!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
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:ASPL0000067538
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
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
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
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: Broad_NEUROSPORA
database: Neurospora crassa Database
object: Identifier for Broad_Ncrassa Loci
example_id: BROAD_NEUROSPORA:7000007580576824
generic_url: http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html
url_syntax: http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S[example_id]
url_example: http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000007580576824

abbreviation: CACAO
database: Community Assessment of Community Annotation with Ontologies
object: accession
example_id: MYCS2:A0QNF5
generic_url: http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
url_syntax: http://gowiki.tamu.edu/wiki/index.php/[example_id]
url_example: http://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5

abbreviation: CAS
database: CAS Chemical Registry
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
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

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

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: CORIELL
database: Coriell Institute for Medical Research
object: Identifier
example_id: GM07892
generic_url: http://ccr.coriell.org/
url_syntax: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=[example_id]
url_example: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07892

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

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
generic_url: http://ecoliwiki.net/
local_id_syntax: ^[A-Za-z]{3,4}$

abbreviation: EMBL
database: EMBL Nucleotide Sequence Database
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
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)
synonym: Ensembl
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

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

! 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
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
database: GeneDB
object: Identifier
example_id: PF3D7_1467300
local_id_syntax: ^LmjF\.\d{2}\.\d{4}$
local_id_syntax: ^PF3D7_\d{7}$
local_id_syntax: ^Tb\d+\.[A-Za-z0-9]+\.\d+$
generic_url: http://www.genedb.org/gene/
url_syntax: http://www.genedb.org/gene/[example_id]
url_example: http://www.genedb.org/gene/PF3D7_1467300

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
is_obsolete: true
replaced_by: GeneDB

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
is_obsolete: true
replaced_by: GeneDB

abbreviation: GeneDB_Pfalciparum
shorthand_name: Pfalcipar
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
is_obsolete: true
replaced_by: GeneDB

! 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
is_obsolete: true
replaced_by: PomBase

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
is_obsolete: true
replaced_by: GeneDB

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: GEO: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

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)
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
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]+$

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: https://en.wikipedia.org/w/index.php?title=Special%3ABookSources&isbn=[example_id]
url_example: https://en.wikipedia.org/w/index.php?title=Special%3ABookSources&isbn=0123456789

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

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
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
generic_url: http://bioinformatics.ustc.edu.cn/locsvmpsi/locsvmpsi.php

abbreviation: MA
database: Adult Mouse Anatomical Dictionary
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
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
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
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
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.
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

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

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

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
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
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
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
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
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;
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

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
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
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
is_obsolete: true
replaced_by: UniProtKB

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
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
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
is_obsolete: true
replaced_by: UniProtKB

abbreviation: UBERON
database: Uber-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

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)
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
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
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
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
object: Accession
synonym: UniProt
example_id: UniProtKB:P51587
local_id_syntax: ^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z]([0-9][A-Z][A-Z0-9]{2}){1,2}[0-9])((-[0-9]+)|:PRO_[0-9]{10}){0,1}$
generic_url: http://www.uniprot.org
url_syntax: http://www.uniprot.org/uniprot/[example_id]
url_example: http://www.uniprot.org/uniprot/P51587

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|RNAi|Transgene)[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

abbreviation: WBbt
database: C. elegans gross anatomy
object: Identifier
example_id: WBbt:0005733
local_id_syntax: [0-9]{7}
generic_url: http://www.wormbase.org/

abbreviation: WBls
database: C. elegans development
object: Identifier
example_id: WBls:0000010
local_id_syntax: [0-9]{7}
generic_url: http://www.wormbase.org/

abbreviation: WBPhenotype
database: WormBase phenotype ontology
object: Gene identifier
example_id: WBPhenotype:0002117
local_id_syntax: ^[0-9]{7}$
generic_url: http://www.wormbase.org/
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

! 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
is_obsolete: true

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|GENO|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
