The data for this page is also available as a YAML file and as a derived plain text file. See the documentation here in the repository for more details.

AgBase resource for functional analysis of agricultural plant and animal gene products
Site
http://www.agbase.msstate.edu/
Object
entity
Example ID
P02264
URL syntax
https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=[example_id]
Arabidopsis Genome Initiative
Site
http://www.arabidopsis.org
Object
gene
Example ID
AGI_LocusCode:At2g17950
URL syntax
http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]
URL example
https://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950
AGRICultural OnLine Access
Site
http://agricola.nal.usda.gov/
Object
entity
Example ID
AGRICOLA_NAL:TP248.2 P76 v.14
AGRICultural OnLine Access
Site
http://agricola.nal.usda.gov/
Object
entity
Example ID
AGRICOLA_IND:IND23252955
Alzheimers Project at University of Toronto
Site
http://www.ims.utoronto.ca/
Object
entity
PlasmoDB Plasmodium Genome Resource
Site
http://plasmodb.org/
Object
entity
Example ID
ApiDB_PlasmoDB:PF11_0344
URL syntax
http://www.plasmodb.org/gene/[example_id]
URL example
https://plasmodb.org/plasmo/app/record/gene/PF11_0344
APSNET Common Names of Plant Diseases
Site
http://www.mobot.org/mobot/research/apweb/
Object
entity
Example ID
APSNET:AfricanDaisy
URL syntax
http://www.apsnet.org/publications/commonnames/Pages/[example_id].aspx
URL example
http://www.apsnet.org/publications/commonnames/Pages/AfricanDaisy.aspx
Angiosperm Phylogeny Website
Site
http://www.mobot.org/mobot/research/apweb/
Object
entity
Example ID
APweb:Glossary
URL syntax
http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
URL example
http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
AraCyc metabolic pathway database for Arabidopsis thaliana
Site
http://www.arabidopsis.org/biocyc/index.jsp
Object
entity
Example ID
AraCyc:PWYQT-62
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
A Systematic Annotation Package for Community Analysis of Genomes
Site
https://asap.genetics.wisc.edu/asap/ASAP1.htm
Object
gene
Example ID
ASAP:ABF-0014586
URL syntax
https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=[example_id]
URL example
https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=ABF-0014586
Aspergillus Genome Database
Site
http://www.aspergillusgenome.org/
Object
gene
Example ID
AspGD:ASPL0000067538
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
Aspergillus Genome Database
Site
http://www.aspergillusgenome.org/
Object
gene
Example ID
AspGD:ASPL0000067538
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
Aspergillus Genome Database
Site
http://www.aspergillusgenome.org/
Object
entity
Example ID
AspGD_LOCUS:AN10942
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
Aspergillus Genome Database
Site
http://www.aspergillusgenome.org/
Object
entity
Example ID
AspGD_REF:90
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

BFO

Basic Formal Ontology
Site
http://purl.obolibrary.org/obo/bfo
Object
entity
Example ID
BFO:0000066
URL syntax
http://purl.obolibrary.org/obo/BFO_[example_id]
URL example
http://purl.obolibrary.org/obo/BFO_0000066
BioCyc collection of metabolic pathway databases
Site
http://biocyc.org/
Object
entity
Example ID
BioCyc:PWY-5271
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
BioModels Database
Site
https://www.ebi.ac.uk/biomodels/
Object
entity
Example ID
BIOMD:BIOMD0000000045
URL syntax
https://www.ebi.ac.uk/biomodels/[example_id]
URL example
https://www.ebi.ac.uk/biomodels/BIOMD0000000045
BioModels Database
Site
https://www.ebi.ac.uk/biomodels/
Object
entity
Example ID
BIOMD:BIOMD0000000045
URL syntax
https://www.ebi.ac.uk/biomodels/[example_id]
URL example
https://www.ebi.ac.uk/biomodels/BIOMD0000000045
bioRxiv
Site
https://www.biorxiv.org/
Object
entity
Example ID
bioRxiv:10.1101/530881v2
URL syntax
https://www.biorxiv.org/content/[example_id]
URL example
https://www.biorxiv.org/content/10.1101/530881v2
BRENDA, The Comprehensive Enzyme Information System
Site
http://www.brenda-enzymes.info
Object
catalytic activity
Example ID
BRENDA:4.2.1.3
URL syntax
https://www.brenda-enzymes.info/enzyme.php?ecno=[example_id]
URL example
https://www.brenda-enzymes.info/enzyme.php?ecno=4.2.1.3
Broad Institute
Site
http://www.broad.mit.edu/
Object
entity
Magnaporthe grisea Database
Site
http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html
Object
entity
Example ID
Broad_MGG:MGG_05132.5
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
Neurospora crassa Database
Site
http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html
Object
entity
Example ID
BROAD_NEUROSPORA:7000007580576824
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

BTO

BRENDA tissue / enzyme ontology
Site
http://purl.obolibrary.org/obo/bto
Object
entity
Example ID
BTO_0002164
URL syntax
http://purl.obolibrary.org/obo/BTO_[example_id]
URL example
http://purl.obolibrary.org/obo/BTO_0002164
Community Assessment of Community Annotation with Ontologies
Site
http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
Object
entity
Example ID
MYCS2:A0QNF5
URL syntax
https://gowiki.tamu.edu/wiki/index.php/[example_id]
URL example
https://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5
Critical Assessment of Protein Function Annotation
Site
http://biofunctionprediction.org/cafa/
Object
entity
Common Anatomy Reference Ontology
Site
http://purl.obolibrary.org/obo/caro
Object
entity
Example ID
CARO:0020003
URL syntax
http://purl.obolibrary.org/obo/CARO_[example_id]
URL example
http://purl.obolibrary.org/obo/CARO_0020003

CAS

CAS Chemical Registry
Site
http://www.cas.org/expertise/cascontent/registry/index.html
Object
entity
Example ID
CAS:58-08-2
Catalog of Fishes genus database
Site
http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
Object
entity
Example ID
CASGEN:1040
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
Catalog of Fishes genus database
Site
http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
Object
entity
Example ID
CASGEN:1040
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
Catalog of Fishes publications database
Site
http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
Object
entity
Example ID
CASREF:2031
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
Catalog of Fishes species database
Site
http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
Object
entity
URL syntax
http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=[example_id]
URL example
http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979
Catalog of Fishes species database
Site
http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
Object
entity
URL syntax
http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=[example_id]
URL example
http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979
Carbohydrate Active EnZYmes
Site
http://www.cazy.org/
Object
entity
Example ID
CAZY:PL11
URL syntax
http://www.cazy.org/[example_id].html
URL example
http://www.cazy.org/PL11.html
Cannabis Genome Browser
Site
http://genome.ccbr.utoronto.ca/
Object
entity
Example ID
CCBR:PK03997.1
URL syntax
http://genome.ccbr.utoronto.ca/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=plant&org=C.+sativa&db=canSat3&position=[example_id]
URL example
http://genome.ccbr.utoronto.ca/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=plant&org=C.+sativa&db=canSat3&position=PK03997.1

CDD

Conserved Domain Database at NCBI
Site
https://www.ncbi.nlm.nih.gov/cdd
Object
entity
Example ID
CDD:34222
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
Candida Genome Database
Site
http://www.candidagenome.org/
Object
gene
Example ID
CGD:CAL0000179664
URL syntax
http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example
http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664

CGD

Candida Genome Database
Site
http://www.candidagenome.org/
Object
gene
Example ID
CGD:CAL0000179664
URL syntax
http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example
http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664
Candida Genome Database
Site
http://www.candidagenome.org/
Object
entity
Example ID
CGD_LOCUS:HWP1
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
Candida Genome Database
Site
http://www.candidagenome.org/
Object
entity
Example ID
CGD_REF:1490
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
CGSC
Site
http://cgsc.biology.yale.edu/
Object
entity
Example ID
CGSC:rbsK
URL example
http://cgsc.biology.yale.edu/Site.php?ID=315
Chemical Entities of Biological Interest
Site
http://www.ebi.ac.uk/chebi/
Object
chemical entity
Example ID
CHEBI:17234
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

CL

Cell Type Ontology
Site
http://cellontology.org
Object
cell
Example ID
CL:0000041
URL syntax
http://purl.obolibrary.org/obo/CL_[example_id]
URL example
http://purl.obolibrary.org/obo/CL_0000041
Crop Ontology CGIAR Musa Anatomy
Site
http://www.cropontology.org/ontology/CO_125:0000000/CGIAR_Musa_anatomy
Object
entity
Example ID
CO_125:0000002
URL example
http://www.cropontology.org/ontology/CO_125:0000000
Coffee Genome Hub
Site
https://coffee-genome.org
Object
entity
Example ID
Coffee-genome:Cc05_g10470
URL syntax
https://coffee-genome.org/[example_id]
URL example
https://coffee-genome.org/Cc05_g10470

COG

NCBI Clusters of Orthologous Groups
Site
http://www.ncbi.nlm.nih.gov/COG/
Object
entity
NCBI COG cluster
Site
http://www.ncbi.nlm.nih.gov/COG/
Object
entity
Example ID
COG_Cluster:COG0001
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
NCBI COG function
Site
http://www.ncbi.nlm.nih.gov/COG/
Object
entity
Example ID
COG_Function:H
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
NCBI COG pathway
Site
http://www.ncbi.nlm.nih.gov/COG/
Object
entity
Example ID
COG_Pathway:14
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
Database of transcription factor binding sites (TFBS) in the Bacteria domain
Site
http://www.collectf.org/
Object
entity
Complex Portal database of macromolecular complexes
Site
https://www.ebi.ac.uk/complexportal
Object
macromolecular complex
Example ID
ComplexPortal:CPX-2158
URL syntax
https://www.ebi.ac.uk/complexportal/complex/[example_id]
URL example
https://www.ebi.ac.uk/complexportal/complex/CPX-2158
Congenie
Site
http://congenie.org
Object
entity
Example ID
Congenie:MA_71765g0010
URL syntax
http://congenie.org/gene?id=[example_id]
URL example
http://congenie.org/gene?id=MA_71765g0010
Coriell Institute for Medical Research
Site
http://ccr.coriell.org/
Object
entity
Example ID
GM07892
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
CORUM - the Comprehensive Resource of Mammalian protein complexes
Site
https://mips.helmholtz-muenchen.de/corum/
Object
entity
Example ID
CORUM:837
URL syntax
https://mips.helmholtz-muenchen.de/corum/?id=[example_id]
URL example
https://mips.helmholtz-muenchen.de/corum/?id=837
plantco.de|cosmoss.org
Site
https://www.cosmoss.org/annotation/genonaut
Object
entity
Example ID
cosmoss_PpV1.2:Pp1s47_77V2.1
URL syntax
https://www.cosmoss.org/annotation/genonaut?accession=[example_id]&version=V1.2
URL example
https://www.cosmoss.org/annotation/genonaut?accession=Pp1s53_22V2.1&version=V1.2
Vitis CRIBI database
Site
http://genomes.cribi.unipd.it
Object
entity
Example ID
VIT_00s0173g00270
URL syntax
http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=[example_id]&release=v1
URL example
http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=VIT_00s0173g00270&release=v1
Cucurbit Genomics
Site
http://cucurbitgenomics.org
Object
entity
Example ID
Cla013087
URL syntax
http://cucurbitgenomics.org/feature/gene/[example_id]
URL example
http://cucurbitgenomics.org/feature/gene/Cla013087
NCBI dbSNP
Site
http://www.ncbi.nlm.nih.gov/projects/SNP
Object
entity
Example ID
dbSNP:rs3131969
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
Dictyostelium discoideum anatomy
Site
http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
Object
anatomical entity
Example ID
DDANAT:0000068
DNA Databank of Japan
Site
https://www.ddbj.nig.ac.jp
Object
entity
Example ID
DDBJ:AA816246
URL syntax
http://getentry.ddbj.nig.ac.jp/getentry/na/[example_id]
URL example
http://getentry.ddbj.nig.ac.jp/getentry/na/AA816246

DDB

dictyBase
Site
http://dictybase.org
Object
gene
Example ID
dictyBase:DDB_G0277859
URL syntax
http://dictybase.org/gene/[example_id]
URL example
http://dictybase.org/gene/DDB_G0277859
dictyBase
Site
http://dictybase.org
Object
gene
Example ID
dictyBase:DDB_G0277859
URL syntax
http://dictybase.org/gene/[example_id]
URL example
http://dictybase.org/gene/DDB_G0277859
dictyBase
Site
http://dictybase.org
Object
entity
Example ID
dictyBase_gene_name:mlcE
URL syntax
http://dictybase.org/gene/[example_id]
URL example
http://dictybase.org/gene/mlcE
dictyBase literature references
Site
http://dictybase.org
Object
entity
Example ID
dictyBase_REF:10157
URL syntax
http://dictybase.org/publication/[example_id]
URL example
http://dictybase.org/publication/10157
dictyBase literature references
Site
http://dictybase.org
Object
entity
Example ID
dictyBase_REF:10157
URL syntax
http://dictybase.org/publication/[example_id]
URL example
http://dictybase.org/publication/10157

DOI

Digital Object Identifier
Site
http://dx.doi.org/
Object
entity
Example ID
DOI:10.1016/S0963-9969(99)00021-6
URL syntax
http://dx.doi.org/[example_id]
URL example
http://dx.doi.org/10.1016/S0963-9969(99)00021-6

DTU

DTU Health Tech Services
Site
http://www.cbs.dtu.dk/services
Object
entity
Example ID
CBS:TMHMM
URL example
http://www.cbs.dtu.dk/services/TMHMM/

EC

Enzyme Commission
Site
http://enzyme.expasy.org/
Object
catalytic activity
Example ID
EC:1.1.1.1
URL syntax
https://enzyme.expasy.org/EC/[example_id]
URL example
https://enzyme.expasy.org/EC/1.1.1.1
EchoBASE post-genomic database for Escherichia coli
Site
https://www.york.ac.uk/res/thomas/
Object
gene
Example ID
EchoBASE:EB0231
URL syntax
https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=[example_id]
URL example
https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=EB0231

ECK

EcoGene Database of Escherichia coli Sequence and Function
Site
http://www.ecogene.org/
Object
gene
Example ID
ECK:ECK3746
URL syntax
http://www.ecogene.org/geneInfo.php?eck_id=[example_id]
URL example
http://www.ecogene.org/geneInfo.php?eck_id=ECK3746

ECO

Evidence Code Ontology
Site
http://www.evidenceontology.org/
Object
entity
Example ID
ECO:0000315
URL syntax
http://www.evidenceontology.org/browse/#ECO_[example_id]
URL example
http://www.evidenceontology.org/browse/#ECO_0000315
Encyclopedia of E. coli metabolism
Site
http://ecocyc.org/
Object
biological_process
Example ID
EcoCyc:P2-PWY
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
Encyclopedia of E. coli metabolism
Site
http://ecocyc.org/
Object
entity
Example ID
EcoCyc_REF:COLISALII
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
EcoGene Database of Escherichia coli Sequence and Function
Site
http://www.ecogene.org/
Object
gene
Example ID
ECOGENE:EG10818
URL syntax
http://www.ecogene.org/geneInfo.php?eg_id=[example_id]
URL example
http://www.ecogene.org/geneInfo.php?eg_id=EG10818
EcoGene Database of Escherichia coli Sequence and Function
Site
http://www.ecogene.org/
Object
entity
Example ID
ECOGENE_G:deoC
EcoliWiki from EcoliHub
Site
http://ecoliwiki.net/
Object
gene
Mouse gross anatomy and development, abstract
Site
http://emouseatlas.org/
Object
anatomical entity
Example ID
EMAPA:16032
URL syntax
http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:[example_id]
URL example
http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16894
EMBL Nucleotide Sequence Database
Site
http://www.ebi.ac.uk/embl/
Object
gene
Example ID
EMBL:AA816246
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

ENA

European Nucleotide Archive
Site
http://www.ebi.ac.uk/ena/
Object
entity
Example ID
ENA:AA816246
URL syntax
http://www.ebi.ac.uk/ena/data/view/[example_id]
URL example
http://www.ebi.ac.uk/ena/data/view/AA816246
Ensembl database of automatically annotated genomic data
Site
http://www.ensembl.org/
Object
transcript
Example ID
ENSEMBL:ENSP00000265949
URL syntax
http://www.ensembl.org/id/[example_id]
URL example
http://www.ensembl.org/id/ENSP00000265949
Ensembl database of automatically annotated genomic data
Site
http://www.ensembl.org/
Object
gene
Example ID
ENSEMBL_GeneID:ENSG00000126016
URL syntax
http://www.ensembl.org/id/[example_id]
URL example
http://www.ensembl.org/id/ENSG00000126016
Ensembl database of automatically annotated genomic data
Site
http://www.ensembl.org/
Object
protein
Example ID
ENSEMBL_ProteinID:ENSP00000361027
URL syntax
http://www.ensembl.org/id/[example_id]
URL example
http://www.ensembl.org/id/ENSP00000361027
Ensembl database of automatically annotated genomic data
Site
http://www.ensembl.org/
Object
transcript
Example ID
ENSEMBL_TranscriptID:ENST00000371959
URL syntax
http://www.ensembl.org/id/[example_id]
URL example
http://www.ensembl.org/id/ENST00000371959
Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
Site
http://fungi.ensembl.org/
Object
gene
Example ID
EnsemblFungi:YOR197W
URL syntax
http://www.ensemblgenomes.org/id/[example_id]
URL example
http://www.ensemblgenomes.org/id/YOR197W
Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
Site
http://metazoa.ensembl.org/
Object
gene
Example ID
EnsemblMetazoa:FBgn0052693
URL syntax
http://www.ensemblgenomes.org/id/[example_id]
URL example
http://www.ensemblgenomes.org/id/FBgn0052693
Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.
Site
http://plants.ensembl.org/
Object
gene
Example ID
EnsemblPlants:LOC_Os01g22954
URL syntax
http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=[example_id];site=ensemblunit
URL example
http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=ESW29762;site=ensemblunit
Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.
Site
http://plants.ensembl.org/
Object
gene
Example ID
EnsemblPlants:LOC_Os01g22954
URL syntax
http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=[example_id];site=ensemblunit
URL example
http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=ESW29762;site=ensemblunit
Ensembl Protists, the Ensembl database for accessing genome-scale data from protists.
Site
http://protists.ensembl.org/
Object
gene
Example ID
EnsemblProtists:PFL2550w
URL syntax
http://www.ensemblgenomes.org/id/[example_id]
URL example
http://www.ensemblgenomes.org/id/PFL2550w
Swiss Institute of Bioinformatics enzyme database
Site
https://enzyme.expasy.org/
Object
entity
Example ID
1.1.1.1
URL syntax
https://enzyme.expasy.org/EC/[example_id]
URL example
https://enzyme.expasy.org/EC/1.1.1.1
GitHub Issue Tracker for EO
Site
https://github.com/Planteome/plant-environment-ontology
Object
entity
Example ID
EO_GIT:76
URL syntax
https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
URL example
https://github.com/Planteome/plant-environment-ontology/issues/76
The Eukaryotic Pathogen Database
Site
http://eupathdb.org
Object
gene
Example ID
EuPathDB:LtaP17.1490
URL syntax
http://eupathdb.org/gene/[example_id]
URL example
http://eupathdb.org/gene/LtaP17.1490
Eurofungbase community annotation
Site
http://www.eurofung.net/option=com_content&task=section&id=3&Itemid=4
Object
entity

FB

FlyBase
Site
http://flybase.org/
Object
gene
Example ID
FB:FBgn0000024
URL syntax
http://flybase.org/reports/[example_id].html
URL example
http://flybase.org/reports/FBgn0000024.html
FlyBase
Site
http://flybase.org/
Object
gene
Example ID
FB:FBgn0000024
URL syntax
http://flybase.org/reports/[example_id].html
URL example
http://flybase.org/reports/FBgn0000024.html
Drosophila gross anatomy
Site
http://flybase.org/
Object
entity
Example ID
FBbt:00005177
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

FMA

Foundational Model of Anatomy
Site
http://sig.biostr.washington.edu/projects/fm/index.html
Object
entity
Example ID
FMA:61905
Fission Yeast Phenotype Ontology
Site
http://www.pombase.org/
Object
entity
Example ID
FYPO:0000001

GB

GenBank
Site
http://www.ncbi.nlm.nih.gov/Genbank/
Object
protein
Example ID
GB:AA816246
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
GenBank
Site
http://www.ncbi.nlm.nih.gov/Genbank/
Object
protein
Example ID
GB:AA816246
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
Domain Architecture Classification
Site
http://gene3d.biochem.ucl.ac.uk/Gene3D/
Object
entity
Example ID
Gene3D:3.30.390.30
URL syntax
http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=[example_id]
URL example
http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=3.30.390.30
GeneDB
Site
http://www.genedb.org/gene/
Object
gene
Example ID
PF3D7_1467300
URL syntax
http://www.genedb.org/gene/[example_id]
URL example
http://www.genedb.org/gene/PF3D7_1467300
Gene DB, Genesys
Site
https://www.genesys-pgr.org/
Object
entity
Example ID
Genesys-pgr:CM1015-16
URL syntax
https://www.genesys-pgr.org/acn/search?q=[example_id]
URL example
https://www.genesys-pgr.org/acn/search?q=CM1015-16

GEO

NCBI Gene Expression Omnibus
Site
http://www.ncbi.nlm.nih.gov/geo/
Object
entity
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

GO

Gene Ontology Database
Site
http://amigo.geneontology.org/
Object
macromolecular complex
Example ID
GO:0044776
URL syntax
http://amigo.geneontology.org/amigo/term/GO:[example_id]
URL example
http://amigo.geneontology.org/amigo/term/GO:0044776
GO Central
Site
http://www.geneontology.org/GO.refgenome.shtml
Object
entity
GO Noctua
Site
https://github.com/geneontology/noctua-models
Object
entity
Gene Ontology Database references
Site
http://current.geneontology.org/metadata/gorefs/index.html
Object
entity
Example ID
0000001
URL syntax
http://purl.obolibrary.org/obo/go/references/[example_id]
URL example
http://purl.obolibrary.org/obo/go/references/0000001

GOC

Gene Ontology Consortium
Site
http://www.geneontology.org/
Object
entity
Gene Ontology Consortium - Logical inferences
Site
http://www.geneontology.org/
Object
entity
Gene Ontology Causal Activity Model Database
Site
http://www.geneontology.org/gocam
Object
model
Example ID
gomodel:5ae3b0f600001522
URL syntax
http://www.geneontology.org/gocam/[example_id]
URL example
http://www.geneontology.org/gocam/gomodel:5ae3b0f600001522
Gene Ontology Normal Usage Tracking System (GONUTS)
Site
http://gowiki.tamu.edu
Object
entity
Example ID
GONUTS:MOUSE:CD28
URL syntax
https://gowiki.tamu.edu/wiki/index.php/[example_id]
URL example
https://gowiki.tamu.edu/wiki/index.php/MOUSE:CD28
GO Extensions to OBO Relation Ontology Ontology
Site
http://purl.obolibrary.org/obo/ro
Object
entity

GR

Gramene
Site
http://www.gramene.org/
Object
protein
Example ID
GR:sd1
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
Gramene
Site
http://www.gramene.org/
Object
entity
Example ID
GR_Ensembl:At1g10040
URL syntax
http://gramene.org/?idList=[example_id]&field=terms
URL example
http://gramene.org/?idList=At1g10040&field=terms
Gramene
Site
http://www.gramene.org/
Object
entity
Example ID
GR_GENE:GR:0060198
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
A Comparative Mapping Resource for Grains
Site
http://www.gramene.org/
Object
entity
Example ID
GR_MUT:GR:0060198
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
Gramene
Site
http://www.gramene.org/
Object
protein
Example ID
GR_PROTEIN:Q6VSV0
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
Gramene
Site
http://www.gramene.org/
Object
entity
Example ID
GR_QTL:CQU7
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
Gramene
Site
http://www.gramene.org/
Object
entity
Example ID
GR_REF:659
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
IRRI Genetic Resources Information Management System
Site
https://www.genesys-pgr.org
Object
germplasm
Example ID
GRIMS:90637
URL syntax
https://www.genesys-pgr.org/acn/search2?q=IRGC+[example_id]
URL example
https://www.genesys-pgr.org/acn/search2?q=IRGC+90637
IRRI Genetic Resources Information Management System
Site
https://www.genesys-pgr.org
Object
germplasm
Example ID
GRIMS:90637
URL syntax
https://www.genesys-pgr.org/acn/search2?q=IRGC+[example_id]
URL example
https://www.genesys-pgr.org/acn/search2?q=IRGC+90637
Germplasm Resources Information Network
Site
https://www.ars-grin.gov/
Object
germplasm
Example ID
GRIN:1882640
URL syntax
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=[example_id]
URL example
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=1882640
Germplasm Resources Information Network
Site
https://www.ars-grin.gov/
Object
germplasm descriptors
Example ID
GRINdesc:89033
URL syntax
https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=[example_id]
URL example
https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=89033
H-invitational Database
Site
http://www.h-invitational.jp/
Object
entity
H-invitational Database
Site
http://www.h-invitational.jp/
Object
entity
Example ID
H-invDB_cDNA:AK093148
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
H-invitational Database
Site
http://www.h-invitational.jp/
Object
entity
Example ID
H-invDB_locus:HIX0014446
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
High-quality Automated and Manual Annotation of microbial Proteomes
Site
http://hamap.expasy.org/
Object
entity
Example ID
HAMAP:MF_00031
URL syntax
http://hamap.expasy.org/unirule/[example_id]
URL example
http://hamap.expasy.org/unirule/MF_00131
HUGO Gene Nomenclature Committee
Site
http://www.genenames.org/
Object
gene
Example ID
HGNC:29
URL syntax
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:[example_id]
URL example
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:29

HPA

Human Protein Atlas tissue profile information
Site
http://www.proteinatlas.org/
Object
entity
Example ID
HPA:HPA000237
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
Human Protein Atlas antibody information
Site
http://www.proteinatlas.org/
Object
entity
Example ID
HPA_antibody:HPA000237
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
Human Genome Organisation
Site
http://www.hugo-international.org/
Object
entity

IMG

Integrated Microbial Genomes; JGI web site for genome annotation
Site
http://img.jgi.doe.gov
Object
entity
Example ID
IMG:640008772
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
IMGT/HLA human major histocompatibility complex sequence database
Site
http://www.ebi.ac.uk/imgt/hla
Object
entity
Example ID
IMGT_HLA:HLA00031
ImMunoGeneTics database covering immunoglobulins and T-cell receptors
Site
http://www.imgt.org/
Object
entity
Example ID
IMGT_LIGM:U03895
IntAct protein interaction database
Site
https://www.ebi.ac.uk/intact/
Object
protein-containing complex
Example ID
IntAct:EBI-10205244
URL syntax
http://www.ebi.ac.uk/complexportal/complex/[example_id]
URL example
http://www.ebi.ac.uk/complexportal/complex/EBI-10205244

IPR

InterPro database of protein domains and motifs
Site
http://www.ebi.ac.uk/interpro/
Object
polypeptide region
Example ID
InterPro:IPR000001
URL syntax
http://www.ebi.ac.uk/interpro/entry/[example_id]
URL example
http://www.ebi.ac.uk/interpro/entry/IPR015421
InterPro database of protein domains and motifs
Site
http://www.ebi.ac.uk/interpro/
Object
polypeptide region
Example ID
InterPro:IPR000001
URL syntax
http://www.ebi.ac.uk/interpro/entry/[example_id]
URL example
http://www.ebi.ac.uk/interpro/entry/IPR015421
iPTMnet protein post-translational modification database
Site
https://research.bioinformatics.udel.edu/iptmnet/
Object
entity
Example ID
iPTM:P06493
URL syntax
https://research.bioinformatics.udel.edu/iptmnet/entry/[example_id]/
URL example
https://research.bioinformatics.udel.edu/iptmnet/entry/P06493/
International Rice Genebank Collection
Site
https://www.genesys-pgr.org
Object
entity
Example ID
IRGC:10012
URL syntax
https://www.genesys-pgr.org/acn/search?q=IRGC+[example_id]
URL example
https://www.genesys-pgr.org/acn/search?q=IRGC+10013
International Rice Research Institute
Site
https://oryzasnp.org
Object
entity
Example ID
IRIS_313-8922
URL syntax
https://oryzasnp.org/_variety.zul?irisid=[example_id]
URL example
https://oryzasnp.org/_variety.zul?irisid=IRIS_313-8922
International Standard Book Number
Site
https://www.worldcat.org
Object
entity
Example ID
ISBN:0781702534
URL syntax
https://www.worldcat.org/search?q=bn%3A[example_id]
URL example
https://www.worldcat.org/search?q=bn%3A0781702534
International Society for Root Research
Site
http://www.rootresearch.org/
Object
entity
Example ID
ISRR:Richard Zobel
URL syntax
http://wiki.plantontology.org/index.php/ISRR_references
URL example
http://wiki.plantontology.org/index.php/ISRR_references
International Standard Serial Number
Site
http://www.issn.org/
Object
entity
Example ID
ISSN:1234-1231
IUPHAR/BPS Guide to Pharmacology
Site
https://www.guidetopharmacology.org/
Object
entity
International Union of Pharmacology
Site
http://www.iuphar.org/
Object
entity
Example ID
IUPHAR_GPCR:13
URL syntax
https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=[example_id]
URL example
https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=13
International Union of Pharmacology
Site
http://www.iuphar.org/
Object
entity
Example ID
IUPHAR_RECEPTOR:56
URL syntax
https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=[example_id]
URL example
https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=56
Jaiswal_Lab
Site
http://wiki.plantontology.org/index.php/PO_REF:00008
Object
entity
Example ID
Jaiswal_Lab:gene00002
URL syntax
http://wiki.plantontology.org/index.php/PO_REF:00008
URL example
http://wiki.plantontology.org/index.php/PO_REF:00008
J. Craig Venter Institute
Site
http://www.jcvi.org/
Object
entity
J. Craig Venter Institute
Site
http://www.jcvi.org/
Object
entity
EGAD database at the J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
protein
Example ID
JCVI_CMR:VCA0557
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
EGAD database at the J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
protein
Example ID
JCVI_CMR:VCA0557
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
EGAD database at the J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
protein
Example ID
JCVI_CMR:VCA0557
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
JCVI CMR Egad
Site
http://cmr.jcvi.org/
Object
entity
Example ID
JCVI_EGAD:74462
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
Genome Properties database at the J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
biological_process
Example ID
JCVI_GenProp:GenProp0120
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
Genome Properties database at the J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
biological_process
Example ID
JCVI_GenProp:GenProp0120
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
Medicago truncatula genome database at the J. Craig Venter Institute
Site
http://medicago.jcvi.org/cgi-bin/medicago/overview.cgi
Object
entity
Example ID
JCVI_Medtr:Medtr5g024510
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
J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
entity
Example ID
JCVI_REF:GO_ref
URL example
http://cmr.jcvi.org/CMR/AnnotationSops.shtml
J. Craig Venter Institute
Site
http://cmr.jcvi.org/
Object
entity
Example ID
JCVI_REF:GO_ref
URL example
http://cmr.jcvi.org/CMR/AnnotationSops.shtml
TIGRFAMs HMM collection at the J. Craig Venter Institute
Site
http://search.jcvi.org/
Object
polypeptide region
Example ID
JCVI_TIGRFAMS:TIGR00254
URL syntax
http://search.jcvi.org/search?p&q=[example_id]
URL example
http://search.jcvi.org/search?p&q=TIGR00254
Digital archive of scholarly articles
Site
https://www.jstor.org/
Object
entity
Example ID
JSTOR:3093870
URL syntax
https://www.jstor.org/stable/[example_id]
URL example
https://www.jstor.org/stable/3093870
Kyoto Encyclopedia of Genes and Genomes
Site
http://www.genome.ad.jp/kegg/
Object
entity
KEGG Enzyme Database
Site
http://www.genome.jp/dbget-bin/www_bfind?enzyme
Object
entity
Example ID
KEGG_ENZYME:2.1.1.4
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
KEGG LIGAND Database
Site
http://www.genome.ad.jp/kegg/docs/upd_ligand.html
Object
chemical entity
Example ID
KEGG_LIGAND:C00577
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
KEGG Pathways Database
Site
http://www.genome.jp/kegg/pathway.html
Object
entity
Example ID
KEGG_PATHWAY:ot00020
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
KEGG Reaction Database
Site
http://www.genome.jp/kegg/reaction/
Object
entity
Example ID
KEGG:R02328
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
LifeDB
Site
http://www.lifedb.de/
Object
entity
Example ID
LIFEdb:DKFZp564O1716
URL syntax
https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=[example_id]
URL example
https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=DKFZp564O1716
Legume Information System
Site
http://legumeinfo.org/
Object
entity
Example ID
Aradu.WUP1N
URL syntax
https://legumeinfo.org/feature/Arachis/duranensis/gene/[example_id]
URL example
https://legumeinfo.org/feature/Arachis/duranensis/gene/Aradu.WUP1N
Legume Information System
Site
http://legumeinfo.org/
Object
entity
Example ID
Araip.9F2SW
URL syntax
https://legumeinfo.org/feature/Arachis/ipaensis/gene/[example_id]
URL example
https://legumeinfo.org/feature/Arachis/ipaensis/gene/Araip.9F2SW
Legume Information System
Site
http://legumeinfo.org/
Object
entity
Example ID
C.cajan_15730
URL syntax
https://legumeinfo.org/feature/Cajanus/cajan/gene/cajca.ICPL87119.gnm1.ann1.[example_id]
URL example
https://legumeinfo.org/feature/Cajanus/cajan/gene/cajca.ICPL87119.gnm1.ann1.C.cajan_15730

MA

Adult Mouse Anatomical Dictionary
Site
http://www.informatics.jax.org/
Object
entity
Example ID
MA:0000003
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
Maize Genetics and Genomics Database
Site
http://www.maizegdb.org/
Object
entity
Example ID
MACSC_REF:78112
URL syntax
http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=[example_id]
URL example
http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112
MaizeGDB
Site
https://www.maizegdb.org/
Object
entity
Example ID
MaizeGDB:12098
URL syntax
https://maizegdb.org/gene_center/gene/[example_id]
URL example
https://maizegdb.org/gene_center/gene/12098
MaizeGDB
Site
https://www.maizegdb.org/
Object
gene
Example ID
MaizeGDB_Locus:25011
URL syntax
https://www.maizegdb.org/gene_center/gene/[example_id]
URL example
https://www.maizegdb.org/gene_center/gene/25011
Maize Genetics and Genomics Database
Site
https://www.maizegdb.org/
Object
entity
Example ID
MaizeGDB_QTL:78112
URL syntax
https://www.maizegdb.org/data_center/trait?id=[example_id]
URL example
https://www.maizegdb.org/data_center/trait?id=78112
Maize Genetics and Genomics Database
Site
https://www.maizegdb.org/
Object
entity
Example ID
MaizeGDB_REF:9021423
URL syntax
http://maizegdb.org/data_center/reference?id=[example_id]
URL example
http://maizegdb.org/data_center/reference?id=9021423
Maize Genetics and Genomics Database
Site
https://www.maizegdb.org/
Object
entity
Example ID
MaizeGDB_stock:282110
URL syntax
https://maizegdb.org/data_center/stock?id=[example_id]
URL example
https://maizegdb.org/data_center/stock?id=282110
Medline literature database
Site
http://www.nlm.nih.gov/databases/databases_medline.html
Object
entity
Example ID
MEDLINE:20572430
MEROPS peptidase database
Site
https://www.ebi.ac.uk/merops
Object
protein
Example ID
MEROPS:A08.001
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
MEROPS peptidase database
Site
https://www.ebi.ac.uk/merops
Object
entity
Example ID
MEROPS_fam:M18
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

MSH

Medical Subject Headings
Site
https://meshb.nlm.nih.gov
Object
entity
Example ID
MeSH:D017209
URL syntax
http://id.nlm.nih.gov/mesh/[example_id]
URL example
http://id.nlm.nih.gov/mesh/D017209
Medical Subject Headings
Site
https://meshb.nlm.nih.gov
Object
entity
Example ID
MeSH:D017209
URL syntax
http://id.nlm.nih.gov/mesh/[example_id]
URL example
http://id.nlm.nih.gov/mesh/D017209
Metabolic Encyclopedia of metabolic and other pathways
Site
http://metacyc.org/
Object
entity
Example ID
MetaCyc:GLUTDEG-PWY
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
Maize Genetics and Genomics Database
Site
http://www.maizegdb.org
Object
entity
Example ID
MGCSC_GENETIC_STOCKS:78112
URL syntax
http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=[example_id]
URL example
http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112

MGD

Mouse Genome Database
Site
http://www.informatics.jax.org/
Object
entity
Example ID
MGD:Adcy9

MGI

Mouse Genome Informatics
Site
http://www.informatics.jax.org/
Object
variation
Example ID
MGI:MGI:3590672
URL syntax
http://www.informatics.jax.org/accession/[example_id]
URL example
http://www.informatics.jax.org/accession/MGI:3590672
MIPS Functional Catalogue
Site
http://mips.gsf.de/proj/funcatDB/
Object
entity
Example ID
MIPS_funcat:11.02
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
The MITRE Corporation
Site
http://www.mitre.org/
Object
entity
ModBase comprehensive Database of Comparative Protein Structure Models
Site
http://modbase.compbio.ucsf.edu/
Object
entity
Example ID
ModBase:P10815
URL syntax
http://salilab.org/modbase/searchbyid?databaseID=[example_id]
URL example
http://salilab.org/modbase/searchbyid?databaseID=P04848
Nottingham Arabidopsis Stock Centre Seeds Database
Site
http://arabidopsis.info
Object
entity
Example ID
NASC_code:N3371
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
Nottingham Arabidopsis Stock Centre Seeds Database
Site
http://arabidopsis.info
Object
entity
Example ID
NASC_code:N3371
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
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
Site
http://www.chem.qmw.ac.uk/iubmb/
Object
entity
National Center for Biotechnology Information
Site
http://www.ncbi.nlm.nih.gov/
Object
entity
Example ID
NCBI:BAA100446
URL syntax
https://www.ncbi.nlm.nih.gov/protein/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/protein/BAA10446
NCBI databases
Site
http://www.ncbi.nlm.nih.gov/
Object
gene
Example ID
NCBI_gi:113194944
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
NCBI GenPept
Site
http://www.ncbi.nlm.nih.gov/
Object
protein
Example ID
NCBI_GP:EAL72968
URL syntax
https://www.ncbi.nlm.nih.gov/protein/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/protein/EAL72968
NCBI locus tag
Site
http://www.ncbi.nlm.nih.gov/
Object
entity
Example ID
NCBI_locus_tag:CTN_0547
NCBI Gene
Site
http://www.ncbi.nlm.nih.gov/
Object
gene
Example ID
NCBI_Gene:4771
URL syntax
https://www.ncbi.nlm.nih.gov/gene[example_id]
URL example
https://www.ncbi.nlm.nih.gov/gene/4771
NCBI Gene
Site
http://www.ncbi.nlm.nih.gov/
Object
gene
Example ID
NCBI_Gene:4771
URL syntax
https://www.ncbi.nlm.nih.gov/gene[example_id]
URL example
https://www.ncbi.nlm.nih.gov/gene/4771
NCBI Gene
Site
http://www.ncbi.nlm.nih.gov/
Object
gene
Example ID
NCBI_Gene:4771
URL syntax
https://www.ncbi.nlm.nih.gov/gene[example_id]
URL example
https://www.ncbi.nlm.nih.gov/gene/4771
NCBI Gene
Site
http://www.ncbi.nlm.nih.gov/
Object
gene
Example ID
NCBI_Gene:4771
URL syntax
https://www.ncbi.nlm.nih.gov/gene[example_id]
URL example
https://www.ncbi.nlm.nih.gov/gene/4771
Neuroscience Information Framework standard ontology, subcellular hierarchy
Site
http://www.neurolex.org/wiki
Object
entity
Example ID
NIF_Subcellular:sao1186862860
URL syntax
http://www.neurolex.org/wiki/[example_id]
URL example
http://www.neurolex.org/wiki/sao1770195789
National Microbial Pathogen Data Resource
Site
http://www.nmpdr.org
Object
entity
Example ID
NMPDR:fig|306254.1.peg.183
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
Norwegian University of Science and Technology, Systems Biology team
Site
http://www.ntnu.edu/nt/systemsbiology
Object
entity

OBI

Ontology for Biomedical Investigations
Site
http://obi-ontology.org/
Object
entity
Example ID
OBI:0000038
URL example
http://purl.obolibrary.org/obo/OBI_0000038
Source Forge OBO plant-experimental-conditions-ontology (PECO) term request tracker
Site
https://sourceforge.net/p/obo/plant-environment-ontology-eo/
Object
entity
Example ID
OBO_SF2_PECO:89
URL syntax
https://sourceforge.net/p/obo/plant-environment-ontology-eo/[example_id]
URL example
https://sourceforge.net/p/obo/plant-environment-ontology-eo/89/
Source Forge OBO Plant Ontology (PO) term request tracker
Site
https://sourceforge.net/p/obo/plant-ontology-po-term-requests/
Object
entity
Example ID
OBO_SF2_PO:500
URL syntax
http://sourceforge.net/p/obo/plant-ontology-po-term-requests/[example_id]
URL example
http://sourceforge.net/p/obo/plant-ontology-po-term-requests/500
Source Forge OBO Plant Ontology (PO) term request tracker
Site
http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555
Object
entity
Example ID
OBO_SF_PO:3184921
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
Mendelian Inheritance in Man
Site
https://omim.org/
Object
entity
Example ID
OMIM:190198
URL syntax
https://omim.org/entry/[example_id]
URL example
https://omim.org/entry/190198

MIM

Mendelian Inheritance in Man
Site
https://omim.org/
Object
entity
Example ID
OMIM:190198
URL syntax
https://omim.org/entry/[example_id]
URL example
https://omim.org/entry/190198
Open Mass Spectrometry Search Algorithm
Site
http://pubchem.ncbi.nlm.nih.gov/omssa/
Object
entity
Phylogenetic Annotation INference Tool References
Site
http://www.pantherdb.org/
Object
entity
Example ID
PAINT_REF:23266
URL syntax
http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR[example_id]
URL example
http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR23266
Plant-Associated Microbe Gene Ontology Interest Group
Site
http://pamgo.vbi.vt.edu/
Object
entity
Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group
Site
http://agro.vbi.vt.edu/public/
Object
entity
Example ID
PAMGO_GAT:Atu0001
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
Magnaporthe grisea database
Site
http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html
Object
entity
Example ID
PAMGO_MGG:MGG_05132
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
Virginia Bioinformatics Institute Microbial Database
Site
http://phytophthora.vbi.vt.edu
Object
entity
Example ID
PAMGO_VMD:109198
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
Protein ANalysis THrough Evolutionary Relationships Classification System
Site
http://www.pantherdb.org/
Object
protein family
Example ID
PANTHER:PTHR11455
URL syntax
http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]
URL example
http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000
Phenotypic quality ontology
Site
http://www.obofoundry.org/ontology/pato.html
Object
entity
Example ID
PATO:0001420
URL example
http://purl.obolibrary.org/obo/PATO_0001420
PathoSystems Resource Integration Center
Site
https://www.patricbrc.org
Object
entity
Example ID
PATRIC:fig%7C83332.12.peg.11
URL syntax
https://www.patricbrc.org/view/Feature/[example_id]
URL example
https://www.patricbrc.org/view/Feature/fig%7C83332.12.peg.1

PDB

Protein Data Bank
Site
https://www.rcsb.org/pdb/
Object
protein
Example ID
PDB:1A4U
URL syntax
https://www.rcsb.org/structure/[example_id]
URL example
https://www.rcsb.org/structure/1A4U
GitHub Issue Tracker for PECO
Site
https://github.com/Planteome/plant-experimental-conditions-ontology
Object
entity
Example ID
PECO_GIT:76
URL syntax
https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
URL example
https://github.com/Planteome/plant-experimental-conditions-ontology/issues/76
Pfam database of protein families
Site
http://pfam.xfam.org
Object
polypeptide region
Example ID
Pfam:PF00046
URL syntax
http://pfam.xfam.org/family/[example_id]
URL example
http://pfam.xfam.org/family/PF00069
Pharmacogenetics and Pharmacogenomics Knowledge Base
Site
https://www.pharmgkb.org
Object
entity
Example ID
PharmGKB:PA267
URL syntax
https://www.pharmgkb.org/do/serve?objId=[example_id]
URL example
https://www.pharmgkb.org/do/serve?objId=PA267
PhenoScape Knowledgebase
Site
http://phenoscape.org/
Object
entity
Phytozome
Site
https://phytozome.jgi.doe.gov
Object
protein
Example ID
Phytozome:Carubv10001290m
URL syntax
https://phytozome.jgi.doe.gov/pz/portal.html#!results?search=0&crown=1&star=1&method=0&offset=0searchText=[example_id]
URL example
https://phytozome.jgi.doe.gov/pz/portal.html#!results?search=0&crown=1&star=1&method=0&offset=0searchText=Carubv10001290m

PIR

Protein Information Resource
Site
https://proteininformationresource.org/
Object
protein
Example ID
PIR:I49499
URL syntax
https://proteininformationresource.org/cgi-bin/nbrfget?uid=[example_id]
URL example
https://proteininformationresource.org/cgi-bin/nbrfget?uid=I49499
PIR Superfamily Classification System
Site
http://pir.georgetown.edu/pirsf/
Object
entity
Example ID
PIRSF:SF002327
URL syntax
http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]
URL example
http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327
Generic planteome genes without homes
Site
http://www.google.com
Object
entity
Example ID
Planteome_gene:AC148152.3_FGT008
URL syntax
http://planteome.org/planteome_dbxrefs
URL example
http://planteome.org/planteome_dbxrefs
PlantSystematics.org
Site
http://plantsystematics.org
Object
entity
Example ID
PlantSystematics_image_archivee:37658
URL syntax
http://www.plantsystematics.org/imagebyid_[example_id].html
URL example
http://www.plantsystematics.org/imagebyid_37658.html

PMC

Pubmed Central
Site
https://www.ncbi.nlm.nih.gov/pmc/
Object
entity
Example ID
PMCID:PMC201377
URL syntax
https://www.ncbi.nlm.nih.gov/pmc/articles/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC201377/
Pubmed Central
Site
https://www.ncbi.nlm.nih.gov/pmc/
Object
entity
Example ID
PMCID:PMC201377
URL syntax
https://www.ncbi.nlm.nih.gov/pmc/articles/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC201377/
PubMed
Site
https://www.ncbi.nlm.nih.gov/pubmed
Object
entity
Example ID
PMID:31931324
URL syntax
http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/pubmed/31931324
PubMed
Site
https://www.ncbi.nlm.nih.gov/pubmed
Object
entity
Example ID
PMID:31931324
URL syntax
http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/pubmed/31931324

PO

Plant Ontology
Site
http://www.planteome.org/
Object
plant structure development stage
Example ID
PO:0025131
URL syntax
http://browser.planteome.org/amigo/term/PO:[example_id]
URL example
http://browser.planteome.org/amigo/term/PO:0025131
GitHub Issue Tracker for PO
Site
https://github.com/Planteome/plant-ontology
Object
entity
Example ID
PO_GIT:626
URL syntax
https://github.com/Planteome/plant-ontology/issues/[example_id]
URL example
https://github.com/Planteome/plant-ontology/issues/626
Plant Ontology custom references
Site
http://planteome.org/po_ref
Object
entity
Example ID
PO_REF:00001
URL syntax
http://planteome.org/po_ref/[example_id]
URL example
http://planteome.org/po_ref/00001

POC

Plant Ontology Consortium
Site
http://www.plantontology.org/
Object
entity
PomBase
Site
https://www.pombase.org/
Object
gene
Example ID
PomBase:SPBC11B10.09
URL syntax
https://www.pombase.org/gene/[example_id]
URL example
https://www.pombase.org/gene/SPBC11B10.09
Schizosaccharomyces pombe protein data
Site
https://www.pombase.org/downloads/protein-datasets
Object
entity
Example ID
Pompep:SPAC890.04C

PPI

Pseudomonas syringae community annotation project
Site
http://www.pseudomonas-syringae.org/
Object
entity

PRO

Protein Ontology
Site
https://proconsortium.org/
Object
protein
Example ID
PR:Q64445
URL syntax
https://proconsortium.org/app/entry/PR_[example_id]
URL example
https://proconsortium.org/app/entry/PR_Q64445

PR

Protein Ontology
Site
https://proconsortium.org/
Object
protein
Example ID
PR:Q64445
URL syntax
https://proconsortium.org/app/entry/PR_[example_id]
URL example
https://proconsortium.org/app/entry/PR_Q64445
PRINTS compendium of protein fingerprints
Site
http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
Object
polypeptide region
Example ID
PRINTS:PR00025
URL syntax
http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=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®expr=off&prints_accn=PR0002
ProDom protein domain families
Site
http://prodom.prabi.fr/prodom/current/html/home.php
Object
entity
Example ID
ProDom:PD000001
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
Prosite database of protein families and domains
Site
https://prosite.expasy.org/
Object
polypeptide region
Example ID
PDOC00314
URL syntax
https://prosite.expasy.org/[example_id]
URL example
https://prosite.expasy.org/PDOC00314
DDBJ / ENA / GenBank
Site
http://www.ddbj.nig.ac.jp/
Object
protein
Example ID
protein_id:CAA71991
Pseudomonas Genome Project
Site
http://www.pseudomonas.com
Object
entity
Example ID
PseudoCAP:PA4756
URL syntax
http://www.pseudomonas.com/feature/show?locus_tag=[example_id]
URL example
http://www.pseudomonas.com/feature/show?locus_tag=PA4756

MI

Proteomic Standard Initiative for Molecular Interaction
Site
http://www.psidev.info/
Object
entity
Example ID
MI_0018
URL syntax
http://purl.obolibrary.org/obo/
URL example
http://purl.obolibrary.org/obo/MI_0018
Proteomic Standard Initiative for Molecular Interaction
Site
http://www.psidev.info/
Object
entity
Example ID
MI_0018
URL syntax
http://purl.obolibrary.org/obo/
URL example
http://purl.obolibrary.org/obo/MI_0018

MOD

Proteomics Standards Initiative protein modification ontology
Site
http://www.psidev.info/groups/protein-modifications
Object
entity
Example ID
MOD_00219
URL syntax
http://purl.obolibrary.org/obo/[example_id]
URL example
http://purl.obolibrary.org/obo/MOD_00219
Proteomics Standards Initiative protein modification ontology
Site
http://www.psidev.info/groups/protein-modifications
Object
entity
Example ID
MOD_00219
URL syntax
http://purl.obolibrary.org/obo/[example_id]
URL example
http://purl.obolibrary.org/obo/MOD_00219
GitHub Issue Tracker for PSO
Site
https://github.com/Planteome/plant-stress-ontology
Object
entity
Example ID
PSO_GIT:169
URL syntax
https://github.com/Planteome/plant-stress-ontology/issues/[example_id]
URL example
https://github.com/Planteome/plant-stress-ontology/issues/169
PSORT protein subcellular localization databases and prediction tools for bacteria
Site
https://www.psort.org/
Object
entity
NCBI PubChem database of bioassay records
Site
https://pubchem.ncbi.nlm.nih.gov
Object
entity
Example ID
PubChem_BioAssay:177
URL syntax
https://pubchem.ncbi.nlm.nih.gov/bioassay/[example_id]
URL example
https://pubchem.ncbi.nlm.nih.gov/bioassay/177
NCBI PubChem database of chemical structures
Site
https://pubchem.ncbi.nlm.nih.gov
Object
chemical entity
Example ID
PubChem_Compound:159296
URL syntax
https://pubchem.ncbi.nlm.nih.gov/compound/[example_id]
URL example
https://pubchem.ncbi.nlm.nih.gov/compound/159296
NCBI PubChem database of chemical substances
Site
https://pubchem.ncbi.nlm.nih.gov
Object
chemical entity
Example ID
PubChem_Substance:4594
URL syntax
https://pubchem.ncbi.nlm.nih.gov/substance/[example_id]
URL example
https://pubchem.ncbi.nlm.nih.gov/substance/4594
Rice annotation Project database
Site
https://rapdb.dna.affrc.go.jp
Object
entity
Example ID
RAP-DB:Os01t0100600-01
URL syntax
https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=[example_id]
URL example
https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=Os01t0100600-01
Reactome - a curated knowledgebase of biological pathways
Site
https://www.reactome.org/
Object
entity
Example ID
Reactome:R-HSA-109582
URL syntax
https://www.reactome.org/content/detail/[example_id]
URL example
https://www.reactome.org/content/detail/R-HSA-109582
Reactome - a curated knowledgebase of biological pathways
Site
https://www.reactome.org/
Object
entity
Example ID
Reactome:R-HSA-109582
URL syntax
https://www.reactome.org/content/detail/[example_id]
URL example
https://www.reactome.org/content/detail/R-HSA-109582
REBASE restriction enzyme database
Site
http://rebase.neb.com/rebase/rebase.html
Object
entity
Example ID
REBASE:EcoRI
URL syntax
http://rebase.neb.com/rebase/enz/[example_id].html
URL example
http://rebase.neb.com/rebase/enz/EcoRI.html
GO Reference Genomes
Site
http://www.geneontology.org/GO.refgenome.shtml
Object
entity
RefSeq
Site
http://www.ncbi.nlm.nih.gov/RefSeq/
Object
protein
Example ID
RefSeq:XP_001068954
URL syntax
https://www.ncbi.nlm.nih.gov/protein/[example_id]
URL example
https://www.ncbi.nlm.nih.gov/protein/NP_001121125
RESID Database of Protein Modifications
Site
https://proteininformationresource.org/resid/resid.shtml
Object
entity
Example ID
RESID:AA0062
URL syntax
https://proteininformationresource.org/cgi-bin/resid?id=[example_id]
URL example
https://proteininformationresource.org/cgi-bin/resid?id=AA0062
Rfam database of RNA families
Site
https://rfam.org
Object
entity
Example ID
Rfam:RF00012
URL syntax
https://rfam.org/family/[example_id]
URL example
https://rfam.org/family/RF00012

RGD

Rat Genome Database
Site
https://rgd.mcw.edu/
Object
gene
Example ID
RGD:2004
URL syntax
https://rgd.mcw.edu/rgdweb/search/search.html?[example_id]
URL example
https://rgd.mcw.edu/rgdweb/search/search.html?term=2004

RAD

Rat Genome Database
Site
https://rgd.mcw.edu/
Object
gene
Example ID
RGD:2004
URL syntax
https://rgd.mcw.edu/rgdweb/search/search.html?[example_id]
URL example
https://rgd.mcw.edu/rgdweb/search/search.html?term=2004
Rat Genome Database
Site
https://rgd.mcw.edu/
Object
gene
Example ID
RGD:2004
URL syntax
https://rgd.mcw.edu/rgdweb/search/search.html?[example_id]
URL example
https://rgd.mcw.edu/rgdweb/search/search.html?term=2004
Rhea, the Annotated Reactions Database
Site
http://www.rhea-db.org
Object
entity
Example ID
RHEA:25811
URL syntax
http://www.rhea-db.org/reaction.xhtml?id=[example_id]
URL example
http://www.rhea-db.org/reaction.xhtml?id=25811
Rice Knowledge Bank
Site
http://www.ncbi.nlm.nih.gov/PubMed/
Object
entity
Example ID
RiceSES:bakanae-diseases-bak
URL syntax
http://www.knowledgebank.irri.org/extension/crop-damage-diseases/[example_id].html
URL example
http://www.knowledgebank.irri.org/extension/crop-damage-diseases/bakanae-diseases-bak.html
RNAcentral
Site
https://rnacentral.org
Object
ribonucleic acid
Example ID
RNAcentral:URS000047C79B_9606
URL syntax
https://rnacentral.org/rna/[example_id]
URL example
https://rnacentral.org/rna/URS000047C79B_9606
RNA Modification Database
Site
https://mods.rna.albany.edu/
Object
entity
Example ID
RNAmods:20
URL syntax
https://mods.rna.albany.edu/mods/modifications/view/[example_id]
URL example
https://mods.rna.albany.edu/mods/modifications/view/20
RNA Modification Database
Site
https://mods.rna.albany.edu/
Object
entity
Example ID
RNAmods:20
URL syntax
https://mods.rna.albany.edu/mods/modifications/view/[example_id]
URL example
https://mods.rna.albany.edu/mods/modifications/view/20

RO

OBO Relation Ontology Ontology
Site
http://purl.obolibrary.org/obo/ro
Object
entity
Example ID
RO:0002211
URL syntax
http://purl.obolibrary.org/obo/RO_[example_id]
URL example
http://purl.obolibrary.org/obo/RO_0002211
SABIO Reaction Kinetics
Site
http://sabio.villa-bosch.de/
Object
entity
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
Wellcome Trust Sanger Institute
Site
http://www.sanger.ac.uk/
Object
entity
The SEED;
Site
http://www.theseed.org
Object
entity
Example ID
SEED:fig|83331.1.peg.1
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
Saccharomyces Genome Database
Site
http://www.yeastgenome.org/
Object
gene
Example ID
SGD:S000006169
URL syntax
https://www.yeastgenome.org/locus/[example_id]
URL example
https://www.yeastgenome.org/locus/S000006169

SGD

Saccharomyces Genome Database
Site
http://www.yeastgenome.org/
Object
gene
Example ID
SGD:S000006169
URL syntax
https://www.yeastgenome.org/locus/[example_id]
URL example
https://www.yeastgenome.org/locus/S000006169
Saccharomyces Genome Database
Site
http://www.yeastgenome.org/
Object
entity
Example ID
SGD_LOCUS:GAL4
URL syntax
http://www.yeastgenome.org/locus/[example_id]/overview
URL example
http://www.yeastgenome.org/locus/S000006169/overview
Saccharomyces Genome Database
Site
http://www.yeastgenome.org/
Object
entity
Example ID
SGD_REF:S000049602
URL syntax
http://www.yeastgenome.org/reference/[example_id]/overview
URL example
http://www.yeastgenome.org/reference/S000049602/overview

SGN

Sol Genomics Network
Site
https://www.sgn.cornell.edu/
Object
gene
Example ID
SGN_gene:7740
URL syntax
http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id]
URL example
http://solgenomics.net/phenome/locus_display.pl?locus_id=7740
Sol Genomics Network
Site
https://www.sgn.cornell.edu/
Object
gene
Example ID
SGN_gene:7740
URL syntax
http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id]
URL example
http://solgenomics.net/phenome/locus_display.pl?locus_id=7740
Sol Genomics Network
Site
https://solgenomics.net/
Object
entity
Example ID
SGN_germplasm:6583
URL syntax
http://solgenomics.net/stock/[example_id]/view/
URL example
http://solgenomics.net/stock/6583/view/
Sol Genomics Network
Site
https://www.sgn.cornell.edu/
Object
entity
Example ID
SGN_ref:861
URL syntax
https://sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]
URL example
https://sgn.cornell.edu/chado/publication.pl?pub_id=861
Simple Modular Architecture Research Tool
Site
http://smart.embl-heidelberg.de/
Object
polypeptide region
Example ID
SMART:SM00005
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

SO

Sequence Ontology
Site
http://www.sequenceontology.org/
Object
sequence feature
Example ID
SO:0000195
URL syntax
http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]
URL example
http://www.sequenceontology.org/browser/current_svn/term/SO:0001850
SoyBase
Site
https://soybase.org/
Object
gene
Example ID
Glyma18g02210
URL syntax
https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=[example_id]
URL example
https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=Glyma18g02210
SoyBase
Site
https://soybase.org/
Object
entity
Example ID
Seedling, abnormal+1-1
URL syntax
https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=[example_id]
URL example
https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Seedling,+abnormal+1-1
SoyBase
Site
https://soybase.org/
Object
entity
Example ID
SOY ref:SoyBase6597900
URL syntax
https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=[example_id]
URL example
https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=SoyBase3142000126
SUPERFAMILY protein annotation database
Site
http://supfam.org/
Object
entity
Example ID
SUPERFAMILY:56994
URL syntax
http://supfam.org/scop/[example_id]
URL example
http://supfam.org/scop/56994
ExPASY Bioinformatics Resource Portal
Site
http://ca.expasy.org
Object
entity
Example ID
SWALL:12345
URL syntax
http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=[example_id]
URL example
http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=12345
Swiss-Prot protein database.
Site
http://ca.expasy.org/sprot/
Object
entity
Example ID
Swiss-Prot:P45867
URL syntax
http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=[example_id]
URL example
http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=P45867
The Synapse Gene Ontology and Annotation Initiative
Site
https://www.syngoportal.org/
Object
entity
Syscilia
Site
http://syscilia.org/
Object
entity
The Arabidopsis Information Resource
Site
http://www.arabidopsis.org/
Object
primary transcript
Example ID
TAIR:locus:2146653
URL syntax
http://arabidopsis.org/servlets/TairObject?accession=[example_id]
URL example
http://arabidopsis.org/servlets/TairObject?accession=locus:2146653
NCBI Taxonomy
Site
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Object
entity
Example ID
taxon:7227
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
NCBI Taxonomy
Site
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Object
entity
Example ID
taxon:7227
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
NCBI Taxonomy
Site
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Object
entity
Example ID
taxon:7227
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

TC

Transport Protein Database
Site
http://www.tcdb.org/
Object
protein
Example ID
TC:9.A.4.1.1
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
TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains
Site
http://tfclass.bioinf.med.uni-goettingen.de/
Object
protein
Example ID
TFCLASS_FAMILY:2.1.1
URL syntax
http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id]
URL example
http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1
TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains
Site
http://tfclass.bioinf.med.uni-goettingen.de/
Object
protein
Example ID
TFCLASS_FAMILY:2.1.1
URL syntax
http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id]
URL example
http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1

TGD

Tetrahymena Genome Database
Site
http://www.ciliate.org/
Object
entity
Tetrahymena Genome Database
Site
http://www.ciliate.org/
Object
entity
Example ID
TGD_LOCUS:PDD1
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
Tetrahymena Genome Database
Site
http://www.ciliate.org/
Object
entity
Example ID
TGD_REF:T000005818
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
TIGRFAMs HMM collection at the J. Craig Venter Institute
Site
http://tigrfams.jcvi.org/cgi-bin/index.cgi
Object
polypeptide region
Example ID
TIGRFAMS:TIGR00254
URL syntax
http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=[example_id]
URL example
http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=TIGR00254
TIGRFAMs HMM collection at the J. Craig Venter Institute
Site
http://tigrfams.jcvi.org/cgi-bin/index.cgi
Object
polypeptide region
Example ID
TIGRFAMS:TIGR00254
URL syntax
http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=[example_id]
URL example
http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=TIGR00254
GitHub Issue Tracker for TO
Site
https://github.com/Planteome/plant-trait-ontology
Object
entity
Example ID
TO_GIT:381
URL syntax
https://github.com/Planteome/plant-trait-ontology/issues/[example_id]
URL example
https://github.com/Planteome/plant-trait-ontology/issues/381

TR

TREMBL
Site
http://www.ebi.ac.uk/swissprot/
Object
entity
Example ID
TrEMBL:Q00177
URL syntax
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]]
URL example
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:Q00177]
TREMBL
Site
http://www.ebi.ac.uk/swissprot/
Object
entity
Example ID
TrEMBL:Q00177
URL syntax
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]]
URL example
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:Q00177]
TREMBL
Site
http://www.ebi.ac.uk/swissprot/
Object
entity
Example ID
TrEMBL:Q00177
URL syntax
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]]
URL example
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:Q00177]
TRANSFAC database of eukaryotic transcription factors
Site
http://www.gene-regulation.com/pub/databases.html#transfac
Object
entity
Forest Tree Genome Database
Site
http://dendrome.ucdavis.edu/treegenes/
Object
entity
Example ID
TreeGenes:254
URL syntax
http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=[example_id]
URL example
http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254
Uber-anatomy ontology
Site
http://uberon.org
Object
life cycle stage
Example ID
UBERON:0000069
URL syntax
http://purl.obolibrary.org/obo/UBERON_[example_id]
EAWAG Biocatalysis/Biodegradation Database
Site
http://eawag-bbd.ethz.ch/
Object
entity
EAWAG Biocatalysis/Biodegradation Database
Site
http://eawag-bbd.ethz.ch/
Object
entity
Example ID
UM-BBD_enzymeID:e0413
URL syntax
http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=[example_id]
URL example
http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=e0230
EAWAG Biocatalysis/Biodegradation Database
Site
http://eawag-bbd.ethz.ch/
Object
entity
Example ID
UM-BBD_pathwayID:acr
URL syntax
http://eawag-bbd.ethz.ch/[example_id]/[example_id]_map.html
URL example
http://eawag-bbd.ethz.ch/acr/acr_map.html
EAWAG Biocatalysis/Biodegradation Database
Site
http://eawag-bbd.ethz.ch/
Object
entity
Example ID
UM-BBD_reactionID:r0129
URL syntax
http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=[example_id]
URL example
http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0129
EAWAG Biocatalysis/Biodegradation Database
Site
http://eawag-bbd.ethz.ch/
Object
entity
Example ID
UM-BBD_ruleID:bt0330
URL syntax
http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=[example_id]
URL example
http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=bt0330
UniGene
Site
http://www.ncbi.nlm.nih.gov/UniGene
Object
entity
Example ID
UniGene:Hs.212293
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
UniProt Archive
Site
https://www.uniprot.org/uniparc/
Object
entity
Example ID
UniParc:UPI000000000A
URL syntax
https://www.uniprot.org/uniparc/[example_id]
URL example
https://www.uniprot.org/uniparc/UPI000000000A
UniPathway
Site
http://www.grenoble.prabi.fr/obiwarehouse/unipathway
Object
biological_process
Example ID
UniPathway:UPA00155
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
Universal Protein Knowledgebase
Site
http://www.uniprot.org
Object
protein
Example ID
UniProtKB:P51587
URL syntax
https://www.uniprot.org/uniprot/[example_id]
URL example
https://www.uniprot.org/uniprot/
UniProt Knowledgebase keywords
Site
http://www.uniprot.org/keywords/
Object
entity
Example ID
UniProtKB-KW:KW-0812
URL syntax
https://www.uniprot.org/keywords/[example_id]
URL example
https://www.uniprot.org/keywords/KW-0812
UniProt Knowledgebase keywords
Site
http://www.uniprot.org/keywords/
Object
entity
Example ID
UniProtKB-KW:KW-0812
URL syntax
https://www.uniprot.org/keywords/[example_id]
URL example
https://www.uniprot.org/keywords/KW-0812
UniProt Knowledgebase Subcellular Location vocabulary
Site
https://www.uniprot.org/locations/
Object
entity
Example ID
UniProtKB-SubCell:SL-0012
URL syntax
http://www.uniprot.org/locations/[example_id]
URL example
http://www.uniprot.org/locations/SL-0012
UniProt Knowledgebase Subcellular Location vocabulary
Site
https://www.uniprot.org/locations/
Object
entity
Example ID
UniProtKB-SubCell:SL-0012
URL syntax
http://www.uniprot.org/locations/[example_id]
URL example
http://www.uniprot.org/locations/SL-0012
Manually curated rules for automatic annotation of UniProtKB unreviewed entries
Site
https://www.uniprot.org/unirule/
Object
entity
Example ID
UniRule:UR000107224
URL syntax
https://www.uniprot.org/unirule/[example_id]
URL example
https://www.uniprot.org/unirule/UR000107224
Viral Bioinformatics Resource Center
Site
http://vbrc.org
Object
entity
Example ID
VBRC:F35742
URL syntax
http://vbrc.org/query.asp?web_id=VBRC:[example_id]
URL example
http://vbrc.org/query.asp?web_id=VBRC:F35742

VMD

Virginia Bioinformatics Institute Microbial Database
Site
http://phytophthora.vbi.vt.edu
Object
entity
Example ID
VMD:109198
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

VZ

ViralZone
Site
http://viralzone.expasy.org/
Object
entity
Example ID
VZ:957
URL syntax
http://viralzone.expasy.org/all_by_protein/[example_id].html
URL example
http://viralzone.expasy.org/all_by_protein/957.html
WormBase database of nematode biology
Site
http://www.wormbase.org/
Object
protein
Example ID
WB:CE00274
URL syntax
http://www.wormbase.org/get?name=[example_id]
URL example
http://www.wormbase.org/get?name=CE00274

WB

WormBase database of nematode biology
Site
http://www.wormbase.org/
Object
protein
Example ID
WB:CE00274
URL syntax
http://www.wormbase.org/get?name=[example_id]
URL example
http://www.wormbase.org/get?name=CE00274
WormBase database of nematode biology
Site
http://www.wormbase.org/
Object
entity
Example ID
WB_REF:WBPaper00004823
URL syntax
http://www.wormbase.org/get?name=[example_id]
URL example
http://www.wormbase.org/get?name=WBPaper00004823
C. elegans gross anatomy
Site
http://www.wormbase.org/
Object
metazoan anatomical entity
Example ID
WBbt:0005733
URL syntax
http://www.wormbase.org/get?name=[example_id]
URL example
http://www.wormbase.org/get?name=WBbt:0005733
C. elegans development
Site
http://www.wormbase.org/
Object
nematoda life stage
Example ID
WBls:0000010
URL syntax
http://www.wormbase.org/get?name=[example_id]
URL example
http://www.wormbase.org/get?name=WBls:0000010
WormBase phenotype ontology
Site
http://www.wormbase.org/
Object
quality
Example ID
WBPhenotype:0002117
URL syntax
http://www.wormbase.org/get?name=[example_id]
URL example
http://www.wormbase.org/get?name=WBPhenotype:0002117
Wikipedia
Site
http://en.wikipedia.org/
Object
entity
Example ID
Wikipedia:Endoplasmic_reticulum
URL syntax
http://en.wikipedia.org/wiki/[example_id]
URL example
http://en.wikipedia.org/wiki/Endoplasmic_reticulum
Xenbase
Site
http://www.xenbase.org/
Object
strain
Example ID
Xenbase:XB-LINE-1248
URL syntax
http://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue=[example_id]
URL example
http://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue=XB-LINE-1248
Yeast Function
Site
http://func.med.harvard.edu/yeast/
Object
entity
Zebrafish Information Network
Site
http://zfin.org/
Object
variation
Example ID
ZDB-GENE-990415-103
URL syntax
http://zfin.org/[example_id]
URL example
http://zfin.org/ZDB-GENE-990415-103