!version: $Revision: 2.302 $
!date: $Date: 2012/09/20 21:04:35 $
!
!Gene Ontology
!Abbreviations for cross-referenced databases.
!
!Note that URLs are not necessarily stable entities and that some
!databases may have many other access routes or mirror sites.
!
!This data is available as a web page at
!http://www.geneontology.org/cgi-bin/xrefs.cgi

abbreviation: AgBase
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?db_pick=[ChickGO/MaizeGO]&uid=[example_id]

abbreviation: AGI_LocusCode
database: Arabidopsis Genome Initiative
description: Comprises TAIR, TIGR and MIPS
object: Locus identifier
example_id: AGI_LocusCode:At2g17950
local_id_syntax: ^AT[MC0-5]G[0-9]{5}(\.[0-9]{1})?$
generic_url: http://www.arabidopsis.org
url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]
url_example: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950
!url_syntax: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=[example_id]
!url_example: http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=At2g17950
!url_syntax: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=[example_id]
!url_example: http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=At2g17950

abbreviation: AGRICOLA_ID
database: AGRICultural OnLine Access
object: AGRICOLA call number
example_id: AGRICOLA_NAL:TP248.2 P76 v.14
generic_url: http://agricola.nal.usda.gov/

abbreviation: AGRICOLA_IND
database: AGRICultural OnLine Access
object: AGRICOLA IND number
example_id: AGRICOLA_IND:IND23252955
generic_url: http://agricola.nal.usda.gov/

abbreviation: ApiDB_PlasmoDB
database: PlasmoDB Plasmodium Genome Resource
object: PlasmoDB Gene ID
example_id: ApiDB_PlasmoDB:PF11_0344
generic_url: http://plasmodb.org/
url_syntax: http://www.plasmodb.org/gene/[example_id]
url_example: http://www.plasmodb.org/gene/PF11_0344

abbreviation: AraCyc
database: AraCyc metabolic pathway database for Arabidopsis thaliana
object: Identifier
example_id: AraCyc:PWYQT-62
generic_url: http://www.arabidopsis.org/biocyc/index.jsp
url_syntax: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=[example_id]
url_example: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=PWYQT-62

abbreviation: ASAP
database: A Systematic Annotation Package for Community Analysis of Genomes
object: Feature identifier
example_id: ASAP:ABE-0000008
generic_url: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
url_syntax: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=[example_id]
url_example: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=ABE-0000008

abbreviation: AspGD
database: Aspergillus Genome Database
object: Identifier for AspGD Loci
synonym: AspGDID
example_id: AspGD:ASPL0005516
generic_url: http://www.aspergillusgenome.org/
url_syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]
url_example: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538

abbreviation: AspGD_LOCUS
database: Aspergillus Genome Database
object: Gene name (gene symbol in mammalian nomenclature)
example_id: AspGD_LOCUS:AN10942
generic_url: http://www.aspergillusgenome.org/
url_syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]
url_example: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942

abbreviation: AspGD_REF
database: Aspergillus Genome Database
object: Literature Reference Identifier
example_id: AspGD_REF:90
generic_url: http://www.aspergillusgenome.org/
url_syntax: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
url_example: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90

abbreviation: BFO
database: Basic Formal Ontology
description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)
example_id: BFO:0000066
generic_url: http://purl.obolibrary.org/obo/bfo
url_syntax: http://purl.obolibrary.org/obo/BFO_[example_id]
url_example: http://purl.obolibrary.org/obo/BFO_0000066

abbreviation: BHF-UCL
database: Cardiovascular Gene Ontology Annotation Initiative
description: The Cardiovascular Gene Ontology Annotation Initiative is supported by the British Heart Foundation (BHF) and located at University College London (UCL).
generic_url: http://www.ucl.ac.uk/cardiovasculargeneontology/

abbreviation: BioCyc
database: BioCyc collection of metabolic pathway databases
object: Identifier
example_id: BioCyc:PWY-5271
generic_url: http://biocyc.org/
url_syntax: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]
url_example: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271

abbreviation: BIOMD
database: BioModels Database
object: Accession
synonym: BIOMDID
example_id: BIOMD:BIOMD0000000045
generic_url: http://www.ebi.ac.uk/biomodels/
url_syntax: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=[example_id]
url_example: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIOMD0000000045

abbreviation: bioPIXIE_MEFIT
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/

abbreviation: BIOSIS
database: BIOSIS previews
object: Identifier
example_id: BIOSIS:200200247281
generic_url: http://www.biosis.org/

abbreviation: BRENDA
database: BRENDA, The Comprehensive Enzyme Information System
object: EC enzyme identifier
example_id: BRENDA:4.2.1.3
generic_url: http://www.brenda-enzymes.info
url_syntax: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=[example_id]
url_example: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3

abbreviation: Broad
database: Broad Institute
generic_url: http://www.broad.mit.edu/

abbreviation: Broad_MGG
database: Magnaporthe grisea Database
description: Magnaporthe grisea Database at the Broad Institute
object: Locus
example_id: Broad_MGG:MGG_05132.5
generic_url: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html
url_syntax: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S[example_id]
url_example: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=SMGG_05132

abbreviation: CAS
database: CAS Chemical Registry
description: CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s.
object: Identifier
example_id: CAS:58-08-2
generic_url: http://www.cas.org/expertise/cascontent/registry/index.html

abbreviation: CASGEN
database: Catalog of Fishes genus database
object: Identifier
synonym: CAS_GEN
example_id: CASGEN:1040
generic_url: http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=[example_id]
url_example: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=1040

abbreviation: CASREF
database: Catalog of Fishes publications database
object: Identifier
example_id: CASREF:2031
generic_url: http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]
url_example: http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031

abbreviation: CASSPC
database: Catalog of Fishes species database
object: Identifier
synonym: CAS_SPC
generic_url: http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=[example_id]
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979

abbreviation: CAZY
database: Carbohydrate Active EnZYmes
description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
object: Identifier
example_id: CAZY:PL11
local_id_syntax: ^(CE|GH|GT|PL)\d+$
generic_url: http://www.cazy.org/
url_syntax: http://www.cazy.org/[example_id].html
url_example: http://www.cazy.org/PL11.html

! Note that CBS examples are not in the traditional accession style because the entities in question are not entries in a database, and don't have accessions

abbreviation: CBS
database: Center for Biological Sequence Analysis
generic_url: http://www.cbs.dtu.dk/
object: prediction tool
example_id: CBS:TMHMM
url_example: http://www.cbs.dtu.dk/services/[example_id]/

! note: CDD contact person is Rob Edwards (RobE@thefig.info); BRC: NMPDR

abbreviation: CDD
database: Conserved Domain Database at NCBI
object: Identifier
example_id: CDD:34222
generic_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
url_syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222

abbreviation: CGD
database: Candida Genome Database
object: Identifier for CGD Loci
synonym: CGDID
example_id: CGD:CAL0005516
local_id_syntax: ^(CAL|CAF)[0-9]{7}$
generic_url: http://www.candidagenome.org/
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
url_example: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0005516

! note: The CGD object also includes the orf19 assembly names, eg. orf19.2475

abbreviation: CGD_LOCUS
database: Candida Genome Database
object: Gene name (gene symbol in mammalian nomenclature)
example_id: CGD_LOCUS:HWP1
generic_url: http://www.candidagenome.org/
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id]
url_example: http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1

abbreviation: CGD_REF
database: Candida Genome Database
object: Literature Reference Identifier
example_id: CGD_REF:1490
generic_url: http://www.candidagenome.org/
url_syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
url_example: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490

! note: also see GO/gene-associations/readme/Compugen.README

abbreviation: CGEN
database: Compugen Gene Ontology Gene Association Data
object: Identifier
example_id: CGEN:PrID131022
generic_url: http://www.cgen.com/

abbreviation: CGSC
database: CGSC: E.coli Genetic Stock Center
object: Gene symbol
example_id: CGSC:rbsK
generic_url: http://cgsc.biology.yale.edu/
url_example: http://cgsc.biology.yale.edu/Site.php?ID=315

abbreviation: CHEBI
database: Chemical Entities of Biological Interest
object: Identifier
synonym: ChEBI
example_id: CHEBI:17234
local_id_syntax: ^[0-9]{1,6}$
generic_url: http://www.ebi.ac.uk/chebi/
url_syntax: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id]
url_example: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234
entity_type: CHEBI:24431 ! chemical entity 

abbreviation: CL
database: Cell Type Ontology
object: Identifier
example_id: CL:0000041
local_id_syntax: ^[0-9]{7}$
generic_url: http://cellontology.org
url_syntax: http://purl.obolibrary.org/obo/CL_[example_id]
url_example: http://purl.obolibrary.org/obo/CL_0000041
entity_type: CL:0000000 ! cell 

abbreviation: COG
database: NCBI Clusters of Orthologous Groups
generic_url: http://www.ncbi.nlm.nih.gov/COG/

abbreviation: COG_Cluster
database: NCBI COG cluster
object: Identifier
example_id: COG_Cluster:COG0001
generic_url: http://www.ncbi.nlm.nih.gov/COG/
url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001

abbreviation: COG_Function
database: NCBI COG function
object: Identifier
example_id: COG_Function:H
generic_url: http://www.ncbi.nlm.nih.gov/COG/
url_syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H

abbreviation: COG_Pathway
database: NCBI COG pathway
object: Identifier
example_id: COG_Pathway:14
generic_url: http://www.ncbi.nlm.nih.gov/COG/
url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14

abbreviation: CORUM
database: CORUM - the Comprehensive Resource of Mammalian protein complexes
object: Identifier
example_id: CORUM:837
generic_url: http://mips.gsf.de/genre/proj/corum/
url_syntax: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=[example_id]
url_example: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=837

abbreviation: dbSNP
database: NCBI dbSNP
object: Identifier
example_id: dbSNP:rs3131969
local_id_syntax: ^\d+$
generic_url: http://www.ncbi.nlm.nih.gov/projects/SNP
url_syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969

abbreviation: DDANAT
database: Dictyostelium discoideum anatomy
object: Identifier
example_id: DDANAT:0000068
local_id_syntax: [0-9]{7}
generic_url: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
entity_type: UBERON:0001062 ! anatomical entity

abbreviation: DDBJ
database: DNA Databank of Japan
object: Sequence accession
example_id: DDBJ:AA816246
generic_url: http://www.ddbj.nig.ac.jp/
url_syntax: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=[example_id]
url_example: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=AA816246

abbreviation: dictyBase
database: dictyBase
object: Identifier
synonym: DDB
synonym: DictyBase
example_id: dictyBase:DDB_G0277859
local_id_syntax: ^DDB_G[0-9]{7}$
generic_url: http://dictybase.org
url_syntax: http://dictybase.org/gene/[example_id]
url_example: http://dictybase.org/gene/DDB_G0277859

abbreviation: dictyBase_gene_name
database: dictyBase
object: Gene name
example_id: dictyBase_gene_name:mlcE
generic_url: http://dictybase.org
url_syntax: http://dictybase.org/gene/[example_id]
url_example: http://dictybase.org/gene/mlcE

abbreviation: dictyBase_REF
database: dictyBase literature references
synonym: DDB_REF
object: Literature Reference Identifier
example_id: dictyBase_REF:10157
generic_url: http://dictybase.org
url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=[example_id]
url_example: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=10157

abbreviation: DFLAT
database: Developmental FunctionaL Annotation at Tufts
generic_url: http://bcb.cs.tufts.edu/dflat/

abbreviation: DOI
database: Digital Object Identifier
object: Identifier
example_id: DOI:10.1016/S0963-9969(99)00021-6
generic_url: http://dx.doi.org/
url_syntax: http://dx.doi.org/DOI:[example_id]
url_example: http://dx.doi.org/DOI:10.1016/S0963-9969(99)00021-6

abbreviation: EC
database: Enzyme Commission
example_id: EC:1.4.3.6
generic_url: http://ww.expasy.org/enzyme/
generic_url: http://www.chem.qmul.ac.uk/iubmb/enzyme/
url_syntax: http://www.expasy.org/enzyme/[example_id]
url_example: http://www.expasy.org/enzyme/1.4.3.6
! url_example: http://www.chem.qmw.ac.uk/iubmb/enzyme/EC1/4/3/6.html

abbreviation: EchoBASE
database: EchoBASE post-genomic database for Escherichia coli
object: Identifier
example_id: EchoBASE:EB0231
local_id_syntax: ^EB[0-9]{4}$
generic_url: http://www.ecoli-york.org/
url_syntax: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=[example_id]
url_example: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=EB0231

abbreviation: ECK
database: EcoGene Database of Escherichia coli Sequence and Function
object: ECK accession (E. coli K-12 gene identifier)
example_id: ECK:ECK3746
local_id_syntax: ^ECK[0-9]{4}$
generic_url: http://www.ecogene.org/
url_syntax: http://www.ecogene.org/geneInfo.php?eck_id=[example_id]
url_example: http://www.ecogene.org/geneInfo.php?eck_id=ECK3746

abbreviation: ECO
database: Evidence Code ontology
object: Identifier
example_id: ECO:0000002
local_id_syntax: ^\d{7}$
generic_url: http://www.geneontology.org/

abbreviation: EcoCyc
database: Encyclopedia of E. coli metabolism
object: Pathway identifier
example_id: EcoCyc:P2-PWY
local_id_syntax: ^EG[0-9]{5}$
generic_url: http://ecocyc.org/
url_syntax: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=[example_id]
url_example: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY

abbreviation: EcoCyc_REF
database: Encyclopedia of E. coli metabolism
object: Reference identifier
synonym: ECOCYC_REF
example_id: EcoCyc_REF:COLISALII
generic_url: http://ecocyc.org/
url_syntax: http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=[example_id]
url_example: http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=COLISALII

abbreviation: ECOGENE
database: EcoGene Database of Escherichia coli Sequence and Function
object: EcoGene accession
example_id: ECOGENE:EG10818
local_id_syntax: ^EG[0-9]{5}$
generic_url: http://www.ecogene.org/
url_syntax: http://www.ecogene.org/geneInfo.php?eg_id=[example_id]
url_example: http://www.ecogene.org/geneInfo.php?eg_id=EG10818

! note: to construct URLs, use EcoGene accessions or ECK accessions

abbreviation: ECOGENE_G
database: EcoGene Database of Escherichia coli Sequence and Function
object: EcoGene Primary Gene Name
example_id: ECOGENE_G:deoC
generic_url: http://www.ecogene.org/

abbreviation: EcoliWiki
database: EcoliWiki from EcoliHub
description: EcoliHub's subsystem for community annotation of E. coli K-12
generic_url: http://ecoliwiki.net/
local_id_syntax: ^[A-Za-z]{3,4}$

abbreviation: EMBL
database: EMBL Nucleotide Sequence Database
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
example_id: EMBL:AA816246
local_id_syntax: ^([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})$
generic_url: http://www.ebi.ac.uk/embl/
url_syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=[example_id]
url_example: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246

abbreviation: ENA
database: European Nucleotide Archive
description: ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
object: Sequence accession
example_id: ENA:AA816246
local_id_syntax: ^([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})$
generic_url: http://www.ebi.ac.uk/ena/
url_syntax: http://www.ebi.ac.uk/ena/data/view/[example_id]
url_example: http://www.ebi.ac.uk/ena/data/view/AA816246

abbreviation: ENSEMBL
database: Ensembl database of automatically annotated genomic data
object: Identifier (unspecified)
example_id: ENSEMBL:ENSP00000265949
local_id_syntax: ^ENS[A-Z0-9]{10,17}$
generic_url: http://www.ensembl.org/
url_syntax: http://www.ensembl.org/id/[example_id]
url_example: http://www.ensembl.org/id/ENSP00000265949
entity_type: SO:0000704 ! gene
entity_type: PR:000000001 ! protein
entity_type: SO:0000673 ! transcript

abbreviation: ENSEMBL_GeneID
database: Ensembl database of automatically annotated genomic data
generic_url: http://www.ensembl.org/
object: Gene identifier
example_id: ENSEMBL_GeneID:ENSG00000126016
local_id_syntax: ^ENSG[0-9]{9,16}$
url_syntax: http://www.ensembl.org/id/[example_id]
url_example: http://www.ensembl.org/id/ENSG00000126016

abbreviation: ENSEMBL_ProteinID
database: Ensembl database of automatically annotated genomic data
generic_url: http://www.ensembl.org/
object: Protein identifier
example_id: ENSEMBL_ProteinID:ENSP00000361027
local_id_syntax: ^ENSP[0-9]{9,16}$
url_syntax: http://www.ensembl.org/id/[example_id]
url_example: http://www.ensembl.org/id/ENSP00000361027

abbreviation: ENSEMBL_TranscriptID
database: Ensembl database of automatically annotated genomic data
generic_url: http://www.ensembl.org/
object: Transcript identifier
example_id: ENSEMBL_TranscriptID:ENST00000371959
local_id_syntax: ^ENST[0-9]{9,16}$
url_syntax: http://www.ensembl.org/id/[example_id]
url_example: http://www.ensembl.org/id/ENST00000371959

abbreviation: EnsemblFungi
database: Ensembl Fungi, the Ensembl Genomes database for accessing fungal genome data
generic_url: http://fungi.ensembl.org/
object: Identifier
example_id: EnsemblFungi:YOR197W
url_syntax: http://www.ensemblgenomes.org/id/[example_ID]
url_example: http://www.ensemblgenomes.org/id/YOR197W

abbreviation: EnsemblPlants/Gramene
synonym: EnsemblPlants
database: Ensembl Plants, the Ensembl Genomes database for accessing plant genome data
generic_url: http://plants.ensembl.org/
object: Identifier
example_id: EnsemblPlants:LOC_Os01g22954
url_syntax: http://www.ensemblgenomes.org/id/[example_ID]
url_example: http://www.ensemblgenomes.org/id/LOC_Os01g22954

abbreviation: ENZYME
database: Swiss Institute of Bioinformatics enzyme database
object: Identifier
example_id: ENZYME:EC 1.1.1.1
generic_url: http://www.expasy.ch/
url_syntax: http://www.expasy.ch/cgi-bin/nicezyme.pl?[example_id]
url_example: http://www.expasy.ch/cgi-bin/nicezyme.pl?1.1.1.1

abbreviation: Eurofung
database: Eurofungbase community annotation
generic_url: http://www.eurofung.net/option=com_content&task=section&id=3&Itemid=4

! note: For FB [NCBI use FLYBASE]

abbreviation: FB
database: FlyBase
object: Identifier
synonym: FlyBase
synonym: FLYBASE
example_id: FB:FBgn0000024
local_id_syntax: ^FBgn[0-9]{7}$
generic_url: http://flybase.org/
url_syntax: http://flybase.org/reports/[example_id].html
url_example: http://flybase.org/reports/FBgn0000024.html
entity_type: SO:0000704 ! gene

! abbreviation: FLYBASE
! database: FlyBase
! object: Gene symbol
! example_id: FLYBASE:Adh
! generic_url: http://flybase.org/
! url_syntax: http://flybase.org/.bin/fbidq.html?[example_id]
!
! is that even correct?!?!

abbreviation: FBbt
database: Drosophila gross anatomy
object: Identifier
example_id: FBbt:00005177
generic_url: http://flybase.org/
url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]
url_example: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00005177

abbreviation: FMA
database: Foundational Model of Anatomy
object: Identifier
example_id: FMA:61905
generic_url: http://sig.biostr.washington.edu/projects/fm/index.html

abbreviation: FYPO
database: Fission Yeast Phenotype Ontology
object: Identifier
example_id: FYPO:0000001
local_id_syntax: ^\d{7}$
generic_url: http://www.pombase.org/

abbreviation: GDB
database: Human Genome Database
object: Accession
example_id: GDB:306600
generic_url: http://www.gdb.org/
url_syntax: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:[example_id]
url_example: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:306600

abbreviation: GenBank
database: GenBank
description: The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
object: Sequence accession
synonym: GB
example_id: GB:AA816246
local_id_syntax: ^[A-Z]{2}[0-9]{6}$
generic_url: http://www.ncbi.nlm.nih.gov/Genbank/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246

abbreviation: Gene3D
database: Domain Architecture Classification
object: Accession
example_id: Gene3D:G3DSA:3.30.390.30
generic_url: http://gene3d.biochem.ucl.ac.uk/Gene3D/
url_syntax: http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=[example_id]
url_example: http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=G3DSA%3A3.30.390.30

abbreviation: GeneDB_Gmorsitans
shorthand_name: Tsetse
database: Glossina morsitans GeneDB
object: Gene identifier
example_id: GeneDB_Gmorsitans:Gmm-0142
generic_url: http://www.genedb.org/genedb/glossina/
url_syntax: http://www.genedb.org/genedb/Search?organism=glossina&name=[example_id]
url_example: http://www.genedb.org/genedb/Search?organism=glossina&name=Gmm-0142

abbreviation: GeneDB_Lmajor
shorthand_name: Lmajor
database: Leishmania major GeneDB
object: Gene identifier
example_id: GeneDB_Lmajor:LM5.32
local_id_syntax: ^LmjF\.\d+\.\d+$
generic_url: http://www.genedb.org/genedb/leish/
url_syntax: http://www.genedb.org/genedb/Search?organism=leish&name=[example_id]
url_example: http://www.genedb.org/genedb/Search?organism=leish&name=LM5.32

abbreviation: GeneDB_Pfalciparum
shorthand_name: Pfalciparum
database: Plasmodium falciparum GeneDB
object: Gene identifier
example_id: GeneDB_Pfalciparum:PFD0755c
local_id_syntax: ^SP[A-Z0-9]+\.[A-Za-z0-9]+$
generic_url: http://www.genedb.org/genedb/malaria/
url_syntax: http://www.genedb.org/genedb/Search?organism=malaria&name=[example_id]
url_example: http://www.genedb.org/genedb/Search?organism=malaria&name=PFD0755c

! note: GeneDB_Spombe is deprecated; PomBase is now the authoritative source for Schizosaccharomyces pombe data

abbreviation: GeneDB_Spombe
shorthand_name: Spombe
database: Schizosaccharomyces pombe GeneDB
object: Gene identifier
example_id: GeneDB_Spombe:SPAC890.04C
local_id_syntax: ^SP[A-Z0-9]+\.[A-Za-z0-9]+$
generic_url: http://old.genedb.org/genedb/pombe/index.jsp
url_syntax: http://old.genedb.org/genedb/Search?organism=pombe&name=[example_id]
url_example: http://old.genedb.org/genedb/Search?organism=pombe&name=SPAC890.04C
entity_type: SO:0000704 ! gene 

abbreviation: GeneDB_Tbrucei
shorthand_name: Tbrucei
database: Trypanosoma brucei GeneDB
object: Gene identifier
example_id: GeneDB_Tbrucei:Tb927.1.5250
local_id_syntax: ^Tb\d+\.\d+\.\d+$
generic_url: http://www.genedb.org/genedb/tryp/
url_syntax: http://www.genedb.org/genedb/Search?organism=tryp&name=[example_id]
url_example: http://www.genedb.org/genedb/Search?organism=tryp&name=Tb927.1.5250

abbreviation: GenProtEC
database: GenProtEC E. coli genome and proteome database
generic_url: http://genprotec.mbl.edu/

abbreviation: GEO
database: NCBI Gene Expression Omnibus
generic_url: http://www.ncbi.nlm.nih.gov/geo/
example_id: GDS2223
url_syntax: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2223

abbreviation: GermOnline
database: GermOnline
generic_url: http://www.germonline.org/

abbreviation: GO
database: Gene Ontology Database
object: Identifier
example_id: GO:0004352
local_id_syntax: ^\d{7}$
generic_url: http://amigo.geneontology.org/
url_syntax: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:[example_id]
url_example: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004352
entity_type: GO:0003674 ! molecular function
entity_type: GO:0008150 ! biological process
entity_type: GO:0005575 ! cellular component

abbreviation: GO_REF
database: Gene Ontology Database references
object: Accession (for reference)
example_id: GO_REF:0000001
local_id_syntax: ^\d{7}$
generic_url: http://www.geneontology.org/
url_syntax: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:[example_id]
url_example: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000001

!abbreviation: GOA
!database: GO Annotation at EBI
!generic_url: http://www.ebi.ac.uk/goa/
!
!abbreviation: GOA_REF
!database: GO Annotation at EBI (UniProtKB-GOA) references
!object: Identifier (for literature reference)
!example_id: GOA_REF:PBT00118838
!generic_url: http://www.ebi.ac.uk/QuickGO
!url_syntax: http://www.ebi.ac.uk/QuickGO/GAnnotation?ref=GOA_REF:[example_id]
!url_example: http://www.ebi.ac.uk/QuickGO/GAnnotation?ref=GOA_REF:PBT00118838

abbreviation: GOC
database: Gene Ontology Consortium
generic_url: http://www.geneontology.org/

abbreviation: GONUTS
database: Gene Ontology Normal Usage Tracking System (GONUTS)
object: Identifier (for gene or gene product)
description: Third party documentation for GO and community annotation system.
example_id: GONUTS:MOUSE:CD28
generic_url: http://gowiki.tamu.edu
url_syntax: http://gowiki.tamu.edu/wiki/index.php/[example_id]
url_example: http://gowiki.tamu.edu/wiki/index.php/MOUSE:CD28

abbreviation: GR
database: Gramene: A Comparative Mapping Resource for Grains
object: Identifier (any)
example_id: GR:sd1
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=[example_id]
url_example: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=sd1

abbreviation: GR_GENE
database: Gramene: A Comparative Mapping Resource for Grains
object: Gene identifier
synonym: GR_gene
example_id: GR_GENE:GR:0060198
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]
url_example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198

abbreviation: GR_PROTEIN
database: Gramene: A Comparative Mapping Resource for Grains
object: Protein identifier
synonym: GR_protein
example_id: GR_PROTEIN:Q6VSV0
local_id_syntax: ^[A-Z][0-9][A-Z0-9]{3}[0-9]$
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id]
url_example: http://www.gramene.org/db/protein/protein_search?acc=Q6VSV0

abbreviation: GR_QTL
database: Gramene: A Comparative Mapping Resource for Grains
object: QTL identifier
example_id: GR_QTL:CQU7
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=[example_id]
url_example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQU7

abbreviation: GR_REF
database: Gramene: A Comparative Mapping Resource for Grains
object: Reference
example_id: GR_REF:659
generic_url: http://www.gramene.org/
url_syntax: http://www.gramene.org/db/literature/pub_search?ref_id=[example_id]
url_example: http://www.gramene.org/db/literature/pub_search?ref_id=659

abbreviation: H-invDB
database: H-invitational Database
generic_url: http://www.h-invitational.jp/

abbreviation: H-invDB_cDNA
database: H-invitational Database
object: Accession
example_id: H-invDB_cDNA:AK093148
generic_url: http://www.h-invitational.jp/
url_syntax: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=[example_id]
url_example: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=AK093149

abbreviation: H-invDB_locus
database: H-invitational Database
object: Cluster identifier
example_id: H-invDB_locus:HIX0014446
generic_url: http://www.h-invitational.jp/
url_syntax: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=[example_id]
url_example: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0014446

abbreviation: HAMAP
database: High-quality Automated and Manual Annotation of microbial Proteomes
object: Identifier
example_id: HAMAP:MF_00031
generic_url: http://us.expasy.org/sprot/hamap/
url_syntax: http://us.expasy.org/unirules/[example_id]
url_example: http://us.expasy.org/unirules/MF_00031

abbreviation: HGNC
database: HUGO Gene Nomenclature Committee
object: Identifier
example_id: HGNC:29
generic_url: http://www.genenames.org/
url_syntax: http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:[example_id]
url_example: http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:29

! note: HGNC:id is preferred over HGNC_gene, because gene symbols are liable to change, resulting in broken links.

abbreviation: HGNC_gene
database: HUGO Gene Nomenclature Committee
object: Gene symbol
example_id: HGNC_gene:ABCA1
generic_url: http://www.genenames.org/
url_syntax: http://www.genenames.org/data/hgnc_data.php?app_sym=[example_id]
url_example: http://www.genenames.org/data/hgnc_data.php?app_sym=ABCA1

! HPA IDs also work with the 'HPA' and leading zeros omitted
! QuickGO links to the #ifcelline anchor within the HPA tissue profile page

abbreviation: HPA
database: Human Protein Atlas tissue profile information
object: Identifier
example_id: HPA:HPA000237
generic_url: http://www.proteinatlas.org/
url_syntax: http://www.proteinatlas.org/tissue_profile.php?antibody_id=[example_id]
url_example: http://www.proteinatlas.org/tissue_profile.php?antibody_id=HPA000237

abbreviation: HPA_antibody
database: Human Protein Atlas antibody information
object: Identifier
example_id: HPA_antibody:HPA000237
generic_url: http://www.proteinatlas.org/
url_syntax: http://www.proteinatlas.org/antibody_info.php?antibody_id=[example_id]
url_example: http://www.proteinatlas.org/antibody_info.php?antibody_id=HPA000237

abbreviation: HUGO
database: Human Genome Organisation
generic_url: http://www.hugo-international.org/

! note: IMG contact person is Rob Edwards (RobE@thefig.info); BRC: NMPDR

abbreviation: IMG
database: Integrated Microbial Genomes; JGI web site for genome annotation
object: Identifier
example_id: IMG:640008772
generic_url: http://img.jgi.doe.gov
url_syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=[example_id]
url_example: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772

abbreviation: IMGT_HLA
database: IMGT/HLA human major histocompatibility complex sequence database
example_id: IMGT_HLA:HLA00031
generic_url: http://www.ebi.ac.uk/imgt/hla

abbreviation: IMGT_LIGM
database: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
description: Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.
example_id: IMGT_LIGM:U03895
generic_url: http://imgt.cines.fr

abbreviation: IntAct
database: IntAct protein interaction database
object: Accession
example_id: IntAct:EBI-17086
generic_url: http://www.ebi.ac.uk/intact/
url_syntax: http://www.ebi.ac.uk/intact/search/do/search?searchString=[example_id]
url_example: http://www.ebi.ac.uk/intact/search/do/search?searchString=EBI-17086
local_id_syntax: ^[0-9]+$
entity_type:  MI:0000 ! molecular interaction
entity_type:  GO:0043234 ! protein complex
entity_type: MI:0315 ! protein complex 

abbreviation: InterPro
database: InterPro database of protein domains and motifs
object: Identifier
synonym: INTERPRO
synonym: IPR
example_id: InterPro:IPR000001
local_id_syntax: ^IPR\d{6}$
generic_url: http://www.ebi.ac.uk/interpro/
url_syntax: http://www.ebi.ac.uk/interpro/entry/[example_id]
url_example: http://www.ebi.ac.uk/interpro/entry/IPR015421

! note: IPI identifiers are in the format ID.version

abbreviation: IPI
database: International Protein Index
object: Identifier
example_id: IPI:IPI00000005.1
generic_url: http://www.ebi.ac.uk/IPI/IPIhelp.html

abbreviation: ISBN
database: International Standard Book Number
generic_url: http://isbntools.com/
object: Identifier
example_id: ISBN:0781702534
url_syntax: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=[example_id]
url_example: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=0781702534

abbreviation: ISSN
database: International Standard Serial Number
object: Identifier
example_id: ISSN:1234-1231
generic_url: http://www.issn.org/

abbreviation: IUPHAR
database: International Union of Pharmacology
generic_url: http://www.iuphar.org/

abbreviation: IUPHAR_GPCR
database: International Union of Pharmacology
object: G-protein-coupled receptor family identifier
example_id: IUPHAR_GPCR:1279
generic_url: http://www.iuphar.org/
url_syntax: http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=[example_id]
url_example: http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=13

abbreviation: IUPHAR_RECEPTOR
database: International Union of Pharmacology
object: Receptor identifier
example_id: IUPHAR_RECEPTOR:2205
generic_url: http://www.iuphar.org/
url_syntax: http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=[example_id]
url_example: http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=56

! JCVI is essentially the same institute formerly named TIGR

abbreviation: JCVI
synonym: TIGR
database: J. Craig Venter Institute
generic_url: http://www.jcvi.org/

abbreviation: JCVI_Ath1
database: Arabidopsis thaliana database at the J. Craig Venter Institute
object: Accession
synonym: TIGR_Ath1
example_id: JCVI_Ath1:At3g01440
generic_url: http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml
is_obsolete: true

abbreviation: JCVI_CMR
database: Comprehensive Microbial Resource at the J. Craig Venter Institute
object: Locus
synonym: TIGR_CMR
example_id: JCVI_CMR:VCA0557
generic_url: http://cmr.jcvi.org/
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=[example_id]
url_example: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=VCA0557

synonym: TIGR_EGAD
database: EGAD database at the J. Craig Venter Institute
abbreviation: JCVI_EGAD
object: Accession
example_id: JCVI_EGAD:74462
generic_url: http://cmr.jcvi.org/
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=[example_id]
url_example: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=74462

abbreviation: JCVI_GenProp
database: Genome Properties database at the J. Craig Venter Institute
object: Accession
synonym: TIGR_GenProp
example_id: JCVI_GenProp:GenProp0120
generic_url: http://cmr.jcvi.org/
local_id_syntax: ^GenProp[0-9]{4}$
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=[example_id]
url_example: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=GenProp0120

abbreviation: JCVI_Medtr
database: Medicago truncatula genome database at the J. Craig Venter Institute 
object: Accession
example_id: JCVI_Medtr:Medtr5g024510
generic_url: http://medicago.jcvi.org/cgi-bin/medicago/overview.cgi
url_syntax: http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=[example_id]
url_example: http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=Medtr5g024510

abbreviation: JCVI_Pfa1
database: Plasmodium falciparum database at the J. Craig Venter Institute
object: Accession
synonym: TIGR_Pfa1
example_id: JCVI_Pfa1:PFB0010w
generic_url: http://www.tigr.org/tdb/e2k1/pfa1/pfa1.shtml
is_obsolete: true

abbreviation: JCVI_REF
database: J. Craig Venter Institute
object: Reference locator
synonym: TIGR_REF
example_id: JCVI_REF:GO_ref
generic_url: http://cmr.jcvi.org/
url_example: http://cmr.jcvi.org/CMR/AnnotationSops.shtml

abbreviation: JCVI_Tba1
database: Trypanosoma brucei database at the J. Craig Venter Institute
object: Accession
synonym: TIGR_Tba1
example_id: JCVI_Tba1:25N14.10
generic_url: http://www.tigr.org/tdb/e2k1/tba1/
is_obsolete: true

abbreviation: JCVI_TIGRFAMS
database: TIGRFAMs HMM collection at the J. Craig Venter Institute
object: Accession
synonym: TIGR_TIGRFAMS
example_id: JCVI_TIGRFAMS:TIGR00254
generic_url: http://search.jcvi.org/
url_syntax: http://search.jcvi.org/search?p&q=[example_id]
url_example: http://search.jcvi.org/search?p&q=TIGR00254

abbreviation: JSTOR
database: Digital archive of scholarly articles
object: journal article
example_id: JSTOR:3093870
generic_url: http://www.jstor.org/
url_syntax: http://www.jstor.org/stable/[example_id]
url_example: http://www.jstor.org/stable/3093870

abbreviation: KEGG
database: Kyoto Encyclopedia of Genes and Genomes
generic_url: http://www.genome.ad.jp/kegg/
object: identifier

abbreviation: KEGG_ENZYME
database: KEGG Enzyme Database
object: Enzyme Commission ID, as stored in KEGG
example_id: KEGG_ENZYME:2.1.1.4
local_id_syntax: ^\d(\.\d{1,2}){2}\.\d{1,3}$
generic_url: http://www.genome.jp/dbget-bin/www_bfind?enzyme
url_syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]
url_example: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4

abbreviation: KEGG_LIGAND
database: KEGG LIGAND Database
object: Compound
generic_url: http://www.genome.ad.jp/kegg/docs/upd_ligand.html
example_id: KEGG_LIGAND:C00577
local_id_syntax: ^C\d{5}$
url_syntax: http://www.genome.jp/dbget-bin/www_bget?cpd:[example_id]
url_example: http://www.genome.jp/dbget-bin/www_bget?cpd:C00577

abbreviation: KEGG_PATHWAY
database: KEGG Pathways Database
object: Pathway
example_id: KEGG_PATHWAY:ot00020
generic_url: http://www.genome.jp/kegg/pathway.html
url_syntax: http://www.genome.jp/dbget-bin/www_bget?path:[example_id]
url_example: http://www.genome.jp/dbget-bin/www_bget?path:ot00020

abbreviation: KEGG_REACTION
database: KEGG Reaction Database
object: Reaction
example_id: KEGG:R02328
local_id_syntax: ^R\d+$
generic_url: http://www.genome.jp/kegg/reaction/
url_syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]
url_example: http://www.genome.jp/dbget-bin/www_bget?rn:R02328

abbreviation: LIFEdb
database: LifeDB
description: LifeDB is a database for information on protein localization, interaction, functional assays and expression.
object: cDNA clone identifier
example_id: LIFEdb:DKFZp564O1716
generic_url: http://www.lifedb.de/
url_syntax: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=[example_id]
url_example: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=DKFZp564O1716

abbreviation: LOCSVMpsi
database: LOCSVMPSI
description: Subcellular localization for eukayotic proteins based on SVM and PSI-BLAST
generic_url: http://bioinformatics.ustc.edu.cn/locsvmpsi/locsvmpsi.php

abbreviation: MA
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_syntax: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:[example_id]
url_example: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003

abbreviation: MaizeGDB
database: MaizeGDB
object: MaizeGDB Object ID Number
example_id: MaizeGDB:881225
generic_url: http://www.maizegdb.org
url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]
url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225

abbreviation: MaizeGDB_Locus
database: MaizeGDB
generic_url: http://www.maizegdb.org
object: Maize gene name
example_id: MaizeGDB_Locus:ZmPK1
local_id_syntax: ^[A-Za-z][A-Za-z0-9]*$
url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=[example_id]
url_example: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=ZmPK1

abbreviation: MEDLINE
database: Medline literature database
generic_url: http://www.nlm.nih.gov/databases/databases_medline.html
object: Identifier
example_id: MEDLINE:20572430

abbreviation: PHI
database: MeGO (Phage and Mobile Element Ontology)
generic_url: http://aclame.ulb.ac.be/Classification/mego.html
example_id: PHI:0000055

abbreviation: MENGO
database: Microbial ENergy processes Gene Ontology Project
generic_url: http://mengo.vbi.vt.edu/

abbreviation: MEROPS
database: MEROPS peptidase database
object: Identifier
example_id: MEROPS:A08.001
generic_url: http://merops.sanger.ac.uk/
url_syntax: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=[example_id]
url_example: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=A08.001

abbreviation: MEROPS_fam
database: MEROPS peptidase database
object: Peptidase family identifier
example_id: MEROPS_fam:M18
generic_url: http://merops.sanger.ac.uk/
url_syntax: http://merops.sanger.ac.uk/cgi-bin/famsum?family=[example_id]
url_example: http://merops.sanger.ac.uk/cgi-bin/famsum?family=m18

abbreviation: MeSH
database: Medical Subject Headings
object: MeSH heading
example_id: MeSH:mitosis
generic_url: http://www.nlm.nih.gov/mesh/2005/MBrowser.html
url_syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id]
url_example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis

abbreviation: MetaCyc
database: Metabolic Encyclopedia of metabolic and other pathways
object: Identifier (pathway or reaction)
example_id: MetaCyc:GLUTDEG-PWY
generic_url: http://metacyc.org/
url_syntax: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=[example_id]
url_example: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY

abbreviation: MGD
database: Mouse Genome Database
object: Gene symbol
example_id: MGD:Adcy9
generic_url: http://www.informatics.jax.org/
! url_syntax: http://www.informatics.jax.org/searches/marker.cgi?

abbreviation: MGI
database: Mouse Genome Informatics
object: Accession
example_id: MGI:MGI:80863
local_id_syntax: ^MGI:[0-9]{5,}$
generic_url: http://www.informatics.jax.org/
url_syntax: http://www.informatics.jax.org/accession/[example_id]
url_example: http://www.informatics.jax.org/accession/MGI:80863

abbreviation: MIPS_funcat
database: MIPS Functional Catalogue
object: Identifier
example_id: MIPS_funcat:11.02
generic_url: http://mips.gsf.de/proj/funcatDB/
url_syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=[example_id]
url_example: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02

abbreviation: MITRE
database: The MITRE Corporation
generic_url: http://www.mitre.org/

abbreviation: MO
database: MGED Ontology
object: ontology term
example_id: MO:Action
generic_url: http://mged.sourceforge.net/ontologies/MGEDontology.php
url_syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#[example_id]
url_example: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action

! ModBase search accepts UniProtKB accessions and some other IDs; latter not shown here for clarity and sanity

abbreviation: ModBase
database: ModBase comprehensive Database of Comparative Protein Structure Models
object: Accession
example_id: ModBase:P10815
generic_url: http://modbase.compbio.ucsf.edu/ 
url_syntax: http://salilab.org/modbase/searchbyid?databaseID=[example_id]
url_example: http://salilab.org/modbase/searchbyid?databaseID=P04848

abbreviation: MTBBASE
database: Collection and Refinement of Physiological Data on Mycobacterium
tuberculosis
generic_url: http://www.ark.in-berlin.de/Site/MTBbase.html

abbreviation: MultiFun
database: MultiFun cell function assignment schema
generic_url: http://genprotec.mbl.edu/files/MultiFun.html

abbreviation: NASC_code
database: Nottingham Arabidopsis Stock Centre Seeds Database
object: NASC code Identifier
example_id: NASC_code:N3371
generic_url: http://arabidopsis.info
url_syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]
url_example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371

abbreviation: NC-IUBMB
database: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
generic_url: http://www.chem.qmw.ac.uk/iubmb/

abbreviation: NCBI
database: National Center for Biotechnology Information
object: Prefix
generic_url: http://www.ncbi.nlm.nih.gov/
! example_id:
! url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
! url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=

! note: LocusID was the abbreviation for LocusLink, which has been superseded by NCBI_Gene (aka Entrez Gene)

abbreviation: NCBI_Gene
database: NCBI Gene
object: Identifier
synonym: GeneID
synonym: LocusID
example_id: NCBI_Gene:4771
local_id_syntax: ^\d+$
generic_url: http://www.ncbi.nlm.nih.gov/
url_syntax: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=4771

abbreviation: NCBI_gi
database: NCBI databases
object: Identifier
example_id: NCBI_gi:113194944
local_id_syntax: ^[0-9]{6,}$
generic_url: http://www.ncbi.nlm.nih.gov/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=113194944

abbreviation: NCBI_GP
database: NCBI GenPept
object: Protein identifier
example_id: NCBI_GP:EAL72968
local_id_syntax: ^[A-Z]{3}[0-9]{5}(\.[0-9]+)?$
generic_url: http://www.ncbi.nlm.nih.gov/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=EAL72968

! An NCBI locus tag includes an organism-specific prefix and a tag value, separated by an underscore; see http://www.ncbi.nlm.nih.gov/genomes/lltp.cgi

abbreviation: NCBI_locus_tag
database: NCBI locus tag
object: Identifier
example_id: NCBI_locus_tag:CTN_0547
generic_url: http://www.ncbi.nlm.nih.gov/

abbreviation: NCBI_NM
database: NCBI RefSeq
object: mRNA identifier
synonym: RefSeq
example_id: NCBI_NM:123456
generic_url: http://www.ncbi.nlm.nih.gov/
is_obsolete: true
replaced_by: RefSeq

abbreviation: NCBI_NP
database: NCBI RefSeq
object: Protein identifier
synonym: RefSeq
example_id: NCBI_NP:123456
generic_url: http://www.ncbi.nlm.nih.gov/
is_obsolete: true
replaced_by: RefSeq

abbreviation: NIF_Subcellular
database: Neuroscience Information Framework standard ontology, subcellular hierarchy
object: ontology term
example_id: NIF_Subcellular:sao1186862860
generic_url: http://www.neurolex.org/wiki
url_syntax: http://www.neurolex.org/wiki/[example_id]
url_example: http://www.neurolex.org/wiki/sao1770195789

abbreviation: NMPDR
database: National Microbial Pathogen Data Resource
object: Identifier
example_id: NMPDR:fig|306254.1.peg.183
generic_url: http://www.nmpdr.org
url_syntax: http://www.nmpdr.org/linkin.cgi?id=[example_id]
url_example: http://www.nmpdr.org/linkin.cgi?id=fig|306254.1.peg.183

abbreviation: NTNU_SB
database: Norwegian University of Science and Technology, Systems Biology team
generic_url: http://www.ntnu.edu/nt/systemsbiology

abbreviation: OBI
database: Ontology for Biomedical Investigations
object: Identifier
example_id: OBI:0000038
local_id_syntax: ^\d{7}$
generic_url: http://obi-ontology.org/page/Main_Page

abbreviation: OBO_REL
database: OBO relation ontology
object: Identifier
example_id: OBO_REL:part_of
generic_url: http://www.obofoundry.org/ro/

abbreviation: OBO_SF_PO
database: Source Forge OBO Plant Ontology (PO) term request tracker
object: Term request
example_id: OBO_SF_PO:3184921
generic_url: http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555
url_syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555
url_example: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555

! note: NCBI uses the synonym MIM for OMIM

abbreviation: OMIM
database: Mendelian Inheritance in Man
object: Identifier
synonym: MIM
example_id: OMIM:190198
generic_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
url_syntax: http://omim.org/entry/[example_id]
url_example: http://omim.org/entry/190198

abbreviation: OMSSA
database: Open Mass Spectrometry Search Algorithm
generic_url: http://pubchem.ncbi.nlm.nih.gov/omssa/

abbreviation: PAMGO
database: Plant-Associated Microbe Gene Ontology Interest Group
generic_url: http://pamgo.vbi.vt.edu/

abbreviation: PAMGO_GAT
database: Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group
object: Gene
example_id: PAMGO_GAT:Atu0001
generic_url: http://agro.vbi.vt.edu/public/
url_syntax: http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=[example_id]
url_example: http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=atu0001

abbreviation: PAMGO_MGG
database: Magnaporthe grisea database
description: Magnaporthe grisea database at North Carolina State University; member of PAMGO Interest Group
object: Locus
example_id: PAMGO_MGG:MGG_05132
generic_url: http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html
url_syntax: http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=[example_id]
url_example: http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=MGG_05132

abbreviation: PAMGO_VMD
database: Virginia Bioinformatics Institute Microbial Database
description: Virginia Bioinformatics Institute Microbial Database; member of PAMGO Interest Group
object: Gene identifier
example_id: PAMGO_VMD:109198
generic_url: http://phytophthora.vbi.vt.edu
url_syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=[example_id]
url_example: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=109198

abbreviation: PAINT_REF
database: Phylogenetic Annotation INference Tool References
generic_url: http://www.pantherdb.org/
object: Reference locator
example_id: PAINT_REF:PTHR10046
url_syntax: http://www.geneontology.org/gene-associations/submission/paint/[example_id]/[example_id].txt
url_example: http://www.geneontology.org/gene-associations/submission/paint/PTHR10046/PTHR10046.txt

abbreviation: PANTHER
database: Protein ANalysis THrough Evolutionary Relationships
Classification System
generic_url: http://www.pantherdb.org/
object: Protein family tree identifier
example_id: PANTHER:PTN000000084
url_syntax: http://pantree.org/node/annotationNode.jsp?id=[example_id]
url_example: http://pantree.org/node/annotationNode.jsp?id=PTN000000084

abbreviation: PATO
database: Phenotypic quality ontology
object: Identifier
example_id: PATO:0001420
generic_url: http://www.bioontology.org/wiki/index.php/PATO:Main_Page

abbreviation: PATRIC
database: PathoSystems Resource Integration Center
description: PathoSystems Resource Integration Center at the Virginia Bioinformatics Institute
object: Feature identifieer
example_id: PATRIC:cds.000002.436951
generic_url: http://patric.vbi.vt.edu
url_syntax: http://patric.vbi.vt.edu/gene/overview.php?fid=[example_id]
url_example: http://patric.vbi.vt.edu/gene/overview.php?fid=cds.000002.436951

abbreviation: PDB
database: Protein Data Bank
object: Identifier
example_id: PDB:1A4U
generic_url: http://www.rcsb.org/pdb/
local_id_syntax: ^[A-Za-z0-9]{4}$
url_syntax: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=[example_id]
url_example: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1A4U

abbreviation: Pfam
database: Pfam database of protein families
description: Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs)
object: Accession
example_id: Pfam:PF00046
generic_url: http://www.sanger.ac.uk/Software/Pfam/
url_syntax: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?[example_id]
url_example: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00046

abbreviation: PfamB
database: Pfam-B supplement to Pfam
object: Accession
example_id: PfamB:PB014624
generic_url: http://www.sanger.ac.uk/Software/Pfam/

abbreviation: PharmGKB
database: Pharmacogenetics and Pharmacogenomics Knowledge Base
example_id: PharmGKB:PA267
generic_url: http://www.pharmgkb.org
url_syntax: http://www.pharmgkb.org/do/serve?objId=[example_id]
url_example: http://www.pharmgkb.org/do/serve?objId=PA267

abbreviation: PhenoScape
database: PhenoScape Knowledgebase
generic_url: http://phenoscape.org/

abbreviation: PINC
database: Proteome Inc.
description: represents GO annotations created in 2001 for NCBI and extracted into UniProtKB-GOA from EntrezGene
generic_url: http://www.proteome.com/

abbreviation: PIR
database: Protein Information Resource
object: Accession
example_id: PIR:I49499
local_id_syntax: ^[A-Z]{1}[0-9]{5}$
generic_url: http://pir.georgetown.edu/
url_syntax: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=[example_id]
url_example: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=I49499

abbreviation: PIRSF
database: PIR Superfamily Classification System
object: Identifier
example_id: PIRSF:SF002327
generic_url: http://pir.georgetown.edu/pirsf/
url_syntax: http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]
url_example: http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327

! Older PMCIDs lacked the PMC prefix (e.g. PMCID:201377), but are being retrofitted

abbreviation: PMCID
database: Pubmed Central
object: Identifier
example_id: PMCID:PMC201377
generic_url: http://www.pubmedcentral.nih.gov/
url_syntax: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC201377
!url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=PMC&term=[example_id]
!url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=PMC&term=PMC201377

abbreviation: PMID
database: PubMed
object: Identifier
synonym: PUBMED
synonym: PubMed
example_id: PMID:4208797
generic_url: http://www.ncbi.nlm.nih.gov/PubMed/
url_syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
url_example: http://www.ncbi.nlm.nih.gov/pubmed/4208797

abbreviation: PO
database: Plant Ontology Consortium Database
object: Identifier
example_id: PO:0009004
local_id_syntax: ^[0-9]{7}$
generic_url: http://www.plantontology.org/
url_syntax: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:[example_id]
url_example: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0009004
entity_type: PO:0025131 ! plant anatomical entity
entity_type: PO:0009012 ! plant structure development stage 

abbreviation: PO_REF
database: Plant Ontology custom references
object: Reference identifier
example_id: PO_REF:00001
generic_url: http://wiki.plantontology.org:8080/index.php/PO_references
url_syntax: http://wiki.plantontology.org:8080/index.php/PO_REF:[example_id]
url_example: http://wiki.plantontology.org:8080/index.php/PO_REF:00001

abbreviation: POC
database: Plant Ontology Consortium
generic_url: http://www.plantontology.org/

abbreviation: PomBase
database: PomBase
object: Identifier
example_id: PomBase:SPBC11B10.09
generic_url: http://www.pombase.org/
local_id_syntax: ^S\w+(\.)?\w+(\.)?$
url_syntax: http://www.pombase.org/spombe/result/[example_id]
url_example: http://www.pombase.org/spombe/result/SPBC11B10.09
entity_type: SO:0000704 ! gene 

abbreviation: Pompep
database: Schizosaccharomyces pombe protein data
object: Gene/protein identifier
example_id: Pompep:SPAC890.04C
generic_url: ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/

abbreviation: PPI
database: Pseudomonas syringae community annotation project
generic_url: http://genome.pseudomonas-syringae.org/

abbreviation: PR
database: Protein Ontology
object: Identifer
synonym: PRO
example_id: PR:000025380
local_id_syntax: ^[0-9]{9}$
generic_url: http://www.proconsortium.org/pro/pro.shtml
url_syntax: http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:[example_id]
url_example: http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:000025380
entity_type: PR:000000001 ! protein 

abbreviation: PRINTS
database: PRINTS compendium of protein fingerprints
object: Accession
example_id: PRINTS:PR00025
generic_url: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
url_syntax: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=[example_id]
url_example: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=PR00025

abbreviation: ProDom
database: ProDom protein domain families
description: ProDom protein domain families automatically generated from UniProtKB
object: Accession
example_id: ProDom:PD000001
generic_url: http://prodom.prabi.fr/prodom/current/html/home.php
url_syntax: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=[example_id]
url_example: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=PD000001

abbreviation: Prosite
database: Prosite database of protein families and domains
object: Accession
example_id: Prosite:PS00365
generic_url: http://www.expasy.ch/prosite/
url_syntax: http://www.expasy.ch/cgi-bin/prosite-search-ac?[example_id]
url_example: http://www.expasy.ch/cgi-bin/prosite-search-ac?PS00365

abbreviation: protein_id
database: DDBJ / EMBL-Bank / GenBank
description: protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases
generic_url: http://www.ddbj.nig.ac.jp/
generic_url: http://www.ebi.ac.uk/embl/
generic_url: http://www.ncbi.nlm.nih.gov/Genbank/
object: Identifier
example_id: protein_id:CAA71991
local_id_syntax: ^[A-Z]{3}[0-9]{5}(\.[0-9]+)?$

abbreviation: PROW
database: Protein Reviews on the Web
generic_url: http://www.ncbi.nlm.nih.gov/prow/

abbreviation: PseudoCAP
database: Pseudomonas Genome Project
object: Identifier
example_id: PseudoCAP:PA4756
generic_url: http://v2.pseudomonas.com/
url_syntax: http://v2.pseudomonas.com/getAnnotation.do?locusID=[example_id]
url_example: http://v2.pseudomonas.com/getAnnotation.do?locusID=PA4756

abbreviation: PSI-MI
database: Proteomic Standard Initiative for Molecular Interaction
object: Interaction identifier
synonym: MI
example_id: MI:0018
generic_url: http://psidev.sourceforge.net/mi/xml/doc/user/index.html

abbreviation: PSI-MOD
database: Proteomics Standards Initiative protein modification ontology
object: Protein modification identifier
synonym: MOD
example_id: MOD:00219
generic_url: http://psidev.sourceforge.net/mod/
url_syntax: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:[example_id]
url_example: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:00219

abbreviation: PSORT
database: PSORT protein subcellular localization databases and prediction tools for bacteria
generic_url: http://www.psort.org/

abbreviation: pTARGET
database: pTARGET Prediction server for protein subcellular localization
generic_url: http://bioinformatics.albany.edu/~ptarget/

abbreviation: PubChem_BioAssay
database: NCBI PubChem database of bioassay records
object: Identifier
example_id: PubChem_BioAssay:177
generic_url: http://pubchem.ncbi.nlm.nih.gov/
url_syntax: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=[example_id]
url_example: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=177

abbreviation: PubChem_Compound
database: NCBI PubChem database of chemical structures
object: Identifier
generic_url: http://pubchem.ncbi.nlm.nih.gov/
example_id: PubChem_Compound:2244
local_id_syntax: ^[0-9]+$
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=2244

abbreviation: PubChem_Substance
database: NCBI PubChem database of chemical substances
object: Identifier
example_id: PubChem_Substance:4594
local_id_syntax: ^[0-9]{4,}$
generic_url: http://pubchem.ncbi.nlm.nih.gov/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=4594

abbreviation: Reactome
database: Reactome - a curated knowledgebase of biological pathways
object: Identifier
example_id: Reactome:REACT_604
generic_url: http://www.reactome.org/
url_syntax: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=[example_id]
url_example: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_604

abbreviation: REBASE
database: REBASE restriction enzyme database
object: Restriction enzyme name
example_id: REBASE:EcoRI
generic_url: http://rebase.neb.com/rebase/rebase.html
url_syntax: http://rebase.neb.com/rebase/enz/[example_id].html
url_example: http://rebase.neb.com/rebase/enz/EcoRI.html

abbreviation: RefGenome
database: GO Reference Genomes
generic_url: http://www.geneontology.org/GO.refgenome.shtml

! note: RefSeq contact person is Guy Plunkett III (guy@genome.wisc.edu); BRC: ERIC

abbreviation: RefSeq
database: RefSeq
object: Identifier
generic_url: http://www.ncbi.nlm.nih.gov/RefSeq/
example_id: RefSeq:XP_001068954
local_id_syntax: ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954

abbreviation: RefSeq_NA
database: RefSeq (Nucleic Acid)
object: Identifier
example_id: RefSeq_NA:NC_000913
generic_url: http://www.ncbi.nlm.nih.gov/RefSeq/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_000913
is_obsolete: true
replaced_by: RefSeq

abbreviation: RefSeq_Prot
database: RefSeq (Protein)
object: Identifier
example_id: RefSeq_Prot:YP_498627
generic_url: http://www.ncbi.nlm.nih.gov/RefSeq/
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=YP_498627
is_obsolete: true
replaced_by: RefSeq

abbreviation: RESID
database: RESID Database of Protein Modifications
object: Identifier
example_id: RESID:AA0062
generic_url: ftp://ftp.ncifcrf.gov/pub/users/residues/

abbreviation: Rfam
database: Rfam database of RNA families
object: accession
example_id: Rfam:RF00012
generic_url: http://rfam.sanger.ac.uk/
url_syntax: http://rfam.sanger.ac.uk/family/[example_id]
url_example: http://rfam.sanger.ac.uk/family/RF00012

abbreviation: RGD
database: Rat Genome Database
object: Accession
synonym: RGDID
example_id: RGD:2004
local_id_syntax: ^[0-9]{4,7}$
generic_url: http://rgd.mcw.edu/
url_syntax: http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=[example_id]
url_example: http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=2004

abbreviation: RHEA
database: Rhea, the Annotated Reactions Database
description: Rhea is a freely available, manually annotated database of chemical reactions created in collaboration with the Swiss Institute of Bioinformatics (SIB).
object: Accession
example_id: RHEA:25811
generic_url: http://www.ebi.ac.uk/rhea/
url_syntax: http://www.ebi.ac.uk/rhea/reaction.xhtml?id=[example_id]
url_example: http://www.ebi.ac.uk/rhea/reaction.xhtml?id=25811

abbreviation: RNAmods
database: RNA Modification Database
object: Identifier
synonym: RNAMDB
example_id: RNAmods:037
generic_url: http://s59.cas.albany.edu/RNAmods/
url_syntax: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?[example_id]
url_example: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?091

! abbreviation: RI  # changing this to Roslin_Institute

abbreviation: Roslin_Institute
database: Roslin Institute
synonym: RI
generic_url: http://www.roslin.ac.uk/

abbreviation: RO
database: OBO Relation Ontology Ontology
description: A collection of relations used across OBO ontologies
generic_url: http://purl.obolibrary.org/obo/ro
example_id: RO:0002211
url_syntax: http://purl.obolibrary.org/obo/RO_[example_id]
url_example: http://purl.obolibrary.org/obo/RO_0002211

abbreviation: SABIO-RK
database: SABIO Reaction Kinetics
description: The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
generic_url: http://sabio.villa-bosch.de/
object: reaction
example_id: SABIO-RK:1858
url_syntax: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=[example_id]
url_example: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=1858

abbreviation: Sanger
database: Wellcome Trust Sanger Institute
generic_url: http://www.sanger.ac.uk/

abbreviation: SEED
database: The SEED;
description: Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices
object: identifier
example_id: SEED:fig|83331.1.peg.1
generic_url: http://www.theseed.org
url_syntax: http://www.theseed.org/linkin.cgi?id=[example_id]
url_example: http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1

! note: SGD is a synonym for the SGDID

abbreviation: SGD
database: Saccharomyces Genome Database
object: Identifier for SGD Loci
synonym: SGDID
example_id: SGD:S000006169
local_id_syntax: ^S[0-9]{9}$
generic_url: http://www.yeastgenome.org/
url_syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=[example_id]
url_example: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006169

! note: The SGD_LOCUS object also includes the systematic S. cerevisiae ORF names, eg. YEL001C

abbreviation: SGD_LOCUS
database: Saccharomyces Genome Database
object: Gene name (gene symbol in mammalian nomenclature)
example_id: SGD_LOCUS:GAL4
generic_url: http://www.yeastgenome.org/
url_syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=[example_id]
url_example: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GAL4

abbreviation: SGD_REF
database: Saccharomyces Genome Database
object: Literature Reference Identifier
example_id: SGD_REF:S000049602
generic_url: http://www.yeastgenome.org/
url_syntax: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
url_example: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000049602

abbreviation: SGN
database: Sol Genomics Network
object: Gene identifier
example_id: SGN:4476
generic_url: http://www.sgn.cornell.edu/
url_syntax: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=[example_id]
url_example: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=4476

abbreviation: SGN_ref
database: Sol Genomics Network
object: Reference identifier
example_id: SGN_ref:861
generic_url: http://www.sgn.cornell.edu/
url_syntax: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]
url_example: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=861

abbreviation: SMART
database: Simple Modular Architecture Research Tool
object: Accession
example_id: SMART:SM00005
generic_url: http://smart.embl-heidelberg.de/
url_syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=[example_id]
url_example: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005

abbreviation: SMD
database: Stanford Microarray Database
generic_url: http://genome-www.stanford.edu/microarray

abbreviation: SO
database: Sequence Ontology
object: Identifier
example_id: SO:0000195
local_id_syntax: ^\d{7}$
generic_url: http://sequenceontology.org/
url_syntax: http://song.sourceforge.net/SOterm_tables.html#SO:[example_id]
url_example: http://song.sourceforge.net/SOterm_tables.html#SO:0000195
entity_type: SO:0000400 ! sequence attribute 

abbreviation: SPD
database: Schizosaccharomyces pombe Postgenome Database at RIKEN; includes Orfeome Localisation data
object: Identifier
example_id: SPD:05/05F01
local_id_syntax: ^[0-9]{2}/[0-9]{2}[A-Z][0-9]{2}$
generic_url: http://www.riken.jp/SPD/
url_syntax: http://www.riken.jp/SPD/[example_id].html
url_example: http://www.riken.jp/SPD/05/05F01.html

abbreviation: SUBTILIST
database: Bacillus subtilis Genome Sequence Project
object: Accession
example_id: SUBTILISTG:BG11384
generic_url: http://genolist.pasteur.fr/SubtiList/

abbreviation: SUBTILISTG
database: Bacillus subtilis Genome Sequence Project
object: Gene symbol
example_id: SUBTILISTG:accC
generic_url: http://genolist.pasteur.fr/SubtiList/

abbreviation: SUPERFAMILY
database: SUPERFAMILY protein annotation database
description: A database of structural and functional protein annotations for completely sequenced genomes
object: Accession
example_id: SUPERFAMILY:51905
generic_url: http://supfam.cs.bris.ac.uk/SUPERFAMILY/index.html
url_syntax: http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF[example_id]
url_example: http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF51905

abbreviation: Swiss-Prot
database: UniProtKB/Swiss-Prot
description: A curated protein sequence database which provides a high level of annotation and a minimal level of redundancy
object: Accession
synonym: UniProtKB/Swiss-Prot
example_id: Swiss-Prot:P51587
generic_url: http://www.uniprot.org
url_syntax: http://www.uniprot.org/uniprot/[example_id]
url_example: http://www.uniprot.org/uniprot/P51587

abbreviation: TAIR
database: The Arabidopsis Information Resource
object: Accession
example_id: TAIR:gene:2062713
example_id: TAIR:locus:2146653
local_id_syntax: ^gene:[0-9]{7,12}$
local_id_syntax: ^locus:[0-9]{7}$
generic_url: http://www.arabidopsis.org/
url_syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id]
url_example: http://arabidopsis.org/servlets/TairObject?accession=gene:2062713
url_example: http://arabidopsis.org/servlets/TairObject?accession=locus:2146653

abbreviation: taxon
database: NCBI Taxonomy
object: Identifier
synonym: NCBITaxon
example_id: taxon:7227
synonym: ncbi_taxid
generic_url: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
url_syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]
url_example: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702

abbreviation: TC
database: Transport Protein Database
object: Identifier
example_id: TC:9.A.4.1.1
generic_url: http://www.tcdb.org/
url_syntax: http://www.tcdb.org/tcdb/index.php?tc=[example_id]
url_example: http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1

abbreviation: TGD
database: Tetrahymena Genome Database
generic_url: http://www.ciliate.org/

! note: The TGD_LOCUS object also includes the systematic T. thermophila ORF names, eg. U66363

abbreviation: TGD_LOCUS
database: Tetrahymena Genome Database
object: Gene name (gene symbol in mammalian nomenclature)
example_id: TGD_LOCUS:PDD1
generic_url: http://www.ciliate.org/
url_syntax: http://db.ciliate.org/cgi-bin/locus.pl?locus=[example_id]
url_example: http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1

abbreviation: TGD_REF
database: Tetrahymena Genome Database
object: Literature Reference Identifier
example_id: TGD_REF:T000005818
generic_url: http://www.ciliate.org/
url_syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=[example_id]
url_example: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818

! abbreviation: TIGR_TGI
! database: TIGR Gene Index from The Institute for Genomic Research
! object: TC accession
! example_id: TIGR_TGI:Cattle_TC123931
! generic_url: http://www.tigr.org/
! url_syntax: http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=[example_id]
! url_example: http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=Cattle_TC123931
!
! moved!

abbreviation: TRAIT
database: TRAnscript Integrated Table
description: an integrated database of transcripts expressed in human skeletal muscle
synonym: MuscleTRAIT
generic_url: http://muscle.cribi.unipd.it/

abbreviation: TRANSFAC
database: TRANSFAC database of eukaryotic transcription factors
generic_url: http://www.gene-regulation.com/pub/databases.html#transfac

abbreviation: TrEMBL
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
object: Accession
synonym: UniProtKB/TrEMBL
example_id: TrEMBL:O31124
generic_url: http://www.uniprot.org
url_syntax: http://www.uniprot.org/uniprot/[example_id]
url_example: http://www.uniprot.org/uniprot/O31124

abbreviation: UBERON
database: Uber-anatomy ontology
description: A multi-species anatomy ontology
object: Identifier
example_id: URBERON:0002398
local_id_syntax: ^[0-9]{7}$
generic_url: http://uberon.org
url_syntax: http://purl.obolibrary.org/obo/UBERON_[example_id]
url_example: http://purl.obolibrary.org/obo/UBERON_0002398
entity_type: UBERON:0001062 ! anatomical entity

abbreviation: UM-BBD
database: University of Minnesota Biocatalysis/Biodegradation Database
object: Prefix
generic_url: http://umbbd.msi.umn.edu/

abbreviation: UM-BBD_enzymeID
database: University of Minnesota Biocatalysis/Biodegradation Database
object: Enzyme identifier
example_id: UM-BBD_enzymeID:e0413
generic_url: http://umbbd.msi.umn.edu/
url_syntax: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=[example_id]
url_example: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=e0230

abbreviation: UM-BBD_pathwayID
database: University of Minnesota Biocatalysis/Biodegradation Database
object: Pathway identifier
example_id: UM-BBD_pathwayID:acr
generic_url: http://umbbd.msi.umn.edu/
url_syntax: http://umbbd.msi.umn.edu/[example_id]/[example_id]_map.html
url_example: http://umbbd.msi.umn.edu/acr/acr_map.html

abbreviation: UM-BBD_reactionID
database: University of Minnesota Biocatalysis/Biodegradation Database
object: Reaction identifier
example_id: UM-BBD_reactionID:r0129
generic_url: http://umbbd.msi.umn.edu/
url_syntax: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=[example_id]
url_example: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=r0129

abbreviation: UM-BBD_ruleID
database: University of Minnesota Biocatalysis/Biodegradation Database
object: Rule identifier
example_id: UM-BBD_ruleID:bt0330
generic_url: http://umbbd.msi.umn.edu/
url_syntax: http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=[example_id]
url_example: http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0330

! Note that UniGene IDs contain an organism abbreviation, which specifies the organism of interest and is required; the ID is split at the dot into organism abbreviation and cluster ID. See http://www.ncbi.nlm.nih.gov/UniGene/FAQ.shtml for more information.

abbreviation: UniGene
database: UniGene
object: Identifier (for transcript cluster)
description: NCBI transcript cluster database, organized by transcriptome. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene).
example_id: UniGene:Hs.212293
generic_url: http://www.ncbi.nlm.nih.gov/UniGene
url_syntax: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=[organism_abbreviation]&CID=[cluster_id]
url_example: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=212293

abbreviation: UniMod
database: UniMod
object: Identifier
description: protein modifications for mass spectrometry
example_id: UniMod:1287
generic_url: http://www.unimod.org/
url_syntax: http://www.unimod.org/modifications_view.php?editid1=[example_id]
url_example: http://www.unimod.org/modifications_view.php?editid1=1287

! note: UniParc supersedes REMTREMBL; the latter is no longer maintained

abbreviation: UniParc
database: UniProt Archive
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
example_id: UniParc:UPI000000000A
generic_url: http://www.uniprot.org/uniparc/
url_syntax: http://www.uniprot.org/uniparc/[example_id]
url_example: http://www.uniprot.org/uniparc/UPI000000000A

abbreviation: UniPathway
database: UniPathway
description: UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.
object: Identifier
example_id: UniPathway:UPA00155
generic_url: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
url_syntax: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=[example_id]
url_example: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00155

abbreviation: UniProtKB
database: Universal Protein Knowledgebase
description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database
object: Accession
synonym: UniProt
example_id: UniProtKB:P51587
local_id_syntax: ^[A-Z][0-9][A-Z0-9]{3}[0-9]((-([0-9]+)|:PRO_[0-9]{10}))?$
generic_url: http://www.uniprot.org
url_syntax: http://www.uniprot.org/uniprot/[example_id]
url_example: http://www.uniprot.org/uniprot/P51587
entity_type: PR:000000001 ! protein 

abbreviation: UniProtKB-KW
synonym: SP_KW
database: UniProt Knowledgebase keywords
object: Identifier
example_id: UniProtKB-KW:KW-0812
generic_url: http://www.uniprot.org/keywords/
url_syntax: http://www.uniprot.org/keywords/[example_id]
url_example: http://www.uniprot.org/keywords/KW-0812

abbreviation: UniProtKB-SubCell
synonym: SP_SL
database: UniProt Knowledgebase Subcellular Location vocabulary
object: Identifier
example_id: UniProtKB-SubCell:SL-0012
generic_url: http://www.uniprot.org/locations/
url_syntax: http://www.uniprot.org/locations/[example_id]
url_example: http://www.uniprot.org/locations/SL-0012

abbreviation: VBRC
database: Viral Bioinformatics Resource Center
object: Identifier
example_id: VBRC:F35742
generic_url: http://vbrc.org
url_syntax: http://vbrc.org/query.asp?web_id=VBRC:[example_id]
url_example: http://vbrc.org/query.asp?web_id=VBRC:F35742

! note: The link URL for VEGA is species specific (much like Ensembl).
! For a direct link you need to translate the abbreviation in the ID
! (eg 'HUM') into 'Homo_sapiens':
!
! http://vega.sanger.ac.uk/Homo_sapiens/protview?peptide=OTTHUMP00000000661&db=core
!
! Therefore to make it easier D. Barrell has given the search URL which
! gives the results of a search on a peptide ID.

abbreviation: VEGA
database: Vertebrate Genome Annotation database
object: Identifier
example_id: VEGA:OTTHUMP00000000661
generic_url: http://vega.sanger.ac.uk/index.html
url_syntax: http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=[example_id]
url_example: http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=OTTHUMP00000000661

abbreviation: VIDA
database: Virus Database at University College London
generic_url: http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html

abbreviation: VZ
database: ViralZone
object: Page Reference Identifier
example_id: VZ:957
generic_url: http://viralzone.expasy.org/
url_syntax: http://viralzone.expasy.org/all_by_protein/[example_id].html
url_example: http://viralzone.expasy.org/all_by_protein/957.html

abbreviation: VMD
database: Virginia Bioinformatics Institute Microbial Database
object: Gene identifier
example_id: VMD:109198
generic_url: http://phytophthora.vbi.vt.edu
url_syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=[example_id]
url_example: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=109198

abbreviation: WB
database: WormBase database of nematode biology
object: Gene identifier
synonym: WormBase
example_id: WB:WBGene00003001
local_id_syntax: ^WP:CE[0-9]{5}$
local_id_syntax: ^WB(Gene|Var)[0-9]{8}$
generic_url: http://www.wormbase.org/
url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
url_example: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
entity_type: SO:0000704 ! gene 

abbreviation: WBbt
database: C. elegans gross anatomy
object: Identifier
example_id: WBbt:0005733
local_id_syntax: [0-9]{7}
entity_type: WBbt:0004017 ! Cell
entity_type: WBbt:0005766 ! Anatomy

abbreviation: WBls
database: C. elegans development
object: Identifier
example_id: WBls:0000010
local_id_syntax: [0-9]{7}
entity_type: WBls:0000075 ! Nematoda Life Stage

abbreviation: WBPhenotype
database: WormBase phenotype ontology
object: Gene identifier
example_id: WBPhenotype:0002117
local_id_syntax: ^[0-9]{7}$
url_syntax: http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype:[example_id]
url_example: http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype:0000154
entity_type: UBERON:0001062 ! anatomical entity

! abbreviation: WB_GENE
! database: WormBase database of nematode biology
! object: Gene symbol
! synonym: WormBase
! example_id: WB_GENE:lin-12
! generic_url: http://www.wormbase.org/
! url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
! url_example: http://www.wormbase.org/db/gene/gene?name=lin-12

abbreviation: WB_REF
database: WormBase database of nematode biology
object: Literature Reference Identifier
example_id: WB_REF:WBPaper00004823
generic_url: http://www.wormbase.org/
url_syntax: http://www.wormbase.org/db/misc/paper?name=[example_id]
url_example: http://www.wormbase.org/db/misc/paper?name=WBPaper00004823

abbreviation: Wikipedia
database: Wikipedia
object: Page Reference Identifier
example_id: Wikipedia:Endoplasmic_reticulum
generic_url: http://en.wikipedia.org/
url_syntax: http://en.wikipedia.org/wiki/[example_id]
url_example: http://en.wikipedia.org/wiki/Endoplasmic_reticulum

abbreviation: WP
database: Wormpep database of proteins of C. elegans
object: Identifier
synonym: Wormpep
example_id: WP:CE25104
generic_url: http://www.wormbase.org/
url_syntax: http://www.wormbase.org/db/get?class=Protein;name=WP:[example_id]
url_example: http://www.wormbase.org/db/get?class=Protein;name=WP:CE15104

abbreviation: YeastFunc
database: Yeast Function
generic_url: http://func.med.harvard.edu/yeast/

abbreviation: ZFIN
database: Zebrafish Information Network
object: Identifier
example_id: ZFIN:ZDB-GENE-990415-103
local_id_syntax: ^ZDB-(GENE|GEN|MRPHLNO)-[0-9]{6}-[0-9]+$
generic_url: http://zfin.org/
url_syntax: http://zfin.org/cgi-bin/ZFIN_jump?record=[example_id]
url_example: http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-990415-103