_transversion:2009-08-18T08-49-12Z julien.wollbrett@cirad.fr SO_pyrimidine_to_purine_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_to_purine_transversion:2009-08-18T08-49-05Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_insert_GU An edit to insert a GU dinucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_GU:2009-08-18T08-42-00Z julien.wollbrett@cirad.fr SO_insert_dinucleotide An edit to insert a dinucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert_dinucleotide:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_number_variation:2009-08-18T08-39-29Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_protein_match A match against a protein sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_match:2009-08-18T08-43-59Z julien.wollbrett@cirad.fr SO_match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. cirad.fr urn:lsid:biomoby.org:objectclass:SO_match:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_genomic_DNA no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_genomic_DNA:2009-08-18T08-43-25Z julien.wollbrett@cirad.fr SO_DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA:2009-08-18T08-41-15Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_overlapping_peptides:2009-08-18T08-44-25Z julien.wollbrett@cirad.fr SO_encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_greater_than_1_polypeptide:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_conformational_change no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_conformational_change:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_3D_structure_of_polypeptide A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_3D_structure_of_polypeptide:2009-08-18T08-39-40Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_linkage_group A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. cirad.fr urn:lsid:biomoby.org:objectclass:SO_linkage_group:2009-08-18T08-42-13Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_translocation_element For some translocations, particularly but not exclusively, reciprocal translocations, the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translocation_element:2009-08-18T08-43-21Z julien.wollbrett@cirad.fr SO_chromosomal_translocation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_translocation:2009-08-18T08-41-30Z julien.wollbrett@cirad.fr SO_interchromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_interchromosomal_mutation:2009-08-18T08-40-33Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNAseI_hypersensitive_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNAseI_hypersensitive_site:2009-08-18T08-46-19Z julien.wollbrett@cirad.fr SO_nuclease_hypersensitive_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_hypersensitive_site:2009-08-18T08-45-56Z julien.wollbrett@cirad.fr SO_nuclease_sensitive_site A region of nucleotide sequence targeted by a nuclease enzyme. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_sensitive_site:2009-08-18T08-45-13Z julien.wollbrett@cirad.fr SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_apicoplast_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_apicoplast_sequence:2009-08-18T08-43-40Z julien.wollbrett@cirad.fr SO_plastid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_plastid_sequence:2009-08-18T08-40-59Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_array An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array:2009-08-18T08-43-00Z julien.wollbrett@cirad.fr SO_gene_group A collection of related genes. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_group:2009-08-18T08-40-42Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_uridine_five_oxyacetic_acid Uridine_5_oxyacetic_acid is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_uridine_five_oxyacetic_acid:2009-08-18T08-47-04Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_trans_spliced An attribute describing transcript sequence that is created by splicing exons from diferent genes. cirad.fr urn:lsid:biomoby.org:objectclass:SO_trans_spliced:2009-08-18T08-41-33Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_G_to_A_transition A transition of a guanine to an adenine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_G_to_A_transition:2009-08-18T08-49-10Z julien.wollbrett@cirad.fr SO_purine_transition A substitution of a purine, A or G, for another purine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_purine_transition:2009-08-18T08-49-06Z julien.wollbrett@cirad.fr SO_transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transition:2009-08-18T08-49-03Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_autoregulated The gene product is involved in its own transcriptional regulation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_autoregulated:2009-08-18T08-44-36Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_recoded_by_translational_bypass Recoded mRNA where a block of nucleotides is not translated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recoded_by_translational_bypass:2009-08-18T08-44-17Z julien.wollbrett@cirad.fr SO_recoded An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recoded:2009-08-18T08-42-34Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_reading_frame A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reading_frame:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_queuosine Queuosine is a modified 7-deazoguanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_queuosine:2009-08-18T08-48-32Z julien.wollbrett@cirad.fr SO_seven_deazaguanosine 7-deazaguanosine is a moddified guanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_deazaguanosine:2009-08-18T08-46-56Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_two_methylthio_N6_isopentenyladenosine 2_methylthio_N6_isopentenyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_methylthio_N6_isopentenyladenosine:2009-08-18T08-47-46Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_microarray_oligo no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_microarray_oligo:2009-08-18T08-45-25Z julien.wollbrett@cirad.fr SO_probe A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. cirad.fr urn:lsid:biomoby.org:objectclass:SO_probe:2009-08-18T08-44-38Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_synthetic_sequence An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_synthetic_sequence:2009-08-18T08-40-21Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N6_methyladenosine N6_methyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_methyladenosine:2009-08-18T08-47-36Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_frameshift_sequence_variation A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift_sequence_variation:2009-08-18T08-44-16Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_reading_frame An umbrella term for terms describing an effect of a sequence variation on the frame of translation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_reading_frame:2009-08-18T08-42-51Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_length_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_length_variation:2009-08-18T08-49-00Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_blocked_reading_frame A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_blocked_reading_frame:2009-08-18T08-43-06Z julien.wollbrett@cirad.fr SO_reading_frame A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reading_frame:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_R_GNA An attribute describing a GNA sequence in the (R)-GNA enantiomer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_R_GNA:2009-08-18T08-43-34Z julien.wollbrett@cirad.fr SO_GNA An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_GNA:2009-08-18T08-41-17Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_pseudogenic_rRNA A non functional descendent of an rRNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pseudogenic_rRNA:2009-08-18T08-42-56Z julien.wollbrett@cirad.fr SO_pseudogenic_region A non-functional descendent of a functional entity. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pseudogenic_region:2009-08-18T08-40-53Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_RNA_hook_turn no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_hook_turn:2009-08-18T08-45-32Z julien.wollbrett@cirad.fr SO_RNA_junction_loop no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_junction_loop:2009-08-18T08-44-29Z julien.wollbrett@cirad.fr SO_RNA_motif A motif that is active in RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_motif:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_uridine_five_oxyacetic_acid_methyl_ester Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_uridine_five_oxyacetic_acid_methyl_ester:2009-08-18T08-47-41Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_three_methylpseudouridine 3_methylpseudouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_three_methylpseudouridine:2009-08-18T08-48-13Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_scRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_scRNA_encoding:2009-08-18T08-42-55Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_cassette_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_cassette_member:2009-08-18T08-42-33Z julien.wollbrett@cirad.fr SO_gene_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array_member:2009-08-18T08-41-24Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_indel A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified. cirad.fr urn:lsid:biomoby.org:objectclass:SO_indel:2009-08-18T08-39-57Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_reagent_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent_attribute:2009-08-18T08-40-25Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_inversion_site A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inversion_site:2009-08-18T08-45-46Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_encodes_1_polypeptide A gene that is alternately spliced, but encodes only one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_1_polypeptide:2009-08-18T08-43-24Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_chromoplast_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromoplast_sequence:2009-08-18T08-42-41Z julien.wollbrett@cirad.fr SO_plastid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_plastid_sequence:2009-08-18T08-40-59Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_cassette_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_cassette_array_member:2009-08-18T08-44-08Z julien.wollbrett@cirad.fr SO_gene_cassette_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_cassette_member:2009-08-18T08-42-33Z julien.wollbrett@cirad.fr SO_gene_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array_member:2009-08-18T08-41-24Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N6_methyl_N6_threonylcarbamoyladenosine N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_methyl_N6_threonylcarbamoyladenosine:2009-08-18T08-47-38Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_two_methyladenosine 2_methyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_methyladenosine:2009-08-18T08-46-52Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_invalidated_by_genomic_contamination An attribute to describe a feature that is invalidated due to genomic contamination. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated_by_genomic_contamination:2009-08-18T08-42-47Z julien.wollbrett@cirad.fr SO_invalidated An attribute describing a feature that is invalidated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated:2009-08-18T08-41-06Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_A_to_T_transversion A transversion from adenine to thymine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_A_to_T_transversion:2009-08-18T08-49-13Z julien.wollbrett@cirad.fr SO_purine_to_pyrimidine_transversion Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. cirad.fr urn:lsid:biomoby.org:objectclass:SO_purine_to_pyrimidine_transversion:2009-08-18T08-49-07Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_chloroplast_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chloroplast_sequence:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_plastid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_plastid_sequence:2009-08-18T08-40-59Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_three_prime_flanking_region A flanking region located three prime of a specific region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_three_prime_flanking_region:2009-08-18T08-43-57Z julien.wollbrett@cirad.fr SO_flanking_region The sequences extending on either side of a specific region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanking_region:2009-08-18T08-41-40Z julien.wollbrett@cirad.fr SO_topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_topologically_defined_region:2009-08-18T08-39-42Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_one_methylguanosine 1_methylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_one_methylguanosine:2009-08-18T08-48-20Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_carbamoylmethyl_two_prime_O_methyluridine 5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carbamoylmethyl_two_prime_O_methyluridine:2009-08-18T08-48-01Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_isowyosine Isowyosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_isowyosine:2009-08-18T08-48-22Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_macronucleus_destined_segment A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_macronucleus_destined_segment:2009-08-18T08-44-00Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_transcript_secondary_structure A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_secondary_structure:2009-08-18T08-41-45Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causes_exon_loss A sequence variant affecting splicing and causes an exon loss. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causes_exon_loss:2009-08-18T08-40-36Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_RNA_sequence_secondary_structure A folded RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_sequence_secondary_structure:2009-08-18T08-43-31Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment:2009-08-18T08-46-10Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transposable_element A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transposable_element:2009-08-18T08-49-36Z julien.wollbrett@cirad.fr SO_integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integrated_mobile_genetic_element:2009-08-18T08-49-32Z julien.wollbrett@cirad.fr SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_encodes_overlapping_polypeptides_different_start_and_stop A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_overlapping_polypeptides_different_start_and_stop:2009-08-18T08-45-20Z julien.wollbrett@cirad.fr SO_encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_overlapping_peptides:2009-08-18T08-44-25Z julien.wollbrett@cirad.fr SO_encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_greater_than_1_polypeptide:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nucleotide_duplication One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_duplication:2009-08-18T08-43-13Z julien.wollbrett@cirad.fr SO_nucleotide_insertion One or more nucleotides are added between two adjacent nucleotides in the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_insertion:2009-08-18T08-41-33Z julien.wollbrett@cirad.fr SO_indel A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified. cirad.fr urn:lsid:biomoby.org:objectclass:SO_indel:2009-08-18T08-39-57Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_S_GNA An attribute describing a GNA sequence in the (S)-GNA enantiomer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_S_GNA:2009-08-18T08-43-11Z julien.wollbrett@cirad.fr SO_GNA An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_GNA:2009-08-18T08-41-17Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_engineered An attribute to describe a region that was modified in vitro. cirad.fr urn:lsid:biomoby.org:objectclass:SO_engineered:2009-08-18T08-40-10Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_silenced_by_DNA_modification An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_DNA_modification:2009-08-18T08-45-43Z julien.wollbrett@cirad.fr SO_silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_amino_acid_coding_codon_change_in_transcript The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_amino_acid_coding_codon_change_in_transcript:2009-08-18T08-43-07Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_synthetic_oligo An oligo composed of synthetic nucleotides. cirad.fr urn:lsid:biomoby.org:objectclass:SO_synthetic_oligo:2009-08-18T08-44-03Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_unoriented_insertional_duplication A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_unoriented_insertional_duplication:2009-08-18T08-44-02Z julien.wollbrett@cirad.fr SO_insertional_duplication A chromosome duplication involving the insertion of a duplicated region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insertional_duplication:2009-08-18T08-42-24Z julien.wollbrett@cirad.fr SO_chromosomal_duplication An extra chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_duplication:2009-08-18T08-40-52Z julien.wollbrett@cirad.fr SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_increasing_transcript_stability Sequence variant increases the stability (half-life) of the transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_increasing_transcript_stability:2009-08-18T08-42-59Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_transcript_stability Sequence variant affects the stability of the transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_stability:2009-08-18T08-41-14Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_plasmid_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_plasmid_location:2009-08-18T08-40-04Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_iDNA Genomic sequence removed from the genome, as a normal event, by a process of recombination. cirad.fr urn:lsid:biomoby.org:objectclass:SO_iDNA:2009-08-18T08-43-35Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_virtual_sequence A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. cirad.fr urn:lsid:biomoby.org:objectclass:SO_virtual_sequence:2009-08-18T08-44-10Z julien.wollbrett@cirad.fr SO_sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_assembly:2009-08-18T08-42-37Z julien.wollbrett@cirad.fr SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_prime_O_ribosyladenosine_phosphate 2prime_O_ribosyladenosine_phosphate is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_prime_O_ribosyladenosine_phosphate:2009-08-18T08-47-27Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_silent_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_silent_mutation:2009-08-18T08-39-31Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_conservative_missense_codon_change_in_transcript The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_conservative_missense_codon_change_in_transcript:2009-08-18T08-46-00Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_missense_codon_change_in_transcript The nucleotide change in the codon leads to a new codon coding for a new amino acid. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_missense_codon_change_in_transcript:2009-08-18T08-45-14Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_non_synonymous_codon_change_in_transcript A DNA point mutation that causes a substitution of an amino acid by an other. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_non_synonymous_codon_change_in_transcript:2009-08-18T08-44-13Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_amino_acid_coding_codon_change_in_transcript The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_amino_acid_coding_codon_change_in_transcript:2009-08-18T08-43-07Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_cryptic_splice_acceptor_activation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_cryptic_splice_acceptor_activation:2009-08-18T08-42-02Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_cryptic_splice_activator A sequence variant causing a new (functional) splice site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_cryptic_splice_activator:2009-08-18T08-40-12Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_increasing_level_of_transcript A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_increasing_level_of_transcript:2009-08-18T08-42-14Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_level_of_transcript A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_level_of_transcript:2009-08-18T08-39-43Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_methylaminomethyluridine 5_methylaminomethyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_methylaminomethyluridine:2009-08-18T08-48-11Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_vertebrate_immune_system_gene_recombination_spacer no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_spacer:2009-08-18T08-46-03Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com CodingSNP_Consequences_Motif Annotated coding SNP with changes in motifs introduced by SNPs. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Consequences_Motif:2010-12-20T09-15-00Z genome@dkfz.de Motif_Changes Includes changes in motifs from a protein sequence caused by SNPs. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:Motif_Changes:2010-12-20T09-04-37Z genome@dkfz.de Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com score String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com motif_mutant consequence method snp_inside motif_ref motif_changes AnnotatedCodingSNP SNP in the context of its location in a protein including annotations. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedCodingSNP:2010-12-01T11-49-27Z genome@dkfz.de wt_aa_seq CodingSNP_Extended An extended version of the former CodingSNP, featuring the additional fields: reference_allele, genotype_allele husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Extended:2010-11-24T14-13-31Z genome@dkfz.de CodingSNP SNPs in coding region with codons and aminoacids www.weigelworld.org urn:lsid:biomoby.org:objectclass:CodingSNP:2006-06-27T14-31-56Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com end start chromosome Position Strain codon_ref aa_ref codon_var aa_var aa_pos Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca aa_change reference_allele genotype_allele mut_aa_seq ext_database_refs Pizza_Hot no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_Hot:2011-10-14T15-17-08Z j@c.fr Pizza_Spiciness A ValuePartition that describes only values from Hot, Medium or Mild. NB Subclasses can themselves be divided up into further partitions. c.fr urn:lsid:biomoby.org:objectclass:Pizza_Spiciness:2011-10-14T15-16-58Z j@c.fr Pizza_ValuePartition A ValuePartition is a pattern that describes a restricted set of classes from which a property can be associated. The parent class is used in restrictions, and the covering axiom means that only members of the subclasses may be used as values. The possible subclasses cannot be extended without updating the ValuePartition class. c.fr urn:lsid:biomoby.org:objectclass:Pizza_ValuePartition:2011-10-14T15-16-57Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pizza_MeatyPizza Any pizza that has at least one meat topping c.fr urn:lsid:biomoby.org:objectclass:Pizza_MeatyPizza:2011-10-14T15-17-19Z j@c.fr Pizza_Pizza no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_Pizza:2011-10-14T15-17-11Z j@c.fr Pizza_DomainConcept no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DomainConcept:2011-10-14T15-16-56Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pizza_PizzaBase no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_PizzaBase:2011-10-14T15-16-59Z j@c.fr hasBase Pizza_MeatTopping no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_MeatTopping:2011-10-14T15-17-02Z j@c.fr Pizza_PizzaTopping no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_PizzaTopping:2011-10-14T15-16-59Z j@c.fr hasTopping Pizza_DeepPanBase no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DeepPanBase:2011-10-14T15-17-01Z j@c.fr Pizza_PizzaBase no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_PizzaBase:2011-10-14T15-16-59Z j@c.fr Pizza_DomainConcept no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DomainConcept:2011-10-14T15-16-56Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pizza_PizzaTopping no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_PizzaTopping:2011-10-14T15-16-59Z j@c.fr Pizza_DomainConcept no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DomainConcept:2011-10-14T15-16-56Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pizza_Pizza no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_Pizza:2011-10-14T15-17-11Z j@c.fr Pizza_DomainConcept no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_DomainConcept:2011-10-14T15-16-56Z j@c.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Pizza_PizzaBase no description available c.fr urn:lsid:biomoby.org:objectclass:Pizza_PizzaBase:2011-10-14T15-16-59Z j@c.fr hasBase SO_minus_1_frameshift A frameshift caused by deleting one base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_minus_1_frameshift:2009-08-18T08-44-46Z julien.wollbrett@cirad.fr SO_frameshift An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift:2009-08-18T08-42-50Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_heptamer_of_recombination_feature_of_vertebrate_immune_system_gene Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene ornJ-gene recombination feature of an immunoglobulin or T-cell receptor gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_heptamer_of_recombination_feature_of_vertebrate_immune_system_gene:2009-08-18T08-46-28Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_signal_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_signal_feature:2009-08-18T08-46-07Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_carboxyhydroxymethyl_uridine 5_carboxyhydroxymethyl_uridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carboxyhydroxymethyl_uridine:2009-08-18T08-48-14Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_affecting_transcript_stability Sequence variant affects the stability of the transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_stability:2009-08-18T08-41-14Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNA_sequence_secondary_structure A folded DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_sequence_secondary_structure:2009-08-18T08-42-40Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_cryptic_splice_activator A sequence variant causing a new (functional) splice site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_cryptic_splice_activator:2009-08-18T08-40-12Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_splicing:2009-08-18T08-39-26Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_isopentenylaminomethyl_two_prime_O_methyluridine 5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_isopentenylaminomethyl_two_prime_O_methyluridine:2009-08-18T08-47-54Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_tmRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_tmRNA_encoding:2009-08-18T08-43-48Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_inversion_site_part A region located within an inversion site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inversion_site_part:2009-08-18T08-45-52Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequencing_primer no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequencing_primer:2009-08-18T08-45-44Z julien.wollbrett@cirad.fr SO_primer A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. cirad.fr urn:lsid:biomoby.org:objectclass:SO_primer:2009-08-18T08-45-16Z julien.wollbrett@cirad.fr SO_ss_oligo A single stranded oligonucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ss_oligo:2009-08-18T08-44-58Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_orthologous An attribute describing a kind of homology where divergence occured after a speciation event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_orthologous:2009-08-18T08-42-45Z julien.wollbrett@cirad.fr SO_homologous Similarity due to common ancestry. cirad.fr urn:lsid:biomoby.org:objectclass:SO_homologous:2009-08-18T08-41-05Z julien.wollbrett@cirad.fr SO_conserved no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved:2009-08-18T08-40-08Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine 2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine:2009-08-18T08-47-28Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_silenced_by_histone_deacetylation An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_histone_deacetylation:2009-08-18T08-46-15Z julien.wollbrett@cirad.fr SO_silenced_by_histone_modification An attribute describing an epigenetic process where a gene is inactivated by histone modification. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced_by_histone_modification:2009-08-18T08-45-47Z julien.wollbrett@cirad.fr SO_silenced An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. cirad.fr urn:lsid:biomoby.org:objectclass:SO_silenced:2009-08-18T08-45-15Z julien.wollbrett@cirad.fr SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mitochondrial_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_mitochondrial_sequence:2009-08-18T08-40-49Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_direction_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_direction_attribute:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_four_thiouridine 4_thiouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_four_thiouridine:2009-08-18T08-48-09Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_capped An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. cirad.fr urn:lsid:biomoby.org:objectclass:SO_capped:2009-08-18T08-41-48Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_forward Forward is an attribute of the feature, where the feature is in the 5' to 3' direction. cirad.fr urn:lsid:biomoby.org:objectclass:SO_forward:2009-08-18T08-42-09Z julien.wollbrett@cirad.fr SO_direction_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_direction_attribute:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_uncharacterised_3D_structural_change no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_uncharacterised_3D_structural_change:2009-08-18T08-40-40Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_3D_structure_of_polypeptide A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_3D_structure_of_polypeptide:2009-08-18T08-39-40Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNAzyme A DNA sequence with catalytic activity. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNAzyme:2009-08-18T08-49-21Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_enzymatic An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_enzymatic:2009-08-18T08-39-58Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_N2_N2_7_trimethylguanosine N2_N2_7_trimethylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N2_N2_7_trimethylguanosine:2009-08-18T08-48-02Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_topologically_defined_region:2009-08-18T08-39-42Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gRNA_encoding A non-protein_coding gene that encodes a guide_RNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gRNA_encoding:2009-08-18T08-43-08Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_stem_loop A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_stem_loop:2009-08-18T08-44-45Z julien.wollbrett@cirad.fr SO_RNA_sequence_secondary_structure A folded RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_sequence_secondary_structure:2009-08-18T08-43-31Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_tRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_tRNA_encoding:2009-08-18T08-42-48Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_intrachromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_intrachromosomal_mutation:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_circular A quality of a nucleotide polymer that has no terminal nucleotide residues. cirad.fr urn:lsid:biomoby.org:objectclass:SO_circular:2009-08-18T08-41-55Z julien.wollbrett@cirad.fr SO_topology_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_topology_attribute:2009-08-18T08-40-06Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_archaeosine Archaeosine is a modified 7-deazoguanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_archaeosine:2009-08-18T08-48-29Z julien.wollbrett@cirad.fr SO_seven_deazaguanosine 7-deazaguanosine is a moddified guanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_deazaguanosine:2009-08-18T08-46-56Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_compensatory_transcript_secondary_structure_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_compensatory_transcript_secondary_structure_mutation:2009-08-18T08-43-58Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_transcript_secondary_structure A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_secondary_structure:2009-08-18T08-41-45Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_prime_O_methylcytidine 2'-O-methylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_prime_O_methylcytidine:2009-08-18T08-47-37Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_pyrimidine_to_purine_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_to_purine_transversion:2009-08-18T08-49-05Z julien.wollbrett@cirad.fr SO_transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transversion:2009-08-18T08-49-02Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_two_prime_O_methylpseudouridine 2prime_O_methylpseudouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_prime_O_methylpseudouridine:2009-08-18T08-47-48Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_translationally_frameshifted Recoding by frameshifting a particular site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translationally_frameshifted:2009-08-18T08-44-14Z julien.wollbrett@cirad.fr SO_recoded An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recoded:2009-08-18T08-42-34Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_assembly:2009-08-18T08-42-37Z julien.wollbrett@cirad.fr SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com NarcisseRegion A NarcisseRegion is a string that describes an unique slice of a chromosome in a particular species.It is composed of 5 elements separated by ':'. 1- Narcisse Species long name with '_' in place of space. 2- chromosome label, string (alphanum). 3- start, integer, where the slice begins. 4- end, integer, where the slice stops. 5- strand, character '+' or '-'. example :'Homo_sapiens:8:1:1000:+' is the forward strand slice from the first base to the base 1000 (included), of the chromosome 8 of Homo sapiens species. narcisse.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:NarcisseRegion:2009-11-05T14-04-30Z Sebastien.Carrere@toulouse.inra.fr text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content SO_SNP SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater. cirad.fr urn:lsid:biomoby.org:objectclass:SO_SNP:2009-08-18T08-49-01Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_cDNA_match A match against cDNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_cDNA_match:2009-08-18T08-45-33Z julien.wollbrett@cirad.fr SO_expressed_sequence_match A match to an EST or cDNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_expressed_sequence_match:2009-08-18T08-44-24Z julien.wollbrett@cirad.fr SO_nucleotide_match A match against a nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_match:2009-08-18T08-42-36Z julien.wollbrett@cirad.fr SO_match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. cirad.fr urn:lsid:biomoby.org:objectclass:SO_match:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_uncharacterised_change_of_translational_product A sequence variant causing an uncharacterized change of translational product. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_uncharacterised_change_of_translational_product:2009-08-18T08-40-14Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_gain_of_function_of_polypeptide no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_gain_of_function_of_polypeptide:2009-08-18T08-40-56Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_ss_oligo A single stranded oligonucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ss_oligo:2009-08-18T08-44-58Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sugar_edge_base_pair A type of non-canonical base-pairing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sugar_edge_base_pair:2009-08-18T08-44-32Z julien.wollbrett@cirad.fr SO_base_pair no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_base_pair:2009-08-18T08-42-42Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_loss_of_function_of_polypeptide no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_loss_of_function_of_polypeptide:2009-08-18T08-41-47Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_peroxywybutosine Peroxywybutosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_peroxywybutosine:2009-08-18T08-47-59Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_J_gene Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_J_gene:2009-08-18T08-46-23Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_segment:2009-08-18T08-46-04Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_carboxyhydroxymethyl_uridine_methyl_ester 5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carboxyhydroxymethyl_uridine_methyl_ester:2009-08-18T08-47-23Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_no_change_in_transcript No effect on the state of the RNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_no_change_in_transcript:2009-08-18T08-40-30Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_prime_flanking_region A flanking region located five prime of a specific region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_prime_flanking_region:2009-08-18T08-43-36Z julien.wollbrett@cirad.fr SO_flanking_region The sequences extending on either side of a specific region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanking_region:2009-08-18T08-41-40Z julien.wollbrett@cirad.fr SO_topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_topologically_defined_region:2009-08-18T08-39-42Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_bound_by_protein An attribute describing a sequence that is bound by a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_bound_by_protein:2009-08-18T08-41-43Z julien.wollbrett@cirad.fr SO_bound_by_factor An attribute describing a sequence that is bound by another molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_bound_by_factor:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_laevosynaptic_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_laevosynaptic_chromosome:2009-08-18T08-42-12Z julien.wollbrett@cirad.fr SO_autosynaptic_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_autosynaptic_chromosome:2009-08-18T08-40-14Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_decreasing_level_of_translation_product no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_decreasing_level_of_translation_product:2009-08-18T08-41-11Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_level_of_translational_product no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_level_of_translational_product:2009-08-18T08-40-02Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transcriptionally_repressed A repressor molecule is required for transcription to stop. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_repressed:2009-08-18T08-44-37Z julien.wollbrett@cirad.fr SO_transcriptionally_regulated An attribute describing a gene that is regulated at transcription. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcriptionally_regulated:2009-08-18T08-42-26Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_isopentenylaminomethyl_two_thiouridine 5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_isopentenylaminomethyl_two_thiouridine:2009-08-18T08-47-17Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_fragmentary An attribute to describe a feature that is incomplete. cirad.fr urn:lsid:biomoby.org:objectclass:SO_fragmentary:2009-08-18T08-42-19Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_free_chromosome_arm no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_free_chromosome_arm:2009-08-18T08-40-19Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_prime_O_methylguanosine 2prime_O_methylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_prime_O_methylguanosine:2009-08-18T08-47-52Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_vertebrate_immunoglobulin_T_cell_receptor_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_segment:2009-08-18T08-46-04Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_subarray A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_subarray:2009-08-18T08-43-43Z julien.wollbrett@cirad.fr SO_gene_group A collection of related genes. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_group:2009-08-18T08-40-42Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_H_ACA_box_snoRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_H_ACA_box_snoRNA_encoding:2009-08-18T08-45-02Z julien.wollbrett@cirad.fr SO_snoRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_snoRNA_encoding:2009-08-18T08-43-53Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_attR_site A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_attR_site:2009-08-18T08-46-20Z julien.wollbrett@cirad.fr SO_integration_excision_site A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integration_excision_site:2009-08-18T08-45-41Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transgenic Attribute describing sequence that has been integrated with foreign sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transgenic:2009-08-18T08-39-47Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mutation_causing_out_of_frame_polypeptide_C_terminal_elongation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_out_of_frame_polypeptide_C_terminal_elongation:2009-08-18T08-44-22Z julien.wollbrett@cirad.fr SO_mutation_causing_polypeptide_C_terminal_elongation . cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_polypeptide_C_terminal_elongation:2009-08-18T08-43-01Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_polypeptide_elongation The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_elongation:2009-08-18T08-41-37Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_replication_mode no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_replication_mode:2009-08-18T08-39-13Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_GNA An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_GNA:2009-08-18T08-41-17Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_supported_by_EST_or_cDNA An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data. cirad.fr urn:lsid:biomoby.org:objectclass:SO_supported_by_EST_or_cDNA:2009-08-18T08-45-03Z julien.wollbrett@cirad.fr SO_supported_by_sequence_similarity An attribute to describe a feature that has been predicted using sequence similarity techniques. cirad.fr urn:lsid:biomoby.org:objectclass:SO_supported_by_sequence_similarity:2009-08-18T08-42-28Z julien.wollbrett@cirad.fr SO_predicted An attribute describing an unverified region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted:2009-08-18T08-40-50Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_hypoploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_hypoploid:2009-08-18T08-40-41Z julien.wollbrett@cirad.fr SO_aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid:2009-08-18T08-39-41Z julien.wollbrett@cirad.fr SO_chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_number_variation:2009-08-18T08-39-29Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_substitute_C_to_U An edit to substitute an U for a C. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute_C_to_U:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_edit_operation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_edit_operation:2009-08-18T08-39-25Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_undermodified_hydroxywybutosine Undermodified_hydroxywybutosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_undermodified_hydroxywybutosine:2009-08-18T08-47-51Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_SRP_RNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_SRP_RNA_encoding:2009-08-18T08-43-42Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_partially_characterised_chromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_partially_characterised_chromosomal_mutation:2009-08-18T08-41-59Z julien.wollbrett@cirad.fr SO_uncharacterised_chromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_uncharacterised_chromosomal_mutation:2009-08-18T08-40-16Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_encodes_different_polypeptides_different_stop A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_different_polypeptides_different_stop:2009-08-18T08-45-39Z julien.wollbrett@cirad.fr SO_encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_overlapping_peptides:2009-08-18T08-44-25Z julien.wollbrett@cirad.fr SO_encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_greater_than_1_polypeptide:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_group_1_intron_homing_endonuclease_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_group_1_intron_homing_endonuclease_target_region:2009-08-18T08-45-58Z julien.wollbrett@cirad.fr SO_nuclease_sensitive_site A region of nucleotide sequence targeted by a nuclease enzyme. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_sensitive_site:2009-08-18T08-45-13Z julien.wollbrett@cirad.fr SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_one_two_prime_O_dimethylguanosine 1_2prime_O_dimethylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_one_two_prime_O_dimethylguanosine:2009-08-18T08-46-59Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_polypeptide_post_translational_processing_change no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_post_translational_processing_change:2009-08-18T08-43-52Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_loss_of_function_of_polypeptide no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_loss_of_function_of_polypeptide:2009-08-18T08-41-47Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_formyl_two_prime_O_methylcytidine 5-formyl-2'-O-methylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_formyl_two_prime_O_methylcytidine:2009-08-18T08-48-06Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_polypeptide_fusion no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_fusion:2009-08-18T08-41-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_three_two_prime_O_dimethyluridine 3_2prime_O_dimethyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_three_two_prime_O_dimethyluridine:2009-08-18T08-47-03Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_inversion_derived_aneuploid_chromosome A chromosome may be generated by recombination between two inverversions; presumed to have a deficiency or duplication at each end of the inversion. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inversion_derived_aneuploid_chromosome:2009-08-18T08-41-01Z julien.wollbrett@cirad.fr SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_affecting_level_of_transcript A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_level_of_transcript:2009-08-18T08-39-43Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_attL_site A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_attL_site:2009-08-18T08-46-21Z julien.wollbrett@cirad.fr SO_integration_excision_site A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integration_excision_site:2009-08-18T08-45-41Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_taurinomethyluridine 5_taurinomethyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_taurinomethyluridine:2009-08-18T08-47-26Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_transposable_element_insertion_site The junction in a genome where a transposable_element has inserted. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transposable_element_insertion_site:2009-08-18T08-48-44Z julien.wollbrett@cirad.fr SO_insertion_site The junction where an insertion occurred. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insertion_site:2009-08-18T08-48-43Z julien.wollbrett@cirad.fr SO_junction A sequence_feature with an extent of zero. cirad.fr urn:lsid:biomoby.org:objectclass:SO_junction:2009-08-18T08-39-22Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insert To insert a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert:2009-08-18T08-39-37Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr position_of SO_FRT_flanked An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. cirad.fr urn:lsid:biomoby.org:objectclass:SO_FRT_flanked:2009-08-18T08-40-42Z julien.wollbrett@cirad.fr SO_flanked An attribute describing a region that is bounded either side by a paricular kind of region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanked:2009-08-18T08-39-43Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_group A collection of related genes. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_group:2009-08-18T08-40-42Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N2_methylguanosine N2_methylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N2_methylguanosine:2009-08-18T08-47-22Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_replicon A region containing at least one unique origin of replication and a unique termination site. cirad.fr urn:lsid:biomoby.org:objectclass:SO_replicon:2009-08-18T08-40-49Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNA_constraint_sequence A double-stranded DNA used to control macromolecular structure and function. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_constraint_sequence:2009-08-18T08-45-23Z julien.wollbrett@cirad.fr SO_ds_oligo A double stranded oligonucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_ds_oligo:2009-08-18T08-44-18Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N2_7_dimethylguanosine N2_7_dimethylguanosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N2_7_dimethylguanosine:2009-08-18T08-48-17Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N6_isopentenyladenosine N6_isopentenyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_isopentenyladenosine:2009-08-18T08-47-00Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_inside_intron_antiparallel An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inside_intron_antiparallel:2009-08-18T08-45-11Z julien.wollbrett@cirad.fr SO_inside_intron An attribute to describe a gene when it is located within the intron of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inside_intron:2009-08-18T08-44-05Z julien.wollbrett@cirad.fr SO_overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_overlapping:2009-08-18T08-42-30Z julien.wollbrett@cirad.fr SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_micronuclear_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_micronuclear_sequence:2009-08-18T08-41-54Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_genome A genome is the sum of genetic material within a cell or virion. cirad.fr urn:lsid:biomoby.org:objectclass:SO_genome:2009-08-18T08-39-34Z julien.wollbrett@cirad.fr SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_seven_aminomethyl_seven_deazaguanosine 7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_aminomethyl_seven_deazaguanosine:2009-08-18T08-48-24Z julien.wollbrett@cirad.fr SO_seven_deazaguanosine 7-deazaguanosine is a moddified guanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_deazaguanosine:2009-08-18T08-46-56Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_floxed An attribute describing sequence that is flanked by Lox-P sites. cirad.fr urn:lsid:biomoby.org:objectclass:SO_floxed:2009-08-18T08-41-22Z julien.wollbrett@cirad.fr SO_flanked An attribute describing a region that is bounded either side by a paricular kind of region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanked:2009-08-18T08-39-43Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_plus_1_frameshift A frameshift caused by inserting one base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_plus_1_frameshift:2009-08-18T08-44-34Z julien.wollbrett@cirad.fr SO_frameshift An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift:2009-08-18T08-42-50Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_conflict Different sources report differing sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_conflict:2009-08-18T08-45-01Z julien.wollbrett@cirad.fr SO_polypeptide_sequencing_information Incompatibility in the sequence due to some experimental problem. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polypeptide_sequencing_information:2009-08-18T08-42-31Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_bound_by_nucleic_acid An attribute describing a sequence that is bound by a nucleic acid. cirad.fr urn:lsid:biomoby.org:objectclass:SO_bound_by_nucleic_acid:2009-08-18T08-41-37Z julien.wollbrett@cirad.fr SO_bound_by_factor An attribute describing a sequence that is bound by another molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_bound_by_factor:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_mutation_causing_polypeptide_C_terminal_elongation . cirad.fr urn:lsid:biomoby.org:objectclass:SO_mutation_causing_polypeptide_C_terminal_elongation:2009-08-18T08-43-01Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_polypeptide_elongation The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_elongation:2009-08-18T08-41-37Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_amino_acid_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_amino_acid_sequence:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DJ_gene Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DJ_gene:2009-08-18T08-46-34Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment:2009-08-18T08-46-10Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_miRNA_target_site A miRNA target site is a binding site where the molecule is a micro RNA. cirad.fr urn:lsid:biomoby.org:objectclass:SO_miRNA_target_site:2009-08-18T08-43-20Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_polyA_junction The boundary between the UTR and the polyA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polyA_junction:2009-08-18T08-40-29Z julien.wollbrett@cirad.fr SO_junction A sequence_feature with an extent of zero. cirad.fr urn:lsid:biomoby.org:objectclass:SO_junction:2009-08-18T08-39-22Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_enzymatic An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_enzymatic:2009-08-18T08-39-58Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_transposition no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transposition:2009-08-18T08-40-18Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_experimentally_determined Attribute to describe a feature that has been experiemntally verified. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimentally_determined:2009-08-18T08-42-53Z julien.wollbrett@cirad.fr SO_validated An attribute to describe a feature that has been proven. cirad.fr urn:lsid:biomoby.org:objectclass:SO_validated:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_gene_to_gene_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_to_gene_feature:2009-08-18T08-41-08Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_non_adjacent_residues Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them. cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_adjacent_residues:2009-08-18T08-44-41Z julien.wollbrett@cirad.fr SO_polypeptide_sequencing_information Incompatibility in the sequence due to some experimental problem. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polypeptide_sequencing_information:2009-08-18T08-42-31Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_polypeptide_localization_change no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_polypeptide_localization_change:2009-08-18T08-42-17Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_partially_characterised_change_of_translational_product A sequence variant causing a partially uncharacterised change in translational product. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_partially_characterised_change_of_translational_product:2009-08-18T08-42-04Z julien.wollbrett@cirad.fr SO_sequence_variant_causing_uncharacterised_change_of_translational_product A sequence variant causing an uncharacterized change of translational product. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_uncharacterised_change_of_translational_product:2009-08-18T08-40-14Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_translocate To translocate a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_translocate:2009-08-18T08-39-36Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_lysidine Lysidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_lysidine:2009-08-18T08-47-31Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_chromosomal_inversion no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_inversion:2009-08-18T08-40-45Z julien.wollbrett@cirad.fr SO_intrachromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_intrachromosomal_mutation:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_post_translationally_regulated_by_protein_modification An attribute describing a gene sequence where the resulting protein is modified to regulate it. cirad.fr urn:lsid:biomoby.org:objectclass:SO_post_translationally_regulated_by_protein_modification:2009-08-18T08-44-54Z julien.wollbrett@cirad.fr SO_post_translationally_regulated An attribute describing a gene that is regulated after it has been translated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_post_translationally_regulated:2009-08-18T08-43-11Z julien.wollbrett@cirad.fr SO_regulated An attribute to describe a sequence that is regulated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_regulated:2009-08-18T08-41-03Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_N6_hydroxynorvalylcarbamoyladenosine N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N6_hydroxynorvalylcarbamoyladenosine:2009-08-18T08-48-15Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_T_to_C_transition no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_T_to_C_transition:2009-08-18T08-49-19Z julien.wollbrett@cirad.fr SO_pyrimidine_transition A substitution of a pyrimidine, C or T, for another pyrimidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_transition:2009-08-18T08-49-08Z julien.wollbrett@cirad.fr SO_transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transition:2009-08-18T08-49-03Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_inosine A modified RNA base in which hypoxanthine is bound to the ribose ring. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inosine:2009-08-18T08-46-49Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_modified_base_site A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_base_site:2009-08-18T08-46-39Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_C_to_T_transition A transition of a cytidine to a thymine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_C_to_T_transition:2009-08-18T08-49-09Z julien.wollbrett@cirad.fr SO_pyrimidine_transition A substitution of a pyrimidine, C or T, for another pyrimidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_transition:2009-08-18T08-49-08Z julien.wollbrett@cirad.fr SO_transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transition:2009-08-18T08-49-03Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_independently_known Attribute to describe a feature that is independently known - not predicted. cirad.fr urn:lsid:biomoby.org:objectclass:SO_independently_known:2009-08-18T08-42-01Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_retrotransposed An attribute of a feature that occured as the product of a reverse transcriptase mediated event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_retrotransposed:2009-08-18T08-39-48Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insert To insert a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert:2009-08-18T08-39-37Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nucleomorphic_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleomorphic_sequence:2009-08-18T08-42-08Z julien.wollbrett@cirad.fr SO_organelle_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_organelle_sequence:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_proviral_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_proviral_location:2009-08-18T08-40-31Z julien.wollbrett@cirad.fr SO_sequence_location no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_location:2009-08-18T08-39-21Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_diplotype A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known. cirad.fr urn:lsid:biomoby.org:objectclass:SO_diplotype:2009-08-18T08-48-41Z julien.wollbrett@cirad.fr SO_genotype A genotype is a variant genome, complete or incomplete. cirad.fr urn:lsid:biomoby.org:objectclass:SO_genotype:2009-08-18T08-48-39Z julien.wollbrett@cirad.fr SO_sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant:2009-08-18T08-39-14Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_genome A genome is the sum of genetic material within a cell or virion. cirad.fr urn:lsid:biomoby.org:objectclass:SO_genome:2009-08-18T08-39-34Z julien.wollbrett@cirad.fr SO_sequence_collection A collection of discontinuous sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_collection:2009-08-18T08-39-10Z julien.wollbrett@cirad.fr variant_of SO_sequence_uncertainty Describes the positions in a sequence where the authors are unsure about the sequence assignment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_uncertainty:2009-08-18T08-44-20Z julien.wollbrett@cirad.fr SO_polypeptide_sequencing_information Incompatibility in the sequence due to some experimental problem. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polypeptide_sequencing_information:2009-08-18T08-42-31Z julien.wollbrett@cirad.fr SO_remark A comment about the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_remark:2009-08-18T08-40-51Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_double_stranded_cDNA no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_double_stranded_cDNA:2009-08-18T08-44-01Z julien.wollbrett@cirad.fr SO_cDNA DNA synthesized by reverse transcriptase using RNA as a template. cirad.fr urn:lsid:biomoby.org:objectclass:SO_cDNA:2009-08-18T08-42-23Z julien.wollbrett@cirad.fr SO_DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA:2009-08-18T08-41-15Z julien.wollbrett@cirad.fr SO_nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleic_acid:2009-08-18T08-40-07Z julien.wollbrett@cirad.fr SO_polymer_attribute An attribute to describe the kind of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polymer_attribute:2009-08-18T08-39-27Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_proviral_region A viral sequence which has integrated into a host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_proviral_region:2009-08-18T08-49-34Z julien.wollbrett@cirad.fr SO_integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_integrated_mobile_genetic_element:2009-08-18T08-49-32Z julien.wollbrett@cirad.fr SO_mobile_genetic_element A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile_genetic_element:2009-08-18T08-49-29Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr Parent SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr has_quality SO_FRT_site An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. cirad.fr urn:lsid:biomoby.org:objectclass:SO_FRT_site:2009-08-18T08-46-11Z julien.wollbrett@cirad.fr SO_inversion_site A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inversion_site:2009-08-18T08-45-46Z julien.wollbrett@cirad.fr SO_site_specific_recombination_target_region no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_site_specific_recombination_target_region:2009-08-18T08-45-12Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_transcript_processing Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_processing:2009-08-18T08-41-41Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_RNA_internal_loop A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_internal_loop:2009-08-18T08-44-06Z julien.wollbrett@cirad.fr SO_RNA_motif A motif that is active in RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_motif:2009-08-18T08-42-29Z julien.wollbrett@cirad.fr SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_dicistronic An attribute describing a sequence that contains the code for two gene products. cirad.fr urn:lsid:biomoby.org:objectclass:SO_dicistronic:2009-08-18T08-43-38Z julien.wollbrett@cirad.fr SO_polycistronic An attribute describing a sequence that contains the code for more than one gene product. cirad.fr urn:lsid:biomoby.org:objectclass:SO_polycistronic:2009-08-18T08-41-56Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_methylinosine A modified RNA base in which methylhypoxanthine is bound to the ribose ring. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylinosine:2009-08-18T08-48-33Z julien.wollbrett@cirad.fr SO_modified_inosine A modified inosine is an inosine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_inosine:2009-08-18T08-47-09Z julien.wollbrett@cirad.fr SO_inosine A modified RNA base in which hypoxanthine is bound to the ribose ring. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inosine:2009-08-18T08-46-49Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_mobile An attribute describing a feature thatnhas either intra-genome or intracellular mobility. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mobile:2009-08-18T08-40-26Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_fragment_assembly A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. cirad.fr urn:lsid:biomoby.org:objectclass:SO_fragment_assembly:2009-08-18T08-42-57Z julien.wollbrett@cirad.fr SO_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly:2009-08-18T08-41-21Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_seven_methylguanine A modified RNA base in which guanine is methylated at the 7- position. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_methylguanine:2009-08-18T08-46-46Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_RNA_aptamer RNA molecules that have been selected from random pools based on their ability to bind other molecules. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_aptamer:2009-08-18T08-45-30Z julien.wollbrett@cirad.fr SO_aptamer DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. cirad.fr urn:lsid:biomoby.org:objectclass:SO_aptamer:2009-08-18T08-44-23Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_snRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_snRNA_encoding:2009-08-18T08-43-22Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_prime_D_recombination_signal_sequence Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_prime_D_recombination_signal_sequence:2009-08-18T08-46-40Z julien.wollbrett@cirad.fr SO_D_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_D_gene_recombination_feature:2009-08-18T08-46-24Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_signal_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_signal_feature:2009-08-18T08-46-07Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_minus_2_frameshift A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_minus_2_frameshift:2009-08-18T08-45-35Z julien.wollbrett@cirad.fr SO_frameshift_sequence_variation A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift_sequence_variation:2009-08-18T08-44-16Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_reading_frame An umbrella term for terms describing an effect of a sequence variation on the frame of translation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_reading_frame:2009-08-18T08-42-51Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_methylwyosine Methylwyosine is a modified guanosine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylwyosine:2009-08-18T08-47-32Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_methylated_base_feature A nucleotide modified by methylation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylated_base_feature:2009-08-18T08-46-48Z julien.wollbrett@cirad.fr SO_modified_base_site A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_base_site:2009-08-18T08-46-39Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_hydroxyuridine 5_hydroxyuridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_hydroxyuridine:2009-08-18T08-47-42Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_plus_1_frameshift_mutation A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_plus_1_frameshift_mutation:2009-08-18T08-45-28Z julien.wollbrett@cirad.fr SO_frameshift_sequence_variation A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift_sequence_variation:2009-08-18T08-44-16Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_reading_frame An umbrella term for terms describing an effect of a sequence variation on the frame of translation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_reading_frame:2009-08-18T08-42-51Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_polyadenylation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polyadenylation:2009-08-18T08-43-19Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_transcript_processing Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_transcript_processing:2009-08-18T08-41-41Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_intergenic_region A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_intergenic_region:2009-08-18T08-41-13Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_methylated_A A modified RNA base in which adenine has been methylated. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylated_A:2009-08-18T08-47-18Z julien.wollbrett@cirad.fr SO_methylated_base_feature A nucleotide modified by methylation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_methylated_base_feature:2009-08-18T08-46-48Z julien.wollbrett@cirad.fr SO_modified_base_site A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_base_site:2009-08-18T08-46-39Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_causing_no_3D_structural_change no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_no_3D_structural_change:2009-08-18T08-41-52Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_3D_structure_of_polypeptide A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_3D_structure_of_polypeptide:2009-08-18T08-39-40Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_G_quartet G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. cirad.fr urn:lsid:biomoby.org:objectclass:SO_G_quartet:2009-08-18T08-42-25Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_causing_gene_fusion A sequence_variant_effect that changes the gene structure by causing a fusion to another gene. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_gene_fusion:2009-08-18T08-40-25Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_gene_structure A sequence_variant_effect that changes the gene structure. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_gene_structure:2009-08-18T08-39-22Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_one_two_prime_O_dimethylinosine 1,2'-O-dimethylinosine is a modified inosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_one_two_prime_O_dimethylinosine:2009-08-18T08-48-31Z julien.wollbrett@cirad.fr SO_modified_inosine A modified inosine is an inosine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_inosine:2009-08-18T08-47-09Z julien.wollbrett@cirad.fr SO_inosine A modified RNA base in which hypoxanthine is bound to the ribose ring. cirad.fr urn:lsid:biomoby.org:objectclass:SO_inosine:2009-08-18T08-46-49Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_N4_methylcytidine N4-methylcytidine is a modified cytidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_N4_methylcytidine:2009-08-18T08-47-40Z julien.wollbrett@cirad.fr SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_vertebrate_immune_system_gene_recombination_signal_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_signal_feature:2009-08-18T08-46-07Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_flanked An attribute describing a region that is bounded either side by a paricular kind of region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_flanked:2009-08-18T08-39-43Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_snoRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_snoRNA_encoding:2009-08-18T08-43-53Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_tag A nucleotide sequence that may be used to identify a larger sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_tag:2009-08-18T08-44-26Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid:2009-08-18T08-39-41Z julien.wollbrett@cirad.fr SO_chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_number_variation:2009-08-18T08-39-29Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_codon_redefined An attribute describing the alteration of codon meaning. cirad.fr urn:lsid:biomoby.org:objectclass:SO_codon_redefined:2009-08-18T08-44-41Z julien.wollbrett@cirad.fr SO_recoded An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. cirad.fr urn:lsid:biomoby.org:objectclass:SO_recoded:2009-08-18T08-42-34Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_single no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_single:2009-08-18T08-41-42Z julien.wollbrett@cirad.fr SO_strand_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_strand_attribute:2009-08-18T08-39-55Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_haplotype_block A region of the genome which is co-inherited as the result of the lack of historic recombination within it. cirad.fr urn:lsid:biomoby.org:objectclass:SO_haplotype_block:2009-08-18T08-42-46Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_consensus no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_consensus:2009-08-18T08-41-35Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_exemplar An attribute describing a sequence is representative of a class of similar sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_exemplar:2009-08-18T08-43-44Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_restriction_enzyme_binding_site A region of a molecule that binds to a restriction enzyme. cirad.fr urn:lsid:biomoby.org:objectclass:SO_restriction_enzyme_binding_site:2009-08-18T08-45-17Z julien.wollbrett@cirad.fr SO_nuclease_binding_site A region of a molecule that binds to a nuclease. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nuclease_binding_site:2009-08-18T08-44-12Z julien.wollbrett@cirad.fr SO_protein_binding_site A region of a molecule that binds to a protein. cirad.fr urn:lsid:biomoby.org:objectclass:SO_protein_binding_site:2009-08-18T08-43-04Z julien.wollbrett@cirad.fr SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_carboxymethylaminomethyl_two_thiouridine 5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_carboxymethylaminomethyl_two_thiouridine:2009-08-18T08-47-30Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_five_methoxycarbonylmethyl_two_prime_O_methyluridine Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_methoxycarbonylmethyl_two_prime_O_methyluridine:2009-08-18T08-47-43Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of ExpressionCore Minimum information from gene expression experiments. www.cnb.uam.es urn:lsid:biomoby.org:objectclass:ExpressionCore:2009-06-17T10-04-40Z natalia@cnb.csic.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com GeneID StructureID TheilerStage ExpressionStatistics Statistics about gene expression www.cnb.uam.es urn:lsid:biomoby.org:objectclass:ExpressionStatistics:2009-06-17T10-04-45Z natalia@cnb.csic.es ExpressionCore Minimum information from gene expression experiments. www.cnb.uam.es urn:lsid:biomoby.org:objectclass:ExpressionCore:2009-06-17T10-04-40Z natalia@cnb.csic.es Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com GeneID StructureID TheilerStage ExpressionPattern ExpressionLevel DevelopmentID SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of iANT_organism-xml iANT organism xml file. This xml format describes an organism (taxonomy,longname,,code,strain,substrain,variety,cultivar,isolate,subspecies,ecotype). iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT_organism-xml:2009-05-18T14-36-21Z Sebastien.Carrere@toulouse.inra.fr iANT-xml iANT xml file (entry, feature, db_entry, db_features) iant.toulouse.inra.fr urn:lsid:biomoby.org:objectclass:iANT-xml:2007-07-18T12-58-41Z Sebastien.Carrere@toulouse.inra.fr text-xml XML formatted text www.illuminae.com urn:lsid:biomoby.org:objectclass:text-xml:2001-09-21T16-00-00Z markw@illuminae.com text-formatted formatted plaintext, where the layout is important to meaning www.illuminae.com urn:lsid:biomoby.org:objectclass:text-formatted:2001-09-21T16-00-00Z markw@illuminae.com text-plain plaintext message www.illuminae.com urn:lsid:biomoby.org:objectclass:text-plain:2001-09-21T16-00-00Z markw@illuminae.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com content MetaboliteMeasurement Metabolite Measurment consisting of measurement value and a metabolite name such as lycopene. This object is registered here due to a probable bug in the BioMoby JAVA API while normal usage of this object is via a private biomoby Repository. We currently use this object to test this probable bug. www.plantbreeding.wur.nl urn:lsid:biomoby.org:objectclass:MetaboliteMeasurement:2009-06-03T08-45-01Z Richard.Fnkers@wur.nl Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com value median min avg max SO_stRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_stRNA_encoding:2009-08-18T08-42-44Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_water_environment The treatment involving an exposure of varying amount of water and watering frequncies, which may depend on regional environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_water_environment:2009-04-30T14-07-08Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com Accession This objects describes some properties of an Accession. www.plantbreeding.wur.nl urn:lsid:biomoby.org:objectclass:Accession:2009-05-06T12-39-50Z richard.finkers@wur.nl Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com collectionCountry accessionSource accessionDescription Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com collectionYear SO_Robertsonian_fusion no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_Robertsonian_fusion:2009-08-18T08-43-10Z julien.wollbrett@cirad.fr SO_chromosomal_translocation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_translocation:2009-08-18T08-41-30Z julien.wollbrett@cirad.fr SO_interchromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_interchromosomal_mutation:2009-08-18T08-40-33Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_Liliopsida The exposure of reference/experimental plant to monocot plants found in its growth environment. These plants may be growing as a weed or as part of normal farming practices. cirad.fr urn:lsid:biomoby.org:objectclass:EO_Liliopsida:2009-04-30T14-08-20Z julien.wollbrett@cirad.fr EO_Viridiplantae Suggests the exposure of plant to other plants found in its growth environment. These plants may be growing as a weed or as part of normal farming practices. This treatmnet is part of an assay of any direct or indirect, harmful or beneficial effect of one plant on another through the production of chemical compounds (allelochemicals) that escape in the environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_Viridiplantae:2009-04-30T14-07-45Z julien.wollbrett@cirad.fr EO_pest-pathogen-animal-plant_environment Treatment involving the exposure of plant to the pest/pathogen/animal/plants present as part of its growth environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_pest-pathogen-animal-plant_environment:2009-04-30T14-07-10Z julien.wollbrett@cirad.fr EO_biotic_environment The treatment involving an exposure to the biotic/biological factors such as pest, pathogens, plants, etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_biotic_environment:2009-04-30T14-07-04Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_Nematoda The treatment involving exposure of plant to the nematode pests. cirad.fr urn:lsid:biomoby.org:objectclass:EO_Nematoda:2009-04-30T14-08-15Z julien.wollbrett@cirad.fr EO_Metazoa The treatment involving exposure of plant to the pests and weeds of higher order. cirad.fr urn:lsid:biomoby.org:objectclass:EO_Metazoa:2009-04-30T14-07-21Z julien.wollbrett@cirad.fr EO_pest-pathogen-animal-plant_environment Treatment involving the exposure of plant to the pest/pathogen/animal/plants present as part of its growth environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_pest-pathogen-animal-plant_environment:2009-04-30T14-07-10Z julien.wollbrett@cirad.fr EO_biotic_environment The treatment involving an exposure to the biotic/biological factors such as pest, pathogens, plants, etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_biotic_environment:2009-04-30T14-07-04Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_modified_cytidine A modified cytidine is a cytidine base feature which has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_cytidine:2009-08-18T08-46-42Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_sequence_variant_affecting_polypeptide_function no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_polypeptide_function:2009-08-18T08-39-54Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_probe A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. cirad.fr urn:lsid:biomoby.org:objectclass:SO_probe:2009-08-18T08-44-38Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_supported_by_domain_match An attribute to describe a feature that has been predicted using sequence similarity of a known domain. cirad.fr urn:lsid:biomoby.org:objectclass:SO_supported_by_domain_match:2009-08-18T08-44-40Z julien.wollbrett@cirad.fr SO_supported_by_sequence_similarity An attribute to describe a feature that has been predicted using sequence similarity techniques. cirad.fr urn:lsid:biomoby.org:objectclass:SO_supported_by_sequence_similarity:2009-08-18T08-42-28Z julien.wollbrett@cirad.fr SO_predicted An attribute describing an unverified region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_predicted:2009-08-18T08-40-50Z julien.wollbrett@cirad.fr SO_status An attribute describing the status of a feature, based on the available evidence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_status:2009-08-18T08-40-01Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_conserved_region Region of sequence similarity by descent from a common ancestor. cirad.fr urn:lsid:biomoby.org:objectclass:SO_conserved_region:2009-08-18T08-41-26Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_member_of_regulon no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_member_of_regulon:2009-08-18T08-43-16Z julien.wollbrett@cirad.fr SO_gene_array_member no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_array_member:2009-08-18T08-41-24Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_epigenetically_modified This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. cirad.fr urn:lsid:biomoby.org:objectclass:SO_epigenetically_modified:2009-08-18T08-40-53Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_assembly_component A region of known length which may be used to manufacture a longer region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assembly_component:2009-08-18T08-40-54Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_hexamethylphosphoramide The treatment involving use of hexamethylphosphoramide for mutagenesis process. cirad.fr urn:lsid:biomoby.org:objectclass:EO_hexamethylphosphoramide:2009-04-30T14-08-35Z julien.wollbrett@cirad.fr EO_chemical_mutagen The treatment involving use of mutagen for the mutagenesis process. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_mutagen:2009-04-30T14-07-16Z julien.wollbrett@cirad.fr EO_chemical_regimen The treatment involving use of chemical(s) to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_regimen:2009-04-30T14-07-06Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_atmospheric_pressure The treatment involving an exposure to a given pressure of the atmosphere at a given point. Its measurement can be expressed in several ways. One is in millibars. Another is in inches or millimeters of mercury (Hg). cirad.fr urn:lsid:biomoby.org:objectclass:EO_atmospheric_pressure:2009-04-30T14-07-56Z julien.wollbrett@cirad.fr EO_ecological_environment The treatment involving an exposure to the various factors that comprise a geographical/regional location. cirad.fr urn:lsid:biomoby.org:objectclass:EO_ecological_environment:2009-04-30T14-07-11Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_isopentenylaminomethyl_uridine 5_isopentenylaminomethyl_uridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_isopentenylaminomethyl_uridine:2009-08-18T08-48-03Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_simple_sequence_length_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_simple_sequence_length_variation:2009-08-18T08-49-04Z julien.wollbrett@cirad.fr SO_sequence_length_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_length_variation:2009-08-18T08-49-00Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of EO_standing_water The treatment involving an exposure to standing water during a plant's life span. This also results in anaerobic soil conditions for a either long or short periods. cirad.fr urn:lsid:biomoby.org:objectclass:EO_standing_water:2009-04-30T14-07-22Z julien.wollbrett@cirad.fr EO_water_environment The treatment involving an exposure of varying amount of water and watering frequncies, which may depend on regional environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_water_environment:2009-04-30T14-07-08Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_uninverted_insertional_duplication A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. cirad.fr urn:lsid:biomoby.org:objectclass:SO_uninverted_insertional_duplication:2009-08-18T08-44-27Z julien.wollbrett@cirad.fr SO_insertional_duplication A chromosome duplication involving the insertion of a duplicated region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insertional_duplication:2009-08-18T08-42-24Z julien.wollbrett@cirad.fr SO_chromosomal_duplication An extra chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_duplication:2009-08-18T08-40-52Z julien.wollbrett@cirad.fr SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_plus_2_framshift A frameshift caused by inserting two bases. cirad.fr urn:lsid:biomoby.org:objectclass:SO_plus_2_framshift:2009-08-18T08-45-04Z julien.wollbrett@cirad.fr SO_frameshift An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. cirad.fr urn:lsid:biomoby.org:objectclass:SO_frameshift:2009-08-18T08-42-50Z julien.wollbrett@cirad.fr SO_mRNA_attribute An attribute describing an mRNA feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_mRNA_attribute:2009-08-18T08-40-55Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_gaseous_environment The use of gasses in a given environment to study various types of responses on their extrinsic and/or intrinsic stimulus. cirad.fr urn:lsid:biomoby.org:objectclass:EO_gaseous_environment:2009-04-30T14-07-14Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_field_study The treatment where the plants were grown under field conditions. This may involve supplemantal treatments in addition to any naturally occurring conditions. cirad.fr urn:lsid:biomoby.org:objectclass:EO_field_study:2009-04-30T14-07-11Z julien.wollbrett@cirad.fr EO_study_type The treatment suggesting what kind of growth facility was used. cirad.fr urn:lsid:biomoby.org:objectclass:EO_study_type:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_alternatively_spliced An attribute describing a situation where a gene may encode for more than 1 transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_alternatively_spliced:2009-08-18T08-42-10Z julien.wollbrett@cirad.fr SO_transcript_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_transcript_attribute:2009-08-18T08-40-03Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_3-H no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_3-H:2009-04-30T14-08-34Z julien.wollbrett@cirad.fr EO_radiation_quality_regimen The treatment involving an exposure to a given type of radiation. Often it is in the form of electromagnetic and ionizing radiation such as light (infrared, visible or ultraviolet), x-rays, gamma rays, etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_quality_regimen:2009-04-30T14-07-17Z julien.wollbrett@cirad.fr EO_radiation_regimen The treatment involving an exposure with a radiation type, intesity or quantity. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_regimen:2009-04-30T14-07-14Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_pH_regimen The treatment involving exposure of plants to varying levels of pH of the growth media. cirad.fr urn:lsid:biomoby.org:objectclass:EO_pH_regimen:2009-04-30T14-07-22Z julien.wollbrett@cirad.fr EO_growth_media The treatment involving use of growth media for growing the plants or tissue cultured samples. cirad.fr urn:lsid:biomoby.org:objectclass:EO_growth_media:2009-04-30T14-07-05Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_assortment_derived_duplication A multi-chromosome duplication aberration generated by reassortment of other aberration components. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assortment_derived_duplication:2009-08-18T08-39-32Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_C_gene Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). cirad.fr urn:lsid:biomoby.org:objectclass:SO_C_gene:2009-08-18T08-46-31Z julien.wollbrett@cirad.fr SO_vertebrate_immunoglobulin_T_cell_receptor_segment no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immunoglobulin_T_cell_receptor_segment:2009-08-18T08-46-04Z julien.wollbrett@cirad.fr SO_vertebrate_immune_system_gene_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_vertebrate_immune_system_gene_recombination_feature:2009-08-18T08-45-40Z julien.wollbrett@cirad.fr SO_recombination_feature_of_rearranged_gene no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature_of_rearranged_gene:2009-08-18T08-45-10Z julien.wollbrett@cirad.fr SO_specific_recombination_site no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_specific_recombination_site:2009-08-18T08-44-04Z julien.wollbrett@cirad.fr SO_sequence_rearrangement_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_rearrangement_feature:2009-08-18T08-42-20Z julien.wollbrett@cirad.fr SO_recombination_feature no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_recombination_feature:2009-08-18T08-41-02Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_copy_number no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_copy_number:2009-08-18T08-39-40Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_chromosomal_deletion An incomplete chromosome. cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosomal_deletion:2009-08-18T08-49-23Z julien.wollbrett@cirad.fr SO_intrachromosomal_mutation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_intrachromosomal_mutation:2009-08-18T08-39-46Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_aneuploid_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_aneuploid_chromosome:2009-08-18T08-39-59Z julien.wollbrett@cirad.fr Parent SO_encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_greater_than_1_polypeptide:2009-08-18T08-43-29Z julien.wollbrett@cirad.fr SO_encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_encodes_alternately_spliced_transcripts:2009-08-18T08-41-44Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_warm-hot_temperature_regimen The treatment involving an exposure to above optimal temperature, which may depend on the study type or the regional environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_warm-hot_temperature_regimen:2009-04-30T14-07-23Z julien.wollbrett@cirad.fr EO_temperature_environment The treatment involving an exposure to varying degree of temperature, which may depend on regional environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_temperature_environment:2009-04-30T14-07-07Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_winter_season The treatment involving an exposure to the winter season. cirad.fr urn:lsid:biomoby.org:objectclass:EO_winter_season:2009-04-30T14-07-36Z julien.wollbrett@cirad.fr EO_seasonal_environment The treatment involving an exposure to a given conditions of regional seasons. cirad.fr urn:lsid:biomoby.org:objectclass:EO_seasonal_environment:2009-04-30T14-07-05Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_assortment_derived_aneuploid A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication. cirad.fr urn:lsid:biomoby.org:objectclass:SO_assortment_derived_aneuploid:2009-08-18T08-39-35Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_insertion A region of sequence that has been inserted. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insertion:2009-08-18T08-48-50Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_insert To insert a subsection of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_insert:2009-08-18T08-39-37Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_pyrimidine_transition A substitution of a pyrimidine, C or T, for another pyrimidine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_pyrimidine_transition:2009-08-18T08-49-08Z julien.wollbrett@cirad.fr SO_transition Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. cirad.fr urn:lsid:biomoby.org:objectclass:SO_transition:2009-08-18T08-49-03Z julien.wollbrett@cirad.fr SO_point_mutation A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_point_mutation:2009-08-18T08-48-56Z julien.wollbrett@cirad.fr SO_substitution Any change in genomic DNA caused by a single event. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitution:2009-08-18T08-48-48Z julien.wollbrett@cirad.fr SO_sequence_alteration A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_alteration:2009-08-18T08-39-18Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr Parent SO_substitute To substitute a subsection of sequence for another. cirad.fr urn:lsid:biomoby.org:objectclass:SO_substitute:2009-08-18T08-39-30Z julien.wollbrett@cirad.fr SO_sequence_operation An operation that can be applied to a sequence, that results in a change. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_operation:2009-08-18T08-39-12Z julien.wollbrett@cirad.fr sequence_of SO_sequence_variant_causing_terminator_codon_change_in_transcript The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_causing_terminator_codon_change_in_transcript:2009-08-18T08-42-54Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_coding_sequence:2009-08-18T08-40-47Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript_sequence no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript_sequence:2009-08-18T08-39-50Z julien.wollbrett@cirad.fr SO_sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variation_affecting_transcript:2009-08-18T08-39-17Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_two_methylthio_N6_threonyl_carbamoyladenosine 2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_two_methylthio_N6_threonyl_carbamoyladenosine:2009-08-18T08-47-05Z julien.wollbrett@cirad.fr SO_modified_adenosine A modified adenine is an adenine base feature that has been altered. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_adenosine:2009-08-18T08-46-41Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of EO_pesticide_regimen The treatment involving use of pesticides to study various types of responses on their application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_pesticide_regimen:2009-04-30T14-07-25Z julien.wollbrett@cirad.fr EO_chemical_regimen The treatment involving use of chemical(s) to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_regimen:2009-04-30T14-07-06Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_light_quantity_regimen In biological experiments often it refer to the length of the exposure time. The treatment also includes the quantity of light falling on a per unit area. This may be expressed either in terms of hours for which teh radiation was available or in the units of luminous flux or the lumens. cirad.fr urn:lsid:biomoby.org:objectclass:EO_light_quantity_regimen:2009-04-30T14-08-14Z julien.wollbrett@cirad.fr EO_radiation_quantity_regimen In biological experiments it refer to the treatment involving radiation in terms of length of the exposure time. It also includes the quantity of radiation falling on a per unit area. This is expressed in the units of luminous flux or the lumens. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_quantity_regimen:2009-04-30T14-07-24Z julien.wollbrett@cirad.fr EO_radiation_regimen The treatment involving an exposure with a radiation type, intesity or quantity. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_regimen:2009-04-30T14-07-14Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_intermediate An attribute to describe a feature between stages of processing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_intermediate:2009-08-18T08-39-49Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_level_of_translational_product no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_level_of_translational_product:2009-08-18T08-40-02Z julien.wollbrett@cirad.fr SO_sequence_variant_affecting_translational_product Mutation causes a change in primary translation product of a transcript. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_translational_product:2009-08-18T08-39-24Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DMv4_motif A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014). cirad.fr urn:lsid:biomoby.org:objectclass:SO_DMv4_motif:2009-08-18T08-44-07Z julien.wollbrett@cirad.fr SO_DNA_motif A motif that is active in the DNA form of the sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_motif:2009-08-18T08-42-32Z julien.wollbrett@cirad.fr SO_nucleotide_motif A region of nucleotide sequence corresponding to a known motif. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_motif:2009-08-18T08-41-00Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_dexstrosynaptic_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_dexstrosynaptic_chromosome:2009-08-18T08-41-48Z julien.wollbrett@cirad.fr SO_autosynaptic_chromosome no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_autosynaptic_chromosome:2009-08-18T08-40-14Z julien.wollbrett@cirad.fr SO_chromosome_structure_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_structure_variation:2009-08-18T08-39-33Z julien.wollbrett@cirad.fr SO_chromosome_variation no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_chromosome_variation:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_tropical_region Exposure to the geographical region of the Earth limited in latitude by the two tropics namely, the Tropic of Cancer and the Tropic of Capricorn, and thus centered on the equator.. This area lies approximately between 23.5 N latitude and 23.5 S latitude, and includes all the parts of the Earth where the sun reaches a point directly overhead at least once during the solar year (north of the Tropic of Cancer and south of the Tropic of Capricorn the sun never reaches an azimuth of 90 or directly overhead). cirad.fr urn:lsid:biomoby.org:objectclass:EO_tropical_region:2009-04-30T14-07-33Z julien.wollbrett@cirad.fr EO_ecological_environment The treatment involving an exposure to the various factors that comprise a geographical/regional location. cirad.fr urn:lsid:biomoby.org:objectclass:EO_ecological_environment:2009-04-30T14-07-11Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_seasonal_environment The treatment involving an exposure to a given conditions of regional seasons. cirad.fr urn:lsid:biomoby.org:objectclass:EO_seasonal_environment:2009-04-30T14-07-05Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_dihydrouridine A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring. cirad.fr urn:lsid:biomoby.org:objectclass:SO_dihydrouridine:2009-08-18T08-47-39Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of EO_fungal_elicitor no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_fungal_elicitor:2009-04-30T14-07-40Z julien.wollbrett@cirad.fr EO_chemical_regimen The treatment involving use of chemical(s) to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_regimen:2009-04-30T14-07-06Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_3-H-thymidine no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_3-H-thymidine:2009-04-30T14-08-38Z julien.wollbrett@cirad.fr EO_radiation_quality_regimen The treatment involving an exposure to a given type of radiation. Often it is in the form of electromagnetic and ionizing radiation such as light (infrared, visible or ultraviolet), x-rays, gamma rays, etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_quality_regimen:2009-04-30T14-07-17Z julien.wollbrett@cirad.fr EO_radiation_regimen The treatment involving an exposure with a radiation type, intesity or quantity. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_regimen:2009-04-30T14-07-14Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_cross_genome_match A nucleotide match against a sequence from another organism. cirad.fr urn:lsid:biomoby.org:objectclass:SO_cross_genome_match:2009-08-18T08-44-47Z julien.wollbrett@cirad.fr SO_nucleotide_match A match against a nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_nucleotide_match:2009-08-18T08-42-36Z julien.wollbrett@cirad.fr SO_match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. cirad.fr urn:lsid:biomoby.org:objectclass:SO_match:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_experimental_feature A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_experimental_feature:2009-08-18T08-39-53Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_deuteron_irradiation no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_deuteron_irradiation:2009-04-30T14-08-06Z julien.wollbrett@cirad.fr EO_radiation_quality_regimen The treatment involving an exposure to a given type of radiation. Often it is in the form of electromagnetic and ionizing radiation such as light (infrared, visible or ultraviolet), x-rays, gamma rays, etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_quality_regimen:2009-04-30T14-07-17Z julien.wollbrett@cirad.fr EO_radiation_regimen The treatment involving an exposure with a radiation type, intesity or quantity. cirad.fr urn:lsid:biomoby.org:objectclass:EO_radiation_regimen:2009-04-30T14-07-14Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_Stramenopiles Treatment involving the exposure of plant to the Stramenopiles (heterokonts) present in the gorowth environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_Stramenopiles:2009-04-30T14-07-29Z julien.wollbrett@cirad.fr EO_pest-pathogen-animal-plant_environment Treatment involving the exposure of plant to the pest/pathogen/animal/plants present as part of its growth environment. cirad.fr urn:lsid:biomoby.org:objectclass:EO_pest-pathogen-animal-plant_environment:2009-04-30T14-07-10Z julien.wollbrett@cirad.fr EO_biotic_environment The treatment involving an exposure to the biotic/biological factors such as pest, pathogens, plants, etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_biotic_environment:2009-04-30T14-07-04Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_five_methylaminomethyl_two_selenouridine 5_methylaminomethyl_2_selenouridine is a modified uridine base feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_five_methylaminomethyl_two_selenouridine:2009-08-18T08-47-53Z julien.wollbrett@cirad.fr SO_modified_uridine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_uridine:2009-08-18T08-46-44Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of EO_1,6-dimethylsulfonoxy_L-mannitol The treatment involving use of 1,6-dimethylsulfonoxy L-mannitol for mutagenesis process. cirad.fr urn:lsid:biomoby.org:objectclass:EO_1,6-dimethylsulfonoxy_L-mannitol:2009-04-30T14-08-18Z julien.wollbrett@cirad.fr EO_chemical_mutagen The treatment involving use of mutagen for the mutagenesis process. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_mutagen:2009-04-30T14-07-16Z julien.wollbrett@cirad.fr EO_chemical_regimen The treatment involving use of chemical(s) to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_regimen:2009-04-30T14-07-06Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_ecological_environment The treatment involving an exposure to the various factors that comprise a geographical/regional location. cirad.fr urn:lsid:biomoby.org:objectclass:EO_ecological_environment:2009-04-30T14-07-11Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com CodingSNP_Consequences_Function Datatype to include the functional consequences of a SNP. Can be used for any prediction tool. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Consequences_Function:2010-12-13T14-31-19Z genome@dkfz.de String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com consequence Float a floating point number openinformatics.com urn:lsid:biomoby.org:objectclass:Float:2001-09-21T16-00-00Z jason@openinformatics.com score method AnnotatedCodingSNP SNP in the context of its location in a protein including annotations. husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:AnnotatedCodingSNP:2010-12-01T11-49-27Z genome@dkfz.de wt_aa_seq CodingSNP_Extended An extended version of the former CodingSNP, featuring the additional fields: reference_allele, genotype_allele husar.gpcf.dkfz.de urn:lsid:biomoby.org:objectclass:CodingSNP_Extended:2010-11-24T14-13-31Z genome@dkfz.de CodingSNP SNPs in coding region with codons and aminoacids www.weigelworld.org urn:lsid:biomoby.org:objectclass:CodingSNP:2006-06-27T14-31-56Z stephan.ossowski@tuebingen.mpg.de GenericSNP Generic SNP with position and strain www.weigelworld.org urn:lsid:biomoby.org:objectclass:GenericSNP:2006-06-27T14-26-28Z stephan.ossowski@tuebingen.mpg.de Position Physical position in chromosome (e.g. chromosome 1,2,..x; position count from 1 ). www.nias.affrc.go.jp urn:lsid:biomoby.org:objectclass:Position:2001-09-21T16-00-00Z kome_web@nias.affrc.go.jp Integer an int openinformatics.com urn:lsid:biomoby.org:objectclass:Integer:2001-09-21T16-00-00Z jason@openinformatics.com end start chromosome Position Strain codon_ref aa_ref codon_var aa_var aa_pos Boolean An object representing a boolean logic value (either "true" or "false") moby.ucalgary.ca urn:lsid:biomoby.org:objectclass:Boolean:2001-09-21T16-00-00Z gordonp@ucalgary.ca aa_change reference_allele genotype_allele mut_aa_seq ext_database_refs BioObjectRelated Object containing information about a related bioobjects in GabiPD www.gabipd.org urn:lsid:biomoby.org:objectclass:BioObjectRelated:2010-06-16T07-01-43Z gabipd@mpimp-golm.mpg.de Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com String a string openinformatics.com urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z jason@openinformatics.com BioObjectSourceDescription BioObject Object containing information about a bioobject www.gabipd.org urn:lsid:biomoby.org:objectclass:BioObject:2010-06-16T06-59-28Z gabipd@mpimp-golm.mpg.de Name Type Description Genotype Strain TaxonName GBIF - Concatenated scientific name, preferrably formed in accordance with a Code of Nomenclature, i. e. a monomial, bionomial, or trinomial plus author(s) or author team(s) and - where relevant - year, or the name of a cultivar or cultivar group, or a hybrid formula, as fully as possible. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:TaxonName:2001-09-21T16-00-00Z jatorre@gmail.com TaxonName FirstEpithet GBIF - The first epithet in a botanical name combination (species epithet or the epithet of the subdivision of a genus. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:FirstEpithet:2001-09-21T16-00-00Z jatorre@gmail.com FirstEpithet FirstEpithet Genus GBIF test - Genus www.mncn.csic.es urn:lsid:biomoby.org:objectclass:Genus:2001-09-21T16-00-00Z jatorre@gmail.com Genus InfraspecificEpithet GBIF - The final epithet of a botanical name of infraspecific rank. AppInfo Nothing found. www.mncn.csic.es urn:lsid:biomoby.org:objectclass:InfraspecificEpithet:2001-09-21T16-00-00Z jatorre@gmail.com InfraspecificEpithet InfraspecificEpithet Species AccessPageUrl BioObjectSource BioObjectTargetDescription BioObjectTarget EO_1-diethylaminoethylethylamino-4-methyl-thioxanthenone The treatment involving use of 1-diethylaminoethylethylamino-4-methyl-thioxanthenone for mutagenesis process. cirad.fr urn:lsid:biomoby.org:objectclass:EO_1-diethylaminoethylethylamino-4-methyl-thioxanthenone:2009-04-30T14-08-27Z julien.wollbrett@cirad.fr EO_chemical_mutagen The treatment involving use of mutagen for the mutagenesis process. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_mutagen:2009-04-30T14-07-16Z julien.wollbrett@cirad.fr EO_chemical_regimen The treatment involving use of chemical(s) to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_regimen:2009-04-30T14-07-06Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_galactosyl_queuosine Galactosyl_queuosine is a modified 7-deazoguanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_galactosyl_queuosine:2009-08-18T08-48-30Z julien.wollbrett@cirad.fr SO_seven_deazaguanosine 7-deazaguanosine is a moddified guanosine. cirad.fr urn:lsid:biomoby.org:objectclass:SO_seven_deazaguanosine:2009-08-18T08-46-56Z julien.wollbrett@cirad.fr SO_modified_guanosine no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_guanosine:2009-08-18T08-46-43Z julien.wollbrett@cirad.fr SO_modified_RNA_base_feature A post_transcriptionally modified base. cirad.fr urn:lsid:biomoby.org:objectclass:SO_modified_RNA_base_feature:2009-08-18T08-46-38Z julien.wollbrett@cirad.fr SO_base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. cirad.fr urn:lsid:biomoby.org:objectclass:SO_base:2009-08-18T08-46-26Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com part_of SO_miRNA_encoding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_miRNA_encoding:2009-08-18T08-43-28Z julien.wollbrett@cirad.fr SO_non_protein_coding no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_non_protein_coding:2009-08-18T08-41-04Z julien.wollbrett@cirad.fr SO_gene_attribute no description available cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_attribute:2009-08-18T08-39-52Z julien.wollbrett@cirad.fr SO_feature_attribute An attribute describing a located_sequence_feature. cirad.fr urn:lsid:biomoby.org:objectclass:SO_feature_attribute:2009-08-18T08-39-19Z julien.wollbrett@cirad.fr SO_sequence_attribute An attribute describes a quality of sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_attribute:2009-08-18T08-39-15Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_tetraloop A base-paired stem with loop of 4 non-hydrogen bonded nucleotides. cirad.fr urn:lsid:biomoby.org:objectclass:SO_tetraloop:2009-08-18T08-45-37Z julien.wollbrett@cirad.fr SO_stem_loop A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. cirad.fr urn:lsid:biomoby.org:objectclass:SO_stem_loop:2009-08-18T08-44-45Z julien.wollbrett@cirad.fr SO_RNA_sequence_secondary_structure A folded RNA sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_RNA_sequence_secondary_structure:2009-08-18T08-43-31Z julien.wollbrett@cirad.fr SO_sequence_secondary_structure A folded sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_secondary_structure:2009-08-18T08-40-46Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_sequence_variant_affecting_gene_structure A sequence_variant_effect that changes the gene structure. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_affecting_gene_structure:2009-08-18T08-39-22Z julien.wollbrett@cirad.fr SO_sequence_variant_effect The effect of a change in nucleotide sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_variant_effect:2009-08-18T08-39-11Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_operon A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. cirad.fr urn:lsid:biomoby.org:objectclass:SO_operon:2009-08-18T08-42-21Z julien.wollbrett@cirad.fr SO_gene_group A collection of related genes. cirad.fr urn:lsid:biomoby.org:objectclass:SO_gene_group:2009-08-18T08-40-42Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_binding_site A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_binding_site:2009-08-18T08-40-57Z julien.wollbrett@cirad.fr SO_biological_region A region defined by its disposition to be involved in a biological process. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biological_region:2009-08-18T08-39-51Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_DNA_aptamer DNA molecules that have been selected from random pools based on their ability to bind other molecules. cirad.fr urn:lsid:biomoby.org:objectclass:SO_DNA_aptamer:2009-08-18T08-45-18Z julien.wollbrett@cirad.fr SO_aptamer DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. cirad.fr urn:lsid:biomoby.org:objectclass:SO_aptamer:2009-08-18T08-44-23Z julien.wollbrett@cirad.fr SO_oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. cirad.fr urn:lsid:biomoby.org:objectclass:SO_oligo:2009-08-18T08-42-22Z julien.wollbrett@cirad.fr SO_reagent A sequence used in experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_reagent:2009-08-18T08-41-07Z julien.wollbrett@cirad.fr SO_biomaterial_region A region which is intended for use in an experiment. cirad.fr urn:lsid:biomoby.org:objectclass:SO_biomaterial_region:2009-08-18T08-40-17Z julien.wollbrett@cirad.fr SO_region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. cirad.fr urn:lsid:biomoby.org:objectclass:SO_region:2009-08-18T08-39-16Z julien.wollbrett@cirad.fr SO_sequence_feature An extent of biological sequence. cirad.fr urn:lsid:biomoby.org:objectclass:SO_sequence_feature:2009-08-18T08-39-09Z julien.wollbrett@cirad.fr SO_Terms Root term of the ontology cirad.fr urn:lsid:biomoby.org:objectclass:SO_Terms:2009-08-18T08-37-20Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com EO_other_nutrient_regimen Treatment involving the exposure of plant to elemental forms of nutrient as supplement to study various types of responses. These are not considered essential elements. cirad.fr urn:lsid:biomoby.org:objectclass:EO_other_nutrient_regimen:2009-04-30T14-08-01Z julien.wollbrett@cirad.fr EO_nutrient_regimen The treatment involving use of nutrients to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_nutrient_regimen:2009-04-30T14-07-43Z julien.wollbrett@cirad.fr EO_chemical_regimen The treatment involving use of chemical(s) to study various types of responses on their extrinsic and/or intrinsic application. cirad.fr urn:lsid:biomoby.org:objectclass:EO_chemical_regimen:2009-04-30T14-07-06Z julien.wollbrett@cirad.fr EO_abiotic_environment The treatment involving an exposure to the abiotic/non-biological factors such as chemicals, location, growth conditions etc. cirad.fr urn:lsid:biomoby.org:objectclass:EO_abiotic_environment:2009-04-30T14-07-02Z julien.wollbrett@cirad.fr EO_plant_environment_ontology A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. cirad.fr urn:lsid:biomoby.org:objectclass:EO_plant_environment_ontology:2009-04-30T14-07-01Z julien.wollbrett@cirad.fr EO_environment_ontology2gcp no description available cirad.fr urn:lsid:biomoby.org:objectclass:EO_environment_ontology2gcp:2009-04-30T14-07-00Z julien.wollbrett@cirad.fr Object a base object class consisting of a namespace and an identifier openinformatics.com urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z jason@openinformatics.com SO_invalidated_by_partial_processing An attribute to describe a feature that is invalidated due to partial processing. cirad.fr urn:lsid:biomoby.org:objectclass:SO_invalidated_b