AGI LocusCode
type: NamedIndividual
type: Database
example id: AGI_LocusCode:At2g17950
database: Arabidopsis Genome Initiative
description: Comprises TAIR, TIGR and MIPS
object: Locus identifier
url example: http://arabidopsis.org/servlets/TairObject
url syntax: http://arabidopsis.org/servlets/TairObject
generic url: http://www.arabidopsis.org

AGRICOLA ID
type: NamedIndividual
type: Database
object: AGRICOLA call number
example id: AGRICOLA_NAL:TP248.2 P76 v.14
database: AGRICultural OnLine Access
generic url: http://agricola.nal.usda.gov/

AGRICOLA IND
type: NamedIndividual
type: Database
object: AGRICOLA IND number
example id: AGRICOLA_IND:IND23252955
database: AGRICultural OnLine Access
generic url: http://agricola.nal.usda.gov/

ASAP
type: NamedIndividual
type: Database
database: A Systematic Annotation Package for Community Analysis of Genomes
example id: ASAP:ABE-0000008
object: Feature identifier
generic url: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
url example: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php
url syntax: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php

AgBase
type: NamedIndividual
type: Database
database: AgBase resource for functional analysis of agricultural plant and animal gene products
generic url: http://www.agbase.msstate.edu/
url syntax: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl

ApiDB PlasmoDB
type: NamedIndividual
type: Database
example id: ApiDB_PlasmoDB:PF11_0344
object: PlasmoDB Gene ID
database: PlasmoDB Plasmodium Genome Resource
generic url: http://plasmodb.org/
url example: http://www.plasmodb.org/gene/PF11_0344
url syntax: http://www.plasmodb.org/gene/[example_id]

AraCyc
type: NamedIndividual
type: Database
database: AraCyc metabolic pathway database for Arabidopsis thaliana
example id: AraCyc:PWYQT-62
object: Identifier
generic url: http://www.arabidopsis.org/biocyc/index.jsp
url example: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE
url syntax: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE

BHF-UCL
type: NamedIndividual
type: Database
database: Cardiovascular Gene Ontology Annotation Initiative; supported by the British Heart Foundation (BHF) at University College London (UCL)
generic url: http://www.cardiovasculargeneontology.com

BIOMD
type: NamedIndividual
type: Database
object: Accession
example id: BIOMD:BIOMD0000000045
synonym: BIOMDID
database: BioModels Database
generic url: http://www.ebi.ac.uk/biomodels/
url example: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do
url syntax: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do

BIOSIS
type: NamedIndividual
type: Database
database: BIOSIS previews
example id: BIOSIS:200200247281
object: Identifier
generic url: http://www.biosis.org/

BRENDA
type: NamedIndividual
type: Database
database: BRENDA, The Comprehensive Enzyme Information System
example id: BRENDA:4.2.1.3
object: EC enzyme identifier
generic url: http://www.brenda-enzymes.info
url example: http://www.brenda-enzymes.info/php/result_flat.php4
url syntax: http://www.brenda-enzymes.info/php/result_flat.php4

Broad
type: NamedIndividual
type: Database
database: Broad Institute
generic url: http://www.broad.mit.edu/

Broad MGG
type: NamedIndividual
type: Database
example id: Broad_MGG:MGG_05132.5
object: Locus
database: Magnaporthe grisea Database
description: Magnaporthe grisea Database at the Broad Institute
url example: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html
url syntax: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html
generic url: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html

CASGEN
type: NamedIndividual
type: Database
example id: CASGEN:1040
synonym: CAS_GEN
database: Catalog of Fishes genus database
object: Identifier
generic url: http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
url example: http://research.calacademy.org/research/ichthyology/catalog/getname.asp
url syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp

CASREF
type: NamedIndividual
type: Database
example id: CASREF:2031
database: Catalog of Fishes publications database
object: Identifier
generic url: http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
url example: http://research.calacademy.org/research/ichthyology/catalog/getref.asp
url syntax: http://research.calacademy.org/research/ichthyology/catalog/getref.asp

CASSPC
type: NamedIndividual
type: Database
synonym: CAS_SPC
database: Catalog of Fishes species database
object: Identifier
generic url: http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
url example: http://research.calacademy.org/research/ichthyology/catalog/getname.asp
url syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp

CBS
type: NamedIndividual
type: Database
example id: CBS:TMHMM
database: Center for Biological Sequence Analysis
generic url: http://www.cbs.dtu.dk/
url example: http://www.cbs.dtu.dk/services/[example_id]/
object: prediction tool

CDD
type: NamedIndividual
type: Database
example id: CDD:34222
database: Conserved Domain Database at NCBI
object: Identifier
url example: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
url syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi
generic url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

CGD
type: NamedIndividual
type: Database
example id: CGD:CAL0005516
synonym: CGDID
database: Candida Genome Database
object: Identifier for CGD Loci
generic url: http://www.candidagenome.org/
url example: http://www.candidagenome.org/cgi-bin/locus.pl
url syntax: http://www.candidagenome.org/cgi-bin/locus.pl

CGD LOCUS
type: NamedIndividual
type: Database
example id: CGD_LOCUS:HWP1
database: Candida Genome Database
object: Gene name (gene symbol in mammalian nomenclature)
generic url: http://www.candidagenome.org/
url example: http://www.candidagenome.org/cgi-bin/locus.pl
url syntax: http://www.candidagenome.org/cgi-bin/locus.pl

CGD REF
type: NamedIndividual
type: Database
example id: CGD_REF:1490
database: Candida Genome Database
object: Literature Reference Identifier
generic url: http://www.candidagenome.org/
url example: http://www.candidagenome.org/cgi-bin/reference/reference.pl
url syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl

CGEN
type: NamedIndividual
type: Database
example id: CGEN:PrID131022
database: Compugen Gene Ontology Gene Association Data
object: Identifier
generic url: http://www.cgen.com/

CGSC
type: NamedIndividual
type: Database
database: CGSC: E.coli Genetic Stock Center
example id: CGSC:rbsK
object: Gene symbol
generic url: http://cgsc.biology.yale.edu/
url example: http://cgsc.biology.yale.edu/Site.php

CL
type: NamedIndividual
type: Database
example id: CL:0000041
database: Cell Type Ontology
object: Identifier
generic url: https://lists.sourceforge.net/lists/listinfo/obo-cell-type

COG
type: NamedIndividual
type: Database
database: NCBI Clusters of Orthologous Groups
generic url: http://www.ncbi.nlm.nih.gov/COG/

COG Cluster
type: NamedIndividual
type: Database
example id: COG_Cluster:COG0001
object: Identifier
database: NCBI COG cluster
generic url: http://www.ncbi.nlm.nih.gov/COG/
url example: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi
url syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi

COG Function
type: NamedIndividual
type: Database
example id: COG_Function:H
object: Identifier
database: NCBI COG function
generic url: http://www.ncbi.nlm.nih.gov/COG/
url example: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi
url syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi

COG Pathway
type: NamedIndividual
type: Database
example id: COG_Pathway:14
object: Identifier
database: NCBI COG pathway
generic url: http://www.ncbi.nlm.nih.gov/COG/
url example: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi
url syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi

CORUM
type: NamedIndividual
type: Database
database: CORUM - the Comprehensive Resource of Mammalian protein complexes
example id: CORUM:837
object: Identifier
generic url: http://mips.gsf.de/genre/proj/corum/
url example: http://mips.gsf.de/genre/proj/corum/complexdetails.html
url syntax: http://mips.gsf.de/genre/proj/corum/complexdetails.html

ChEBI
type: NamedIndividual
type: Database
example id: ChEBI:17234
database: Chemical Entities of Biological Interest
object: Identifier
generic url: http://www.ebi.ac.uk/chebi/
url example: http://www.ebi.ac.uk/chebi/searchId.do
url syntax: http://www.ebi.ac.uk/chebi/searchId.do

DDBJ
type: NamedIndividual
type: Database
example id: DDBJ:AA816246
database: DNA Databank of Japan
object: Sequence accession number
url example: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch
url syntax: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch
generic url: http://www.ddbj.nig.ac.jp/

DOI
type: NamedIndividual
type: Database
example id: DOI:10.1016/S0963-9969(99)00021-6
database: Digital Object Identifier
object: Identifier
generic url: http://dx.doi.org/
url example: http://dx.doi.org/DOI:10.1016/S0963-9969(99)00021-6
url syntax: http://dx.doi.org/[example_id]

EC
type: NamedIndividual
type: Database
example id: EC:1.4.3.6
database: Enzyme Commission
generic url: http://ww.expasy.org/enzyme/
generic url: http://www.chem.qmul.ac.uk/iubmb/enzyme/
url example: http://www.expasy.org/enzyme/1.4.3.6
url syntax: http://www.expasy.org/enzyme/[example_id]

ECK
type: NamedIndividual
type: Database
object: ECK accession number (E. coli K-12 gene identifier)
example id: ECK:ECK3746
database: EcoGene Database of Escherichia coli Sequence and Function
generic url: http://www.ecogene.org/
url example: http://www.ecogene.org/geneInfo.php
url syntax: http://www.ecogene.org/geneInfo.php

ECOGENE
type: NamedIndividual
type: Database
example id: ECOGENE:EG10818
object: EcoGene Accession Number
database: EcoGene Database of Escherichia coli Sequence and Function
generic url: http://www.ecogene.org/
url example: http://www.ecogene.org/geneInfo.php
url syntax: http://www.ecogene.org/geneInfo.php

ECOGENE G
type: NamedIndividual
type: Database
example id: ECOGENE_G:deoC
database: EcoGene Database of Escherichia coli Sequence and Function
object: EcoGene Primary Gene Name
generic url: http://www.ecogene.org/

EMBL
type: NamedIndividual
type: Database
database: EMBL Nucleotide Sequence Database
example id: EMBL:AA816246
description: International nucleotide sequence database collaboration, comprising EMBL-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
object: Sequence accession number
url example: http://www.ebi.ac.uk/cgi-bin/emblfetch
url syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch
generic url: http://www.ebi.ac.uk/embl/

ENSEMBL
type: NamedIndividual
type: Database
example id: ENSEMBL:ENSP00000265949
database: Ensembl database of automatically annotated genomic data
object: Identifier
generic url: http://www.ensembl.org/
url example: http://www.ensembl.org/perl/protview
url syntax: http://www.ensembl.org/perl/protview

ENZYME
type: NamedIndividual
type: Database
example id: ENZYME:EC 1.1.1.1
object: Identifier
database: Swiss Institute of Bioinformatics enzyme database
generic url: http://www.expasy.ch/
url example: http://www.expasy.ch/cgi-bin/nicezyme.pl
url syntax: http://www.expasy.ch/cgi-bin/nicezyme.pl

EchoBASE
type: NamedIndividual
type: Database
database: EchoBASE post-genomic database for Escherichia coli
example id: EchoBASE:EB0231
object: Identifier
url example: http://www.biolws1.york.ac.uk/echobase/Gene.cfm
url syntax: http://www.biolws1.york.ac.uk/echobase/Gene.cfm
generic url: http://www.ecoli-york.org/

EcoCyc
type: NamedIndividual
type: Database
example id: EcoCyc:P2-PWY
database: Encyclopedia of E. coli metabolism
object: Pathway identifier
url example: http://biocyc.org/ECOLI/NEW-IMAGE
url syntax: http://biocyc.org/ECOLI/NEW-IMAGE
generic url: http://ecocyc.org/

EcoCyc REF
type: NamedIndividual
type: Database
synonym: ECOCYC_REF
example id: EcoCyc_REF:COLISALII
database: Encyclopedia of E. coli metabolism
object: Reference identifier
url example: http://biocyc.org/ECOLI/reference.html
url syntax: http://biocyc.org/ECOLI/reference.html
generic url: http://ecocyc.org/

EcoliWiki
type: NamedIndividual
type: Database
description: EcoliHub's subsystem for community annotation of E. coli K-12
database: EcoliWiki from EcoliHub
generic url: http://ecoliwiki.net/

FB
type: NamedIndividual
type: Database
example id: FB:FBgn0000024
database: FlyBase
synonym: FlyBase
object: Gene identifier
generic url: http://flybase.org/
url example: http://flybase.org/reports/FBgn0000024.html
url syntax: http://flybase.org/reports/[example_id].html

GDB
type: NamedIndividual
type: Database
object: Accession number
example id: GDB:306600
database: Human Genome Database
generic url: http://www.gdb.org/
url example: http://www.gdb.org/gdb-bin/genera/accno
url syntax: http://www.gdb.org/gdb-bin/genera/accno

GO
type: NamedIndividual
type: Database
example id: GO:0004352
database: Gene Ontology Database
object: Identifier
local id format: ^\d{7}$
generic url: http://amigo.geneontology.org/
url example: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi
url syntax: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi

GOA
type: NamedIndividual
type: Database
database: GO Annotation at EBI
generic url: http://www.ebi.ac.uk/goa/

GOC
type: NamedIndividual
type: Database
database: Gene Ontology Consortium
generic url: http://www.geneontology.org/

GO REF
type: NamedIndividual
type: Database
object: Accession (for reference)
example id: GO_REF:0000001
database: Gene Ontology Database references
local id format: ^\d{7}$
generic url: http://www.geneontology.org/
url example: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000001
url syntax: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:[example_id]

GR
type: NamedIndividual
type: Database
example id: GR:sd1
database: Gramene: A Comparative Mapping Resource for Grains
object: Identifier (any)
generic url: http://www.gramene.org/
url syntax: http://www.gramene.org/db/searches/browser
url example: http://www.gramene.org/db/searches/browser

GR GENE
type: NamedIndividual
type: Database
example id: GR_GENE:GR:0060198
synonym: GR_gene
object: Gene identifier
database: Gramene: A Comparative Mapping Resource for Grains
generic url: http://www.gramene.org/
url example: http://www.gramene.org/db/genes/search_gene
url syntax: http://www.gramene.org/db/genes/search_gene

GR PROTEIN
type: NamedIndividual
type: Database
example id: GR_PROTEIN:Q6VSV0
synonym: GR_protein
database: Gramene: A Comparative Mapping Resource for Grains
object: Protein identifier
generic url: http://www.gramene.org/
url example: http://www.gramene.org/db/protein/protein_search
url syntax: http://www.gramene.org/db/protein/protein_search

GR QTL
type: NamedIndividual
type: Database
example id: GR_QTL:CQU7
database: Gramene: A Comparative Mapping Resource for Grains
object: QTL identifier
generic url: http://www.gramene.org/
url example: http://www.gramene.org/db/qtl/qtl_display
url syntax: http://www.gramene.org/db/qtl/qtl_display

GR REF
type: NamedIndividual
type: Database
example id: GR_REF:659
database: Gramene: A Comparative Mapping Resource for Grains
object: Reference
generic url: http://www.gramene.org/
url example: http://www.gramene.org/db/literature/pub_search
url syntax: http://www.gramene.org/db/literature/pub_search

GenBank
type: NamedIndividual
type: Database
synonym: GB
example id: GB:AA816246
database: GenBank
object: Sequence accession number
description: The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
generic url: http://www.ncbi.nlm.nih.gov/Genbank/
url example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi

GenProtEC
type: NamedIndividual
type: Database
database: GenProtEC E. coli genome and proteome database
generic url: http://genprotec.mbl.edu/

Gene3D
type: NamedIndividual
type: Database
database: Domain Architecture Classification
generic url: http://gene3d.biochem.ucl.ac.uk/Gene3D/

GeneDB Gmorsitans
type: NamedIndividual
type: Database
object: Gene identifier
example id: GeneDB_Gmorsitans:Gmm-0142
database: Glossina morsitans GeneDB
shorthand name: Tsetse
url example: http://www.genedb.org/genedb/Search
url syntax: http://www.genedb.org/genedb/Search
generic url: http://www.genedb.org/genedb/glossina/

GeneDB Lmajor
type: NamedIndividual
type: Database
object: Gene identifier
example id: GeneDB_Lmajor:LM5.32
database: Leishmania major GeneDB
shorthand name: Lmajor
url example: http://www.genedb.org/genedb/Search
url syntax: http://www.genedb.org/genedb/Search
generic url: http://www.genedb.org/genedb/leish/

GeneDB Pfalciparum
type: NamedIndividual
type: Database
object: Gene identifier
example id: GeneDB_Pfalciparum:PFD0755c
shorthand name: Pfalciparum
database: Plasmodium falciparum GeneDB
url example: http://www.genedb.org/genedb/Search
url syntax: http://www.genedb.org/genedb/Search
generic url: http://www.genedb.org/genedb/malaria/

GeneDB Spombe
type: NamedIndividual
type: Database
object: Gene identifier
example id: GeneDB_Spombe:SPAC890.04C
database: Schizosaccharomyces pombe GeneDB
shorthand name: Spombe
url example: http://www.genedb.org/genedb/Search
url syntax: http://www.genedb.org/genedb/Search
generic url: http://www.genedb.org/genedb/pombe/

GeneDB Tbrucei
type: NamedIndividual
type: Database
object: Gene identifier
example id: GeneDB_Tbrucei:Tb927.1.5250
shorthand name: Tbrucei
database: Trypanosoma brucei GeneDB
url example: http://www.genedb.org/genedb/Search
url syntax: http://www.genedb.org/genedb/Search
generic url: http://www.genedb.org/genedb/tryp/

GermOnline
type: NamedIndividual
type: Database
database: GermOnline
generic url: http://www.germonline.org/

H-invDB
type: NamedIndividual
type: Database
database: H-invitational Database
generic url: http://www.h-invitational.jp/

H-invDB cDNA
type: NamedIndividual
type: Database
object: Accession
example id: H-invDB_cDNA:AK093148
database: H-invitational Database
generic url: http://www.h-invitational.jp/
url example: http://www.h-invitational.jp/hinv/spsoup/transcript_view
url syntax: http://www.h-invitational.jp/hinv/spsoup/transcript_view

H-invDB locus
type: NamedIndividual
type: Database
object: Cluster identifier
example id: H-invDB_locus:HIX0014446
database: H-invitational Database
generic url: http://www.h-invitational.jp/
url example: http://www.h-invitational.jp/hinv/spsoup/locus_view
url syntax: http://www.h-invitational.jp/hinv/spsoup/locus_view

HAMAP
type: NamedIndividual
type: Database
example id: HAMAP:MF_00031
database: High-quality Automated and Manual Annotation of microbial Proteomes
object: Identifier
generic url: http://us.expasy.org/sprot/hamap/
url example: http://us.expasy.org/unirules/MF_00031
url syntax: http://us.expasy.org/unirules/[example_id]

HGNC
type: NamedIndividual
type: Database
example id: HGNC:29
database: HUGO Gene Nomenclature Committee
object: Identifier
generic url: http://www.genenames.org/
url example: http://www.genenames.org/data/hgnc_data.php
url syntax: http://www.genenames.org/data/hgnc_data.php

HGNC gene
type: NamedIndividual
type: Database
object: Gene symbol
example id: HGNC_gene:ABCA1
database: HUGO Gene Nomenclature Committee
generic url: http://www.genenames.org/
url example: http://www.genenames.org/data/hgnc_data.php
url syntax: http://www.genenames.org/data/hgnc_data.php

HPA
type: NamedIndividual
type: Database
example id: HPA:HPA000237
database: Human Protein Atlas tissue profile information
object: Identifier
generic url: http://www.proteinatlas.org/
url example: http://www.proteinatlas.org/tissue_profile.php
url syntax: http://www.proteinatlas.org/tissue_profile.php

HPA antibody
type: NamedIndividual
type: Database
example id: HPA_antibody:HPA000237
database: Human Protein Atlas antibody information
object: Identifier
generic url: http://www.proteinatlas.org/
url example: http://www.proteinatlas.org/antibody_info.php
url syntax: http://www.proteinatlas.org/antibody_info.php

HUGO
type: NamedIndividual
type: Database
database: Human Genome Organisation
generic url: http://www.hugo-international.org/

IMG
type: NamedIndividual
type: Database
example id: IMG:640008772
object: Identifier
database: Integrated Microbial Genomes; JGI web site for genome annotation
generic url: http://img.jgi.doe.gov
url example: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi
url syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

IMGT HLA
type: NamedIndividual
type: Database
database: IMGT/HLA human major histocompatibility complex sequence database
example id: IMGT_HLA:HLA00031
generic url: http://www.ebi.ac.uk/imgt/hla

IMGT LIGM
type: NamedIndividual
type: Database
description: Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.
example id: IMGT_LIGM:U03895
database: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
generic url: http://imgt.cines.fr

IPI
type: NamedIndividual
type: Database
example id: IPI:IPI00000005.1
object: Identifier
database: International Protein Index
generic url: http://www.ebi.ac.uk/IPI/IPIhelp.html

ISBN
type: NamedIndividual
type: Database
example id: ISBN:0781702534
object: Identifier
database: International Standard Book Number
generic url: http://isbntools.com/
url example: http://my.linkbaton.com/get
url syntax: http://my.linkbaton.com/get

ISSN
type: NamedIndividual
type: Database
example id: ISSN:1234-1231
object: Identifier
database: International Standard Serial Number
generic url: http://www.issn.org/

IUPHAR
type: NamedIndividual
type: Database
database: International Union of Pharmacology
generic url: http://www.iuphar.org/

IUPHAR GPCR
type: NamedIndividual
type: Database
object: G-protein-coupled receptor family identifier
example id: IUPHAR_GPCR:1279
database: International Union of Pharmacology
url example: http://www.iuphar-db.org/GPCR/ChapterMenuForward
url syntax: http://www.iuphar-db.org/GPCR/ChapterMenuForward
generic url: http://www.iuphar.org/

IUPHAR RECEPTOR
type: NamedIndividual
type: Database
example id: IUPHAR_RECEPTOR:2205
database: International Union of Pharmacology
object: Receptor identifier
url example: http://www.iuphar-db.org/GPCR/ReceptorDisplayForward
url syntax: http://www.iuphar-db.org/GPCR/ReceptorDisplayForward
generic url: http://www.iuphar.org/

IntAct
type: NamedIndividual
type: Database
object: Accession
database: IntAct protein interaction database
example id: IntAct:EBI-17086
generic url: http://www.ebi.ac.uk/intact/
url example: http://www.ebi.ac.uk/intact/search/do/search
url syntax: http://www.ebi.ac.uk/intact/search/do/search

InterPro
type: NamedIndividual
type: Database
synonym: INTERPRO
synonym: IPR
object: Identifier
database: InterPro database of protein domains and motifs
example id: InterPro:IPR000001
local id format: ^IPR\d{6}$
generic url: http://www.ebi.ac.uk/interpro/
url example: http://www.ebi.ac.uk/interpro/DisplayIproEntry
url syntax: http://www.ebi.ac.uk/interpro/DisplayIproEntry

JCVI
type: NamedIndividual
type: Database
database: J. Craig Venter Institute
synonym: TIGR
generic url: http://www.jcvi.org/

JCVI Ath1
type: NamedIndividual
type: Database
object: Accession
database: Arabidopsis thaliana database at the J. Craig Venter Institute
example id: JCVI_Ath1:At3g01440
synonym: TIGR_Ath1
generic url: http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml
url example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi
url syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi

JCVI CMR
type: NamedIndividual
type: Database
database: Comprehensive Microbial Resource at the J. Craig Venter Institute
example id: JCVI_CMR:VCA0557
object: Locus
synonym: TIGR_CMR
generic url: http://cmr.jcvi.org/
url example: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi
url syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi

JCVI EGAD
type: NamedIndividual
type: Database
object: Accession
database: EGAD database at the J. Craig Venter Institute
example id: JCVI_EGAD:74462
synonym: TIGR_EGAD
generic url: http://cmr.jcvi.org/
url example: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi
url syntax: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi

JCVI GenProp
type: NamedIndividual
type: Database
object: Accession
database: Genome Properties database at the J. Craig Venter Institute
example id: JCVI_GenProp:GenProp0120
synonym: TIGR_GenProp
generic url: http://cmr.jcvi.org/
url example: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi
url syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi

JCVI Pfa1
type: NamedIndividual
type: Database
object: Accession
example id: JCVI_Pfa1:PFB0010w
database: Plasmodium falciparum database at the J. Craig Venter Institute
synonym: TIGR_Pfa1
generic url: http://www.tigr.org/tdb/e2k1/pfa1/pfa1.shtml
url example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi
url syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi

JCVI REF
type: NamedIndividual
type: Database
database: J. Craig Venter Institute
example id: JCVI_REF:GO_ref
object: Reference locator
synonym: TIGR_REF
generic url: http://cmr.jcvi.org/
url example: http://cmr.jcvi.org/CMR/AnnotationSops.shtml

JCVI TIGRFAMS
type: NamedIndividual
type: Database
object: Accession
example id: JCVI_TIGRFAMS:TIGR00254
database: TIGRFAMs HMM collection at the J. Craig Venter Institute
synonym: TIGR_TIGRFAMS
generic url: http://cmr.jcvi.org/
url example: http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi
url syntax: http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi

JCVI Tba1
type: NamedIndividual
type: Database
object: Accession
example id: JCVI_Tba1:25N14.10
synonym: TIGR_Tba1
database: Trypanosoma brucei database at the J. Craig Venter Institute
generic url: http://www.tigr.org/tdb/e2k1/tba1/
url example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi
url syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi

KEGG
type: NamedIndividual
type: Database
database: Kyoto Encyclopedia of Genes and Genomes
generic url: http://www.genome.ad.jp/kegg/

KEGG LIGAND
type: NamedIndividual
type: Database
object: Compound
database: KEGG LIGAND Database
example id: KEGG_LIGAND:C00577
url example: http://www.genome.ad.jp/dbget-bin/www_bget
url syntax: http://www.genome.ad.jp/dbget-bin/www_bget
generic url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html

KEGG PATHWAY
type: NamedIndividual
type: Database
database: KEGG Pathways Database
example id: KEGG_PATHWAY:ot00020
object: Pathway
url syntax: http://www.genome.ad.jp/dbget-bin/www_bget
url example: http://www.genome.ad.jp/dbget-bin/www_bget
generic url: http://www.genome.ad.jp/kegg/docs/upd_pathway.html

LIFEdb
type: NamedIndividual
type: Database
description: Database for Localization, Interaction, Functional assays and Expression of Proteins
example id: LIFEdb:DKFZp564O1716
object: cDNA clone identifier
url example: http://www.dkfz.de/LIFEdb/LIFEdb.aspx
url syntax: http://www.dkfz.de/LIFEdb/LIFEdb.aspx
generic url: http://www.lifedb.de/
database: lifedb

LOCSVMpsi
type: NamedIndividual
type: Database
database: LOCSVMPSI: subcellular localization for eukayotic proteins based on SVM and PSI-BLAST
generic url: http://bioinformatics.ustc.edu.cn/locsvmpsi/locsvmpsi.php

MA
type: NamedIndividual
type: Database
database: Adult Mouse Anatomical Dictionary
description: Adult Mouse Anatomical Dictionary; part of Gene Expression Database
object: Identifier
example id: MA:0000003
generic url: http://www.informatics.jax.org/
url example: http://www.informatics.jax.org/searches/AMA.cgi
url syntax: http://www.informatics.jax.org/searches/AMA.cgi

MEDLINE
type: NamedIndividual
type: Database
object: Identifier
example id: MEDLINE:20572430
database: Medline literature database

MEROPS
type: NamedIndividual
type: Database
object: Identifier
database: MEROPS peptidase database
example id: MEROPS:A08.001
generic url: http://merops.sanger.ac.uk/
url example: http://merops.sanger.ac.uk/cgi-bin/pepsum
url syntax: http://merops.sanger.ac.uk/cgi-bin/pepsum

MEROPS fam
type: NamedIndividual
type: Database
database: MEROPS peptidase database
example id: MEROPS_fam:M18
object: Peptidase family identifier
generic url: http://merops.sanger.ac.uk/
url syntax: http://merops.sanger.ac.uk/cgi-bin/famsum
url example: http://merops.sanger.ac.uk/cgi-bin/famsum

MGD
type: NamedIndividual
type: Database
object: Gene symbol
example id: MGD:Adcy9
database: Mouse Genome Database
generic url: http://www.informatics.jax.org/

MGI
type: NamedIndividual
type: Database
object: Accession number
example id: MGI:80863
database: Mouse Genome Informatics
generic url: http://www.informatics.jax.org/
url example: http://www.informatics.jax.org/searches/accession_report.cgi
url syntax: http://www.informatics.jax.org/searches/accession_report.cgi

MIPS funcat
type: NamedIndividual
type: Database
object: Identifier
database: MIPS Functional Catalogue
example id: MIPS_funcat:11.02
url example: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl
url syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl
generic url: http://mips.gsf.de/proj/funcatDB/

MO
type: NamedIndividual
type: Database
database: MGED Ontology
example id: MO:Action
generic url: http://mged.sourceforge.net/ontologies/MGEDontology.php
url example: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action
url syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#[example_id]
object: ontology term

MaizeGDB
type: NamedIndividual
type: Database
database: MaizeGDB
object: MaizeGDB Object ID Number
example id: MaizeGDB:881225
generic url: http://www.maizegdb.org
url example: http://www.maizegdb.org/cgi-bin/id_search.cgi
url syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi

MaizeGDB Locus
type: NamedIndividual
type: Database
object: Maize gene name
database: MaizeGDB
example id: MaizeGDB_Locus:ZmPK1
generic url: http://www.maizegdb.org
url example: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi
url syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi

MeSH
type: NamedIndividual
type: Database
object: MeSH heading
example id: MeSH:mitosis
database: Medical Subject Headings
url syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi
url example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi
generic url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html

MetaCyc
type: NamedIndividual
type: Database
object: Identifier (pathway or reaction)
example id: MetaCyc:GLUTDEG-PWY
database: Metabolic Encyclopedia of metabolic and other pathways
url example: http://biocyc.org/META/NEW-IMAGE
url syntax: http://biocyc.org/META/NEW-IMAGE
generic url: http://metacyc.org/

MultiFun
type: NamedIndividual
type: Database
database: MultiFun cell function assignment schema
generic url: http://genprotec.mbl.edu/files/MultiFun.html

NASC code
type: NamedIndividual
type: Database
object: NASC code Identifier
example id: NASC_code:N3371
database: Nottingham Arabidopsis Stock Centre Seeds Database
generic url: http://arabidopsis.info
url example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso
url syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso

NC-IUBMB
type: NamedIndividual
type: Database
database: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
generic url: http://www.chem.qmw.ac.uk/iubmb/

NCBI
type: NamedIndividual
type: Database
database: National Center for Biotechnology Information
object: Prefix
generic url: http://www.ncbi.nlm.nih.gov/

NCBI GP
type: NamedIndividual
type: Database
database: NCBI GenPept
example id: NCBI_GP:EAL72968
object: Protein identifier
generic url: http://www.ncbi.nlm.nih.gov/
url example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi

NCBI Gene
type: NamedIndividual
type: Database
object: Identifier
synonym: LocusID
database: NCBI Gene
example id: NCBI_Gene:4771
local id syntax: ^\d+$
generic url: http://www.ncbi.nlm.nih.gov/
url example: http://www.ncbi.nlm.nih.gov/sites/entrez
url syntax: http://www.ncbi.nlm.nih.gov/sites/entrez

NCBI NM
type: NamedIndividual
type: Database
database: NCBI RefSeq
example id: NCBI_NM:123456
synonym: RefSeq
replaced by: RefSeq
generic url: http://www.ncbi.nlm.nih.gov/
object: mRNA identifier
is obsolete: true

NCBI NP
type: NamedIndividual
type: Database
database: NCBI RefSeq
example id: NCBI_NP:123456
object: Protein identifier
synonym: RefSeq
replaced by: RefSeq
generic url: http://www.ncbi.nlm.nih.gov/
is obsolete: true

NCBI gi
type: NamedIndividual
type: Database
object: Identifier
database: NCBI databases
example id: NCBI_gi:113194944
local id syntax: ^\d+$
generic url: http://www.ncbi.nlm.nih.gov/
url example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi

NMPDR
type: NamedIndividual
type: Database
object: Identifier
example id: NMPDR:fig|306254.1.peg.183
database: National Microbial Pathogen Data Resource
generic url: http://www.nmpdr.org
url syntax: http://www.nmpdr.org/linkin.cgi
url example: http://www.nmpdr.org/linkin.cgi

OMIM
type: NamedIndividual
type: Database
object: Identifier
synonym: MIM
database: Mendelian Inheritance in Man
example id: OMIM:190198
url syntax: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi
generic url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
url example: http://www.ncbi.nlm.nih.gov/htbin-post/entrez/dispomim.cgi

PAMGO
type: NamedIndividual
type: Database
database: Plant-Associated Microbe Gene Ontology Interest Group
generic url: http://pamgo.vbi.vt.edu/

PAMGO GAT
type: NamedIndividual
type: Database
object: Gene
database: Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group
example id: PAMGO_GAT:Atu0001
generic url: http://agro.vbi.vt.edu/public/
url syntax: http://agro.vbi.vt.edu/public/servlet/GeneEdit
url example: http://agro.vbi.vt.edu/public/servlet/GeneEdit

PAMGO MGG
type: NamedIndividual
type: Database
object: Locus
database: Magnaporthe grisea database
description: Magnaporthe grisea database at North Carolina State University; member of PAMGO Interest Group
example id: PAMGO_MGG:MGG_05132
url example: http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi
url syntax: http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi
generic url: http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html

PAMGO VMD
type: NamedIndividual
type: Database
object: Gene identifier
example id: PAMGO_VMD:109198
database: Virginia Bioinformatics Institute Microbial Database
description: Virginia Bioinformatics Institute Microbial Database; member of PAMGO Interest Group
generic url: http://phytophthora.vbi.vt.edu
url example: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi
url syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi

PANTHER
type: NamedIndividual
type: Database
database: Protein ANalysis THrough Evolutionary Relationships Classification System
generic url: http://www.pantherdb.org/

PATO
type: NamedIndividual
type: Database
object: Identifier
example id: PATO:0001420
database: Phenotypic quality ontology
generic url: http://www.bioontology.org/wiki/index.php/PATO:Main_Page

PATRIC
type: NamedIndividual
type: Database
object: Feature identifieer
example id: PATRIC:cds.000002.436951
database: PathoSystems Resource Integration Center
description: PathoSystems Resource Integration Center at the Virginia Bioinformatics Institute
generic url: http://patric.vbi.vt.edu
url syntax: http://patric.vbi.vt.edu/gene/overview.php
url example: http://patric.vbi.vt.edu/gene/overview.php

PDB
type: NamedIndividual
type: Database
object: Identifier
example id: PDB:1A4U
database: Protein Data Bank
generic url: http://www.rcsb.org/pdb/
url example: http://www.rcsb.org/pdb/cgi/explore.cgi
url syntax: http://www.rcsb.org/pdb/cgi/explore.cgi

PINC
type: NamedIndividual
type: Database
database: Proteome Inc.
generic url: http://www.proteome.com/
description: represents GO annotations created in 2001 for NCBI and extracted into GOA from EntrezGene

PIR
type: NamedIndividual
type: Database
object: Accession number
example id: PIR:I49499
database: Protein Information Resource
generic url: http://pir.georgetown.edu/
url example: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget
url syntax: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget

PIRSF
type: NamedIndividual
type: Database
object: Identifier
database: PIR Superfamily Classification System
example id: PIRSF:SF002327
url example: http://pir.georgetown.edu/cgi-bin/ipcSF
url syntax: http://pir.georgetown.edu/cgi-bin/ipcSF
generic url: http://pir.georgetown.edu/pirsf/

PMCID
type: NamedIndividual
type: Database
object: Identifier
example id: PMCID:PMC201377
database: Pubmed Central
url example: http://www.ncbi.nlm.nih.gov/sites/entrez
url syntax: http://www.ncbi.nlm.nih.gov/sites/entrez
generic url: http://www.pubmedcentral.nih.gov/

PMID
type: NamedIndividual
type: Database
object: Identifier
example id: PMID:4208797
synonym: PUBMED
database: PubMed
synonym: PubMed
generic url: http://www.ncbi.nlm.nih.gov/PubMed/
url example: http://www.ncbi.nlm.nih.gov/pubmed/4208797
url syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]

PO
type: NamedIndividual
type: Database
object: Identifier
example id: PO:0009004
database: Plant Ontology Consortium Database
generic url: http://www.plantontology.org/
url example: http://www.plantontology.org/amigo/go.cgi
url syntax: http://www.plantontology.org/amigo/go.cgi

POC
type: NamedIndividual
type: Database
database: Plant Ontology Consortium

PPI
type: NamedIndividual
type: Database
database: Pseudomonas syringae community annotation project
generic url: http://genome.pseudomonas-syringae.org/

PRINTS
type: NamedIndividual
type: Database
object: Accession
database: PRINTS compendium of protein fingerprints
example id: PRINTS:PR00025
url example: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi
url syntax: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi
generic url: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/

PROW
type: NamedIndividual
type: Database
database: Protein Reviews on the Web
generic url: http://www.ncbi.nlm.nih.gov/prow/

PSI-MI
type: NamedIndividual
type: Database
object: Interaction identifier
synonym: MI
example id: MI:0018
database: Proteomic Standard Initiative for Molecular Interaction
generic url: http://psidev.sourceforge.net/mi/xml/doc/user/index.html

PSI-MOD
type: NamedIndividual
type: Database
synonym: MOD
example id: MOD:00219
object: Protein modification identifier
database: Proteomics Standards Initiative protein modification ontology
generic url: http://psidev.sourceforge.net/mod/
url example: http://www.ebi.ac.uk/ontology-lookup/
url syntax: http://www.ebi.ac.uk/ontology-lookup/

PSORT
type: NamedIndividual
type: Database
database: PSORT protein subcellular localization databases and prediction tools for bacteria
generic url: http://www.psort.org/

Pfam
type: NamedIndividual
type: Database
object: Accession number
database: Pfam database of protein families
description: Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs)
example id: Pfam:PF00046
generic url: http://www.sanger.ac.uk/Software/Pfam/
url example: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc
url syntax: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc

PfamB
type: NamedIndividual
type: Database
object: Accession number
database: Pfam-B supplement to Pfam
example id: PfamB:PB014624
generic url: http://www.sanger.ac.uk/Software/Pfam/

PharmGKB PA
type: NamedIndividual
type: Database
example id: PharmGKB_PA:PA267
database: Pharmacogenetics and Pharmacogenomics Knowledge Base
generic url: http://www.pharmgkb.org
url example: http://www.pharmgkb.org/do/serve
url syntax: http://www.pharmgkb.org/do/serve

PharmGKB PGKB
type: NamedIndividual
type: Database
example id: PharmGKB_PGKB:PA267
database: Pharmacogenetics and Pharmacogenomics Knowledge Base
generic url: http://www.pharmgkb.org
url example: http://www.pharmgkb.org/do/serve
url syntax: http://www.pharmgkb.org/do/serve

Pompep
type: NamedIndividual
type: Database
object: Gene/protein identifier
example id: Pompep:SPAC890.04C
database: Schizosaccharomyces pombe protein data
generic url: ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/

ProDom
type: NamedIndividual
type: Database
object: Accession
database: ProDom protein domain families
description: ProDom protein domain families automatically generated from Swiss-Prot and TrEMBL
example id: ProDom:PD000001
url example: http://prodes.toulouse.inra.fr/prodom/current/cgi-bin/request.pl
url syntax: http://prodes.toulouse.inra.fr/prodom/current/cgi-bin/request.pl
generic url: http://prodes.toulouse.inra.fr/prodom/current/html/home.php

Prosite
type: NamedIndividual
type: Database
object: Accession number
database: Prosite database of protein families and domains
example id: Prosite:PS00365
url example: http://www.expasy.ch/cgi-bin/prosite-search-ac
url syntax: http://www.expasy.ch/cgi-bin/prosite-search-ac
generic url: http://www.expasy.ch/prosite/

PseudoCAP
type: NamedIndividual
type: Database
object: Identifier
example id: PseudoCAP:PA4756
database: Pseudomonas Genome Project
generic url: http://v2.pseudomonas.com/
url example: http://v2.pseudomonas.com/getAnnotation.do
url syntax: http://v2.pseudomonas.com/getAnnotation.do

PubChem BioAssay
type: NamedIndividual
type: Database
object: Identifier
database: NCBI PubChem database of bioassay records
example id: PubChem_BioAssay:177
generic url: http://pubchem.ncbi.nlm.nih.gov/
url example: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi
url syntax: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi

PubChem Compound
type: NamedIndividual
type: Database
object: Identifier
database: NCBI PubChem database of chemical structures
example id: PubChem_Compound:2244
generic url: http://pubchem.ncbi.nlm.nih.gov/
url example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

PubChem Substance
type: NamedIndividual
type: Database
object: Identifier
database: NCBI PubChem database of chemical substances
example id: PubChem_Substance:4594
generic url: http://pubchem.ncbi.nlm.nih.gov/
url example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

REBASE
type: NamedIndividual
type: Database
database: REBASE restriction enzyme database
example id: REBASE:EcoRI
object: Restriction enzyme name
url example: http://rebase.neb.com/rebase/enz/EcoRI.html
url syntax: http://rebase.neb.com/rebase/enz/[example_id].html
generic url: http://rebase.neb.com/rebase/rebase.html

RESID
type: NamedIndividual
type: Database
object: Identifier
database: RESID Database of Protein Modifications
example id: RESID:AA0062
generic url: ftp://ftp.ncifcrf.gov/pub/users/residues/

RGD
type: NamedIndividual
type: Database
object: Accession Number
example id: RGD:2004
synonym: RGDID
database: Rat Genome Database
generic url: http://rgd.mcw.edu/
url example: http://rgd.mcw.edu/generalSearch/RgdSearch.jsp
url syntax: http://rgd.mcw.edu/generalSearch/RgdSearch.jsp

RNAmods
type: NamedIndividual
type: Database
object: Identifier
database: RNA Modification Database
example id: RNAmods:037
generic url: http://medlib.med.utah.edu/RNAmods/
url example: http://medlib.med.utah.edu/cgi-bin/rnashow.cgi
url syntax: http://medlib.med.utah.edu/cgi-bin/rnashow.cgi

Reactome
type: NamedIndividual
type: Database
object: Identifier
database: Reactome - a curated knowledgebase of biological pathways
example id: Reactome:REACT_1240.1
generic url: http://www.reactome.org/
url example: http://www.reactome.org/cgi-bin/eventbrowser_st_id
url syntax: http://www.reactome.org/cgi-bin/eventbrowser_st_id

RefSeq
type: NamedIndividual
type: Database
object: Identifier
database: RefSeq
example id: RefSeq:XP_001068954
local id syntax: ^[A-Z]{2}_([A_Z]{4})?\d+$
generic url: http://www.ncbi.nlm.nih.gov/RefSeq/
url example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi

RefSeq NA
type: NamedIndividual
type: Database
object: Identifier
replaced by: RefSeq
database: RefSeq (Nucleic Acid)
example id: RefSeq_NA:NC_000913
generic url: http://www.ncbi.nlm.nih.gov/RefSeq/
url example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
is obsolete: true

RefSeq Prot
type: NamedIndividual
type: Database
object: Identifier
replaced by: RefSeq
database: RefSeq (Protein)
example id: RefSeq_Prot:YP_498627
generic url: http://www.ncbi.nlm.nih.gov/RefSeq/
url example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
url syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi
is obsolete: true

Roslin Institute
type: NamedIndividual
type: Database
synonym: RI
database: Roslin Institute
generic url: http://www.roslin.ac.uk/

SEED
type: NamedIndividual
type: Database
description: Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices
example id: SEED:fig|83331.1.peg.1
database: The SEED;
generic url: http://www.theseed.org
url syntax: http://www.theseed.org/linkin.cgi
url example: http://www.theseed.org/linkin.cgi
object: identifier

SGD
type: NamedIndividual
type: Database
object: Identifier for SGD Loci
example id: SGD:S000006169
synonym: SGDID
database: Saccharomyces Genome Database
url example: http://db.yeastgenome.org/cgi-bin/locus.pl
url syntax: http://db.yeastgenome.org/cgi-bin/locus.pl
generic url: http://www.yeastgenome.org/

SGD LOCUS
type: NamedIndividual
type: Database
object: Gene name (gene symbol in mammalian nomenclature)
example id: SGD_LOCUS:GAL4
database: Saccharomyces Genome Database
url example: http://db.yeastgenome.org/cgi-bin/locus.pl
url syntax: http://db.yeastgenome.org/cgi-bin/locus.pl
generic url: http://www.yeastgenome.org/

SGD REF
type: NamedIndividual
type: Database
object: Literature Reference Identifier
example id: SGD_REF:S000049602
database: Saccharomyces Genome Database
url example: http://db.yeastgenome.org/cgi-bin/reference/reference.pl
url syntax: http://db.yeastgenome.org/cgi-bin/reference/reference.pl
generic url: http://www.yeastgenome.org/

SGN
type: NamedIndividual
type: Database
object: Gene identifier
example id: SGN:4476
database: Sol Genomics Network
generic url: http://www.sgn.cornell.edu/
url example: http://www.sgn.cornell.edu/phenome/locus_display.pl
url syntax: http://www.sgn.cornell.edu/phenome/locus_display.pl

SGN ref
type: NamedIndividual
type: Database
object: Reference identifier
example id: SGN_ref:861
database: Sol Genomics Network
generic url: http://www.sgn.cornell.edu/
url example: http://www.sgn.cornell.edu/chado/publication.pl
url syntax: http://www.sgn.cornell.edu/chado/publication.pl

SMART
type: NamedIndividual
type: Database
object: Accession
example id: SMART:SM00005
database: Simple Modular Architecture Research Tool
generic url: http://smart.embl-heidelberg.de/
url example: http://smart.embl-heidelberg.de/smart/do_annotation.pl
url syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl

SMD
type: NamedIndividual
type: Database
database: Stanford Microarray Database
generic url: http://genome-www.stanford.edu/microarray

SO
type: NamedIndividual
type: Database
object: Identifier
example id: SO:0000195
database: Sequence Ontology
generic url: http://sequenceontology.org/
url example: http://song.sourceforge.net/SOterm_tables.html#SO:0000195
url syntax: http://song.sourceforge.net/SOterm_tables.html#[example_id]

SP KW
type: NamedIndividual
type: Database
object: Identifier
example id: SP_KW:KW-0812
database: UniProt Knowledgebase keywords
generic url: http://www.uniprot.org/keywords/
url example: http://www.uniprot.org/keywords/KW-0812
url syntax: http://www.uniprot.org/keywords/[example_id]

SP SL
type: NamedIndividual
type: Database
object: Identifier
example id: SP_SL:SL-0012
database: UniProt Subcellular Location vocabulary
generic url: http://beta.uniprot.org/docs/subcell

SUBTILIST
type: NamedIndividual
type: Database
object: Accession number
database: Bacillus subtilis Genome Sequence Project
example id: SUBTILISTG:BG11384
generic url: http://genolist.pasteur.fr/SubtiList/

SUBTILISTG
type: NamedIndividual
type: Database
database: Bacillus subtilis Genome Sequence Project
object: Gene symbol
example id: SUBTILISTG:accC
generic url: http://genolist.pasteur.fr/SubtiList/

SUPERFAMILY
type: NamedIndividual
type: Database
description: A database of structural and functional protein annotations for completely sequenced genomes
database: SUPERFAMILY protein annotation database
generic url: http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

Sanger
type: NamedIndividual
type: Database
database: Wellcome Trust Sanger Institute
generic url: http://www.sanger.ac.uk/

Swiss-Prot
type: NamedIndividual
type: Database
description: A curated protein sequence database which provides a high level of annotation and a minimal level of redundancy
object: Accession number
example id: Swiss-Prot:P51587
database: UniProtKB/Swiss-Prot
url example: http://www.ebi.uniprot.org/entry/P51587
url syntax: http://www.ebi.uniprot.org/entry/[example_id]
generic url: http://www.uniprot.org

TAIR
type: NamedIndividual
type: Database
object: Accession number
example id: TAIR:gene:2062713
example id: TAIR:locus:2146653
database: The Arabidopsis Information Resource
url syntax: http://arabidopsis.org/servlets/TairObject
url example: http://arabidopsis.org/servlets/TairObject
generic url: http://www.arabidopsis.org/

TC
type: NamedIndividual
type: Database
object: Identifier
example id: TC:9.A.4.1.1
database: Transport Protein Database
generic url: http://www.tcdb.org/
url example: http://www.tcdb.org/tcdb/index.php
url syntax: http://www.tcdb.org/tcdb/index.php

TGD
type: NamedIndividual
type: Database
database: Tetrahymena Genome Database
generic url: http://www.ciliate.org/

TGD LOCUS
type: NamedIndividual
type: Database
object: Gene name (gene symbol in mammalian nomenclature)
example id: TGD_LOCUS:PDD1
database: Tetrahymena Genome Database
url example: http://db.ciliate.org/cgi-bin/locus.pl
url syntax: http://db.ciliate.org/cgi-bin/locus.pl
generic url: http://www.ciliate.org/

TGD REF
type: NamedIndividual
type: Database
object: Literature Reference Identifier
example id: TGD_REF:T000005818
database: Tetrahymena Genome Database
url example: http://db.ciliate.org/cgi-bin/reference/reference.pl
url syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl
generic url: http://www.ciliate.org/

TRAIT
type: NamedIndividual
type: Database
synonym: Muscle TRAIT
database: TRAnscript Integrated Table
description: an integrated database of transcripts expressed in human skeletal muscle
generic url: http://muscle.cribi.unipd.it/

TRANSFAC
type: NamedIndividual
type: Database
database: TRANSFAC database of eukaryotic transcription factors
generic url: http://www.gene-regulation.com/pub/databases.html#transfac

TrEMBL
type: NamedIndividual
type: Database
object: Accession number
example id: TrEMBL:O31124
database: UniProtKB-TrEMBL protein sequence database
description: UniProtKB-TrEMBL, a computer-annotated protein sequence database supplementing UniProtKB and containing the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database but not yet integrated in UniProtKB/Swiss-Prot
url example: http://www.ebi.uniprot.org/entry/O31124
url syntax: http://www.ebi.uniprot.org/entry/[example_id]
generic url: http://www.uniprot.org

UM-BBD
type: NamedIndividual
type: Database
object: Prefix
database: University of Minnesota Biocatalysis/Biodegradation Database
generic url: http://umbbd.msi.umn.edu/

UM-BBD enzymeID
type: NamedIndividual
type: Database
object: Enzyme identifier
example id: UM-BBD_enzymeID:e0413
database: University of Minnesota Biocatalysis/Biodegradation Database
generic url: http://umbbd.msi.umn.edu/
url syntax: http://umbbd.msi.umn.edu/servlets/pageservlet
url example: http://umbbd.msi.umn.edu/servlets/pageservlet

UM-BBD pathwayID
type: NamedIndividual
type: Database
object: Pathway identifier
example id: UM-BBD_pathwayID:acr
database: University of Minnesota Biocatalysis/Biodegradation Database
generic url: http://umbbd.msi.umn.edu/
url example: http://umbbd.msi.umn.edu/acr/acr_map.html

UM-BBD reactionID
type: NamedIndividual
type: Database
object: Reaction identifier
example id: UM-BBD_reactionID:r0129
database: University of Minnesota Biocatalysis/Biodegradation Database
generic url: http://umbbd.msi.umn.edu/
url syntax: http://umbbd.msi.umn.edu/servlets/pageservlet
url example: http://umbbd.msi.umn.edu/servlets/pageservlet

UM-BBD ruleID
type: NamedIndividual
type: Database
object: Rule identifier
example id: UM-BBD_ruleID:bt0330
database: University of Minnesota Biocatalysis/Biodegradation Database
generic url: http://umbbd.msi.umn.edu/
url syntax: http://umbbd.msi.umn.edu/servlets/rule.jsp
url example: http://umbbd.msi.umn.edu/servlets/rule.jsp

UniParc
type: NamedIndividual
type: Database
description: A non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office
object: Accession number
example id: UniParc:UPI000000000A
database: UniProt Archive
url example: http://www.ebi.ac.uk/cgi-bin/dbfetch
url syntax: http://www.ebi.ac.uk/cgi-bin/dbfetch
generic url: http://www.ebi.ac.uk/uniparc/

UniProtKB
type: NamedIndividual
type: Database
description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR
object: Accession number
synonym: UniProt
example id: UniProtKB:P51587
database: Universal Protein Knowledgebase
url example: http://www.ebi.uniprot.org/entry/P51587
url syntax: http://www.ebi.uniprot.org/entry/[example_id]
generic url: http://www.uniprot.org

VBRC
type: NamedIndividual
type: Database
object: Identifier
example id: VBRC:F35742
database: Viral Bioinformatics Resource Center
generic url: http://vbrc.org
url example: http://vbrc.org/query.asp
url syntax: http://vbrc.org/query.asp

VEGA
type: NamedIndividual
type: Database
object: Identifier
example id: VEGA:OTTHUMP00000000661
database: Vertebrate Genome Annotation database
generic url: http://vega.sanger.ac.uk/index.html
url example: http://vega.sanger.ac.uk/perl/searchview
url syntax: http://vega.sanger.ac.uk/perl/searchview

VIDA
type: NamedIndividual
type: Database
database: Virus Database at University College London
generic url: http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html

VMD
type: NamedIndividual
type: Database
object: Gene identifier
example id: VMD:109198
database: Virginia Bioinformatics Institute Microbial Database
generic url: http://phytophthora.vbi.vt.edu
url example: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi
url syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi

WB
type: NamedIndividual
type: Database
object: Gene identifier
example id: WB:WBGene00003001
synonym: WormBase
database: WormBase database of nematode biology
generic url: http://www.wormbase.org/
url syntax: http://www.wormbase.org/db/gene/gene
url example: http://www.wormbase.org/db/get

WB REF
type: NamedIndividual
type: Database
object: Literature Reference Identifier
example id: WB_REF:WBPaper00004823
database: WormBase database of nematode biology
generic url: http://www.wormbase.org/
url example: http://www.wormbase.org/db/misc/paper
url syntax: http://www.wormbase.org/db/misc/paper

WP
type: NamedIndividual
type: Database
object: Identifier
example id: WP:CE25104
synonym: Wormpep
database: Wormpep database of proteins of C. elegans
generic url: http://www.wormbase.org/
url example: http://www.wormbase.org/db/get
url syntax: http://www.wormbase.org/db/get

YeastFunc
type: NamedIndividual
type: Database
database: Yeast Function
generic url: http://func.med.harvard.edu/yeast/

ZFIN
type: NamedIndividual
type: Database
object: Accession ID
example id: ZFIN:ZDB-GENE-990415-103
database: Zebrafish Information Network
generic url: http://zfin.org/
url example: http://zfin.org/cgi-bin/ZFIN_jump
url syntax: http://zfin.org/cgi-bin/ZFIN_jump

bioPIXIE MEFIT
type: NamedIndividual
type: Database
database: biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
generic url: http://avis.princeton.edu/mefit/
generic url: http://pixie.princeton.edu/pixie/

dictyBase
type: NamedIndividual
type: Database
synonym: DDB
synonym: DictyBase
object: Identifier
database: dictyBase
example id: dictyBase:DDB0001836
generic url: http://dictybase.org
url example: http://dictybase.org/db/cgi-bin/gene_page.pl
url syntax: http://dictybase.org/db/cgi-bin/gene_page.pl

dictyBase REF
type: NamedIndividual
type: Database
synonym: DDB_REF
object: Literature Reference Identifier
database: dictyBase literature references
example id: dictyBase_REF:10157
generic url: http://dictybase.org
url example: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl
url syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl

dictyBase gene name
type: NamedIndividual
type: Database
object: Gene name
database: dictyBase
example id: dictyBase_gene_name:mlcE
generic url: http://dictybase.org
url syntax: http://dictybase.org/db/cgi-bin/gene_page.pl
url example: http://dictybase.org/db/cgi-bin/gene_page.pl

pTARGET
type: NamedIndividual
type: Database
generic url: http://bioinformatics.albany.edu/~ptarget/
database: pTARGET Prediction server for protein subcellular localization

protein id
type: NamedIndividual
type: Database
database: DDBJ / EMBL-Bank / GenBank
object: Identifier
description: protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases
example id: protein_id:CAA71991

taxon
type: NamedIndividual
type: Database
object: Identifier
database: NCBI Taxonomy
url example: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
url syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
generic url: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
synonym: ncbi_taxid
example id: taxon:7227