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 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 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