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# Metadata on databases and database prefixes of relevances to the GOC
# See the README.md in this directory for more details.
#
- database: AgBase
name: AgBase resource for functional analysis of agricultural plant and animal gene products
generic_urls:
- http://www.agbase.msstate.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=[example_id]
- database: AGI_LocusCode
name: Arabidopsis Genome Initiative
description: Comprises TAIR, TIGR and MIPS
generic_urls:
- http://www.arabidopsis.org
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})?
url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]
example_id: AGI_LocusCode:At2g17950
example_url: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950
- database: AGRICOLA_ID
name: AGRICultural OnLine Access
generic_urls:
- http://agricola.nal.usda.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: AGRICOLA_NAL:TP248.2 P76 v.14
- database: AGRICOLA_IND
name: AGRICultural OnLine Access
generic_urls:
- http://agricola.nal.usda.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: AGRICOLA_IND:IND23252955
- database: Alzheimers_University_of_Toronto
name: Alzheimers Project at University of Toronto
generic_urls:
- http://www.ims.utoronto.ca/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: ApiDB_PlasmoDB
name: PlasmoDB Plasmodium Genome Resource
generic_urls:
- http://plasmodb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.plasmodb.org/gene/[example_id]
example_id: ApiDB_PlasmoDB:PF11_0344
example_url: http://www.plasmodb.org/gene/PF11_0344
- database: APSNET
name: APSNET Common Names of Plant Diseases
generic_urls:
- http://www.mobot.org/mobot/research/apweb/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.apsnet.org/publications/commonnames/Pages/[example_id].aspx
example_id: APSNET:AfricanDaisy
example_url: http://www.apsnet.org/publications/commonnames/Pages/AfricanDaisy.aspx
- database: APweb
name: Angiosperm Phylogeny Website
generic_urls:
- http://www.mobot.org/mobot/research/apweb/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
example_id: APweb:Glossary
example_url: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
- database: AraCyc
name: AraCyc metabolic pathway database for Arabidopsis thaliana
generic_urls:
- http://www.arabidopsis.org/biocyc/index.jsp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=[example_id]
example_id: AraCyc:PWYQT-62
example_url: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=PWYQT-62
- database: ARUK-UCL
name: Alzheimers Research Gene Ontology Initiative
generic_urls:
- http://www.ucl.ac.uk/functional-gene-annotation/neurological
entity_types:
- type_name: entity
type_id: BET:0000000
- database: ASAP
name: A Systematic Annotation Package for Community Analysis of Genomes
generic_urls:
- https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=[example_id]
example_id: ASAP:ABE-0000008
example_url: https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=ABE-0000008
- database: AspGD
name: Aspergillus Genome Database
synonyms:
- ASPGD
- AspGDID
generic_urls:
- http://www.aspergillusgenome.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ASPL[0-9]{10}
url_syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]
example_id: AspGD:ASPL0000067538
example_url: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538
- database: AspGD_LOCUS
name: Aspergillus Genome Database
rdf_uri_prefix: http://identifiers.org/aspgd.locus/
generic_urls:
- http://www.aspergillusgenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]
example_id: AspGD_LOCUS:AN10942
example_url: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942
- database: AspGD_REF
name: Aspergillus Genome Database
generic_urls:
- http://www.aspergillusgenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
example_id: AspGD_REF:90
example_url: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90
- database: BFO
name: Basic Formal Ontology
description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)
rdf_uri_prefix: http://purl.obolibrary.org/obo/BFO_
generic_urls:
- http://purl.obolibrary.org/obo/bfo
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/BFO_[example_id]
example_id: BFO:0000066
example_url: http://purl.obolibrary.org/obo/BFO_0000066
- database: BHF-UCL
name: Cardiovascular Gene Ontology Annotation Initiative
description: The Cardiovascular Gene Ontology Annotation Initiative is supported by the British Heart Foundation (BHF) and located at University College London (UCL).
generic_urls:
- http://www.ucl.ac.uk/cardiovasculargeneontology/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: BioCyc
name: BioCyc collection of metabolic pathway databases
generic_urls:
- http://biocyc.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]
example_id: BioCyc:PWY-5271
example_url: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271
- database: BIOMD
name: BioModels Database
synonyms:
- BIOMDID
generic_urls:
- http://www.ebi.ac.uk/biomodels/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=[example_id]
example_id: BIOMD:BIOMD0000000045
example_url: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIOMD0000000045
- database: bioPIXIE_MEFIT
name: biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology
generic_urls:
- http://avis.princeton.edu/mefit/
- http://pixie.princeton.edu/pixie/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: BIOSIS
name: BIOSIS previews
generic_urls:
- http://www.biosis.org/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: BIOSIS:200200247281
- database: BRENDA
name: BRENDA, The Comprehensive Enzyme Information System
generic_urls:
- http://www.brenda-enzymes.info
entity_types:
- type_name: catalytic activity
type_id: GO:0003824
url_syntax: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=[example_id]
example_id: BRENDA:4.2.1.3
example_url: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3
- database: BTO
name: BRENDA tissue / enzyme ontology
description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
rdf_uri_prefix: http://purl.obolibrary.org/obo/BTO_
generic_urls:
- http://purl.obolibrary.org/obo/bto
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/BTO_[example_id]
example_id: BTO_0002164
example_url: http://purl.obolibrary.org/obo/BTO_0002164
- database: Broad
name: Broad Institute
generic_urls:
- http://www.broad.mit.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: Broad_MGG
name: Magnaporthe grisea Database
description: Magnaporthe grisea Database at the Broad Institute
generic_urls:
- http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S[example_id]
example_id: Broad_MGG:MGG_05132.5
example_url: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=SMGG_05132
- database: Broad_NEUROSPORA
name: Neurospora crassa Database
description: Neurospora crassa database at the Broad Institute
generic_urls:
- http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S[example_id]
example_id: BROAD_NEUROSPORA:7000007580576824
example_url: http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000007580576824
- database: CACAO
name: Community Assessment of Community Annotation with Ontologies
description: The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.
generic_urls:
- http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://gowiki.tamu.edu/wiki/index.php/[example_id]
example_id: MYCS2:A0QNF5
example_url: http://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5
- database: CAFA
name: Critical Assessment of Protein Function Annotation
generic_urls:
- http://biofunctionprediction.org/cafa/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: CAS
name: CAS Chemical Registry
description: CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s.
rdf_uri_prefix: http://identifiers.org/cas/
generic_urls:
- http://www.cas.org/expertise/cascontent/registry/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CAS:58-08-2
- database: CASGEN
name: Catalog of Fishes genus database
synonyms:
- CAS_GEN
generic_urls:
- http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=[example_id]
example_id: CASGEN:1040
example_url: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=1040
- database: CASREF
name: Catalog of Fishes publications database
generic_urls:
- http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]
example_id: CASREF:2031
example_url: http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031
- database: CASSPC
name: Catalog of Fishes species database
synonyms:
- CAS_SPC
generic_urls:
- http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=[example_id]
example_url: http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979
- database: CAZY
name: Carbohydrate Active EnZYmes
description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
generic_urls:
- http://www.cazy.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: (CE|GH|GT|PL)\d+
url_syntax: http://www.cazy.org/[example_id].html
example_id: CAZY:PL11
example_url: http://www.cazy.org/PL11.html
- database: CBS
name: Center for Biological Sequence Analysis
generic_urls:
- http://www.cbs.dtu.dk/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CBS:TMHMM
example_url: http://www.cbs.dtu.dk/services/[example_id]/
- database: CDD
name: Conserved Domain Database at NCBI
generic_urls:
- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id]
example_id: CDD:34222
example_url: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222
- database: CGD
name: Candida Genome Database
synonyms:
- CGDID
rdf_uri_prefix: http://identifiers.org/cgd/
generic_urls:
- http://www.candidagenome.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: (CAL|CAF)[0-9]{10}
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
example_id: CGD:CAL0000179664
example_url: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664
- database: CGD_LOCUS
name: Candida Genome Database
generic_urls:
- http://www.candidagenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id]
example_id: CGD_LOCUS:HWP1
example_url: http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1
- database: CGD_REF
name: Candida Genome Database
generic_urls:
- http://www.candidagenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
example_id: CGD_REF:1490
example_url: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490
- database: CGEN
name: Compugen Gene Ontology Gene Association Data
generic_urls:
- http://www.cgen.com/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CGEN:PrID131022
- database: CGSC
name: CGSC
generic_urls:
- http://cgsc.biology.yale.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CGSC:rbsK
example_url: http://cgsc.biology.yale.edu/Site.php?ID=315
- database: CHEBI
name: Chemical Entities of Biological Interest
synonyms:
- ChEBI
rdf_uri_prefix: http://purl.obolibrary.org/obo/CHEBI_
generic_urls:
- http://www.ebi.ac.uk/chebi/
entity_types:
- type_name: chemical entity
type_id: CHEBI:24431
id_syntax: '[0-9]{1,6}'
url_syntax: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id]
example_id: CHEBI:17234
example_url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234
- database: CL
name: Cell Type Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/CL_
generic_urls:
- http://cellontology.org
entity_types:
- type_name: cell
type_id: GO:0005623
id_syntax: '[0-9]{7}'
url_syntax: http://purl.obolibrary.org/obo/CL_[example_id]
example_id: CL:0000041
example_url: http://purl.obolibrary.org/obo/CL_0000041
- database: CO_125
name: Crop Ontology CGIAR Musa Anatomy
generic_urls:
- http://www.cropontology.org/ontology/CO_125:0000000/CGIAR_Musa_anatomy
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CO_125:0000002
example_url: http://www.cropontology.org/ontology/CO_125:0000000
- database: COG
name: NCBI Clusters of Orthologous Groups
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: COG_Cluster
name: NCBI COG cluster
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id]
example_id: COG_Cluster:COG0001
example_url: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001
- database: COG_Function
name: NCBI COG function
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id]
example_id: COG_Function:H
example_url: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H
- database: COG_Pathway
name: NCBI COG pathway
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id]
example_id: COG_Pathway:14
example_url: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14
- database: CollecTF
name: Database of transcription factor binding sites (TFBS) in the Bacteria domain
generic_urls:
- http://www.collectf.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: ComplexPortal
name: Complex Portal database of macromolecular complexes
generic_urls:
- https://www.ebi.ac.uk/complexportal
entity_types:
- type_name: macromolecular complex
type_id: GO:0032991
id_syntax: CPX-[0-9]+
url_syntax: https://www.ebi.ac.uk/complexportal/complex/[example_id]
example_id: ComplexPortal:CPX-2158
example_url: https://www.ebi.ac.uk/complexportal/complex/CPX-2158
- database: CORIELL
name: Coriell Institute for Medical Research
description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.
generic_urls:
- http://ccr.coriell.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=[example_id]
example_id: GM07892
example_url: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07892
- database: CORUM
name: CORUM - the Comprehensive Resource of Mammalian protein complexes
generic_urls:
- http://mips.gsf.de/genre/proj/corum/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=[example_id]
example_id: CORUM:837
example_url: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=837
- database: cosmoss_PpV1.2
name: plantco.de|cosmoss.org
generic_urls:
- https://www.cosmoss.org/annotation/genonaut
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.cosmoss.org/annotation/genonaut?accession=[example_id]&version=V1.2
example_id: cosmoss_PpV1.2:Pp1s47_77V2.1
example_url: https://www.cosmoss.org/annotation/genonaut?accession=Pp1s53_22V2.1&version=V1.2
- database: cribi_vitis
name: Vitis CRIBI database
generic_urls:
- http://genomes.cribi.unipd.it
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=[example_id]&release=v1
example_id: VIT_00s0173g00270
example_url: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=VIT_00s0173g00270&release=v1
- database: dbSNP
name: NCBI dbSNP
rdf_uri_prefix: http://identifiers.org/dbsnp/
generic_urls:
- http://www.ncbi.nlm.nih.gov/projects/SNP
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d+
url_syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]
example_id: dbSNP:rs3131969
example_url: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969
- database: DDANAT
name: Dictyostelium discoideum anatomy
rdf_uri_prefix: http://purl.obolibrary.org/obo/DDANAT_
generic_urls:
- http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
entity_types:
- type_name: anatomical entity
type_id: CARO:0000000
id_syntax: '[0-9]{7}'
example_id: DDANAT:0000068
- database: DDBJ
name: DNA Databank of Japan
generic_urls:
- http://www.ddbj.nig.ac.jp/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=[example_id]
example_id: DDBJ:AA816246
example_url: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=AA816246
- database: DFLAT
name: Developmental FunctionaL Annotation at Tufts
generic_urls:
- http://bcb.cs.tufts.edu/dflat/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: dictyBase
name: dictyBase
synonyms:
- DDB
- DictyBase
rdf_uri_prefix: http://identifiers.org/dictybase.gene/
generic_urls:
- http://dictybase.org
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: DDB_G[0-9]{7}
url_syntax: http://dictybase.org/gene/[example_id]
example_id: dictyBase:DDB_G0277859
example_url: http://dictybase.org/gene/DDB_G0277859
- database: dictyBase_gene_name
name: dictyBase
generic_urls:
- http://dictybase.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://dictybase.org/gene/[example_id]
example_id: dictyBase_gene_name:mlcE
example_url: http://dictybase.org/gene/mlcE
- database: dictyBase_REF
name: dictyBase literature references
synonyms:
- DDB_REF
generic_urls:
- http://dictybase.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=[example_id]
example_id: dictyBase_REF:10157
example_url: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=10157
- database: DOI
name: Digital Object Identifier
generic_urls:
- http://dx.doi.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: 10\.[0-9]+\/.*
url_syntax: http://dx.doi.org/[example_id]
example_id: DOI:10.1016/S0963-9969(99)00021-6
example_url: http://dx.doi.org/10.1016/S0963-9969(99)00021-6
- database: EC
name: Enzyme Commission
generic_urls:
- http://enzyme.expasy.org/
- http://www.chem.qmul.ac.uk/iubmb/enzyme/
entity_types:
- type_name: catalytic activity
type_id: GO:0003824
url_syntax: http://www.expasy.org/enzyme/[example_id]
example_id: EC:1.4.3.6
example_url: http://www.expasy.org/enzyme/1.4.3.6
- database: EchoBASE
name: EchoBASE post-genomic database for Escherichia coli
generic_urls:
- http://www.ecoli-york.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: EB[0-9]{4}
url_syntax: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=[example_id]
example_id: EchoBASE:EB0231
example_url: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=EB0231
- database: ECK
name: EcoGene Database of Escherichia coli Sequence and Function
generic_urls:
- http://www.ecogene.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ECK[0-9]{4}
url_syntax: http://www.ecogene.org/geneInfo.php?eck_id=[example_id]
example_id: ECK:ECK3746
example_url: http://www.ecogene.org/geneInfo.php?eck_id=ECK3746
- database: ECO
name: Evidence Code ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/ECO_
generic_urls:
- http://www.geneontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
example_id: ECO:0000002
- database: EcoCyc
name: Encyclopedia of E. coli metabolism
generic_urls:
- http://ecocyc.org/
entity_types:
- type_name: biological_process
type_id: GO:0008150
id_syntax: EG[0-9]{5}
url_syntax: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=[example_id]
example_id: EcoCyc:P2-PWY
example_url: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY
- database: EcoCyc_REF
name: Encyclopedia of E. coli metabolism
synonyms:
- ECOCYC_REF
generic_urls:
- http://ecocyc.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=[example_id]
example_id: EcoCyc_REF:COLISALII
example_url: http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=COLISALII
- database: ECOGENE
name: EcoGene Database of Escherichia coli Sequence and Function
synonyms:
- EcoGene
generic_urls:
- http://www.ecogene.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: EG[0-9]{5}
url_syntax: http://www.ecogene.org/geneInfo.php?eg_id=[example_id]
example_id: ECOGENE:EG10818
example_url: http://www.ecogene.org/geneInfo.php?eg_id=EG10818
- database: ECOGENE_G
name: EcoGene Database of Escherichia coli Sequence and Function
generic_urls:
- http://www.ecogene.org/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: ECOGENE_G:deoC
- database: EcoliWiki
name: EcoliWiki from EcoliHub
description: EcoliHub\'s subsystem for community annotation of E. coli K-12
generic_urls:
- http://ecoliwiki.net/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[A-Za-z]{3,4}'
- database: EMAPA
name: Mouse gross anatomy and development, abstract
description: "A time-independent Mouse Anatomical Dictionary; part of Gene Expression Database"
rdf_uri_prefix: http://purl.obolibrary.org/obo/EMAPA_
generic_urls:
- http://emouseatlas.org/
entity_types:
- type_name: anatomical entity
type_id: CARO:0000000
id_syntax: '[0-9]{5}'
url_syntax: "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:[example_id]"
example_id: EMAPA:16032
example_url: "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16894"
- database: EMBL
name: EMBL Nucleotide Sequence Database
description: International nucleotide sequence database collaboration, comprising EMBL-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
generic_urls:
- http://www.ebi.ac.uk/embl/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})
url_syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=[example_id]
example_id: EMBL:AA816246
example_url: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246
- database: ENA
name: European Nucleotide Archive
description: ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
generic_urls:
- http://www.ebi.ac.uk/ena/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: ([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})
url_syntax: http://www.ebi.ac.uk/ena/data/view/[example_id]
example_id: ENA:AA816246
example_url: http://www.ebi.ac.uk/ena/data/view/AA816246
- database: ENSEMBL
name: Ensembl database of automatically annotated genomic data
synonyms:
- Ensembl
- ensembl
rdf_uri_prefix: http://identifiers.org/ensembl/
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ENS[A-Z0-9]{10,17}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL:ENSP00000265949
example_url: http://www.ensembl.org/id/ENSP00000265949
- type_name: protein
type_id: PR:000000001
id_syntax: ENS[A-Z0-9]{10,17}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL:ENSP00000265949
example_url: http://www.ensembl.org/id/ENSP00000265949
- type_name: transcript
type_id: SO:0000673
id_syntax: ENS[A-Z0-9]{10,17}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL:ENSP00000265949
example_url: http://www.ensembl.org/id/ENSP00000265949
- database: ENSEMBL_GeneID
name: Ensembl database of automatically annotated genomic data
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ENSG[0-9]{9,16}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL_GeneID:ENSG00000126016
example_url: http://www.ensembl.org/id/ENSG00000126016
- database: ENSEMBL_ProteinID
name: Ensembl database of automatically annotated genomic data
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: ENSP[0-9]{9,16}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL_ProteinID:ENSP00000361027
example_url: http://www.ensembl.org/id/ENSP00000361027
- database: ENSEMBL_TranscriptID
name: Ensembl database of automatically annotated genomic data
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: transcript
type_id: SO:0000673
id_syntax: ENST[0-9]{9,16}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL_TranscriptID:ENST00000371959
example_url: http://www.ensembl.org/id/ENST00000371959
- database: EnsemblFungi
name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
generic_urls:
- http://fungi.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblFungi:YOR197W
example_url: http://www.ensemblgenomes.org/id/YOR197W
- database: EnsemblMetazoa
name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
generic_urls:
- http://metazoa.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblMetazoa:FBgn0052693
example_url: http://www.ensemblgenomes.org/id/FBgn0052693
- database: EnsemblPlants
name: Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.
synonyms:
- EnsemblPlants/Gramene
generic_urls:
- http://plants.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblPlants:LOC_Os01g22954
example_url: http://www.ensemblgenomes.org/id/LOC_Os01g22954
- database: EnsemblProtists
name: Ensembl Protists, the Ensembl database for accessing genome-scale data from protists.
generic_urls:
- http://protists.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblProtists:PFL2550w
example_url: http://www.ensemblgenomes.org/id/PFL2550w
- database: ENZYME
name: Swiss Institute of Bioinformatics enzyme database
generic_urls:
- http://www.expasy.ch/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.expasy.ch/cgi-bin/nicezyme.pl?[example_id]
example_id: ENZYME:EC 1.1.1.1
example_url: http://www.expasy.ch/cgi-bin/nicezyme.pl?1.1.1.1
- database: EO_GIT
name: GitHub Issue Tracker for EO
generic_urls:
- https://github.com/Planteome/plant-environment-ontology
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
example_id: EO_GIT:76
example_url: https://github.com/Planteome/plant-environment-ontology/issues/76
- database: EuPathDB
name: The Eukaryotic Pathogen Database
generic_urls:
- http://eupathdb.org
entity_types:
- type_name: gene
type_id: BET:0000000
url_syntax: http://eupathdb.org/gene/[example_id]
example_id: EuPathDB:LtaP17.1490
example_url: http://eupathdb.org/gene/LtaP17.1490
- database: Eurofung
name: Eurofungbase community annotation
generic_urls:
- http://www.eurofung.net/option=com_content&task=section&id=3&Itemid=4
entity_types:
- type_name: entity
type_id: BET:0000000
- database: FB
name: FlyBase
synonyms:
- FlyBase
- FLYBASE
rdf_uri_prefix: http://identifiers.org/flybase/
generic_urls:
- http://flybase.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: FBgn[0-9]{7}
url_syntax: http://flybase.org/reports/[example_id].html
example_id: FB:FBgn0000024
example_url: http://flybase.org/reports/FBgn0000024.html
- database: FBbt
name: Drosophila gross anatomy
rdf_uri_prefix: http://purl.obolibrary.org/obo/FBbt_
generic_urls:
- http://flybase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]
example_id: FBbt:00005177
example_url: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00005177
- database: FMA
name: Foundational Model of Anatomy
rdf_uri_prefix: http://purl.obolibrary.org/obo/FMA_
generic_urls:
- http://sig.biostr.washington.edu/projects/fm/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: FMA:61905
- database: FYPO
name: Fission Yeast Phenotype Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/FYPO_
generic_urls:
- http://www.pombase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
example_id: FYPO:0000001
- database: GDB
name: Human Genome Database
generic_urls:
- http://www.gdb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:[example_id]
example_id: GDB:306600
example_url: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:306600
- database: GenBank
name: GenBank
description: The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
synonyms:
- GB
generic_urls:
- http://www.ncbi.nlm.nih.gov/Genbank/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ([A-Z]{2}[0-9]{6})|([A-Z]{1}[0-9]{5})
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
example_id: GB:AA816246
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246
- type_name: protein
type_id: PR:000000001
id_syntax: ([A-Z]{2}[0-9]{6})|([A-Z]{1}[0-9]{5})
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
example_id: GB:AA816246
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246
- database: Gene3D
name: Domain Architecture Classification
generic_urls:
- http://gene3d.biochem.ucl.ac.uk/Gene3D/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=[example_id]
example_id: Gene3D:3.30.390.30
example_url: http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=3.30.390.30
- database: GeneDB
name: GeneDB
rdf_uri_prefix: http://identifiers.org/genedb/
generic_urls:
- http://www.genedb.org/gene/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ((LmjF|LinJ|LmxM)\.[0-9]{2}\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\.[A-Za-z0-9]+\.[0-9]+)|(TcCLB\.[0-9]{6}\.[0-9]+)
url_syntax: http://www.genedb.org/gene/[example_id]
example_id: PF3D7_1467300
example_url: http://www.genedb.org/gene/PF3D7_1467300
- database: Genesys-pgr
name: Gene DB, Genesys
generic_urls:
- https://www.genesys-pgr.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.genesys-pgr.org/acn/search?q=[example_id]
example_id: Genesys-pgr:CM1015-16
example_url: https://www.genesys-pgr.org/acn/search?q=CM1015-16
- database: GenProtEC
name: GenProtEC E. coli genome and proteome database
generic_urls:
- http://genprotec.mbl.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GEO
name: NCBI Gene Expression Omnibus
generic_urls:
- http://www.ncbi.nlm.nih.gov/geo/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=[example_id]
example_id: GEO:GDS2223
example_url: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2223
- database: GermOnline
name: GermOnline
generic_urls:
- http://www.germonline.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GO
name: Gene Ontology Database
rdf_uri_prefix: http://purl.obolibrary.org/obo/GO_
generic_urls:
- http://amigo.geneontology.org/
entity_types:
- type_name: molecular_function
type_id: GO:0003674
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0004352
example_url: http://amigo.geneontology.org/amigo/term/GO:0004352
- type_name: biological_process
type_id: GO:0008150
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0004352
example_url: http://amigo.geneontology.org/amigo/term/GO:0004352
- type_name: cellular_component
type_id: GO:0005575
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0004352
example_url: http://amigo.geneontology.org/amigo/term/GO:0004352
- type_name: macromolecular complex
type_id: GO:0032991
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0004352
example_url: http://amigo.geneontology.org/amigo/term/GO:0004352
- database: GO_Central
name: GO Central
synonyms:
- GO_CENTRAL
description: Manual annotation from PAINT curators into the UniProt Protein2GO curation tool.
generic_urls:
- http://www.geneontology.org/GO.refgenome.shtml
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GO_Noctua
name: GO Noctua
description: Manual annotation derived from LEGO annotations
generic_urls:
- https://github.com/geneontology/noctua-models
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GO_REF
name: Gene Ontology Database references
generic_urls:
- http://purl.obolibrary.org/obo/go/references/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
url_syntax: http://purl.obolibrary.org/obo/go/references/[example_id]
example_id: "0000001"
example_url: http://purl.obolibrary.org/obo/go/references/0000001
- database: gomodel
name: Gene Ontology Causal Activity Model Database
rdf_uri_prefix: http://model.geneontology.org/
generic_urls:
- http://www.geneontology.org/gocam
entity_types:
- type_name: model
type_id: BET:0000000
url_syntax: http://www.geneontology.org/gocam/[example_id]
example_id: gomodel:5ae3b0f600001522
example_url: http://www.geneontology.org/gocam/gomodel:5ae3b0f600001522
- database: GOC
name: Gene Ontology Consortium
generic_urls:
- http://www.geneontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GOC-OWL
name: Gene Ontology Consortium - Logical inferences
generic_urls:
- http://www.geneontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GONUTS
name: Gene Ontology Normal Usage Tracking System (GONUTS)
description: Third party documentation for GO and community annotation system.
generic_urls:
- http://gowiki.tamu.edu
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://gowiki.tamu.edu/wiki/index.php/[example_id]
example_id: GONUTS:MOUSE:CD28
example_url: http://gowiki.tamu.edu/wiki/index.php/MOUSE:CD28
- database: GOREL
name: GO Extensions to OBO Relation Ontology Ontology
description: Additional relations pending addition into RO
generic_urls:
- http://purl.obolibrary.org/obo/ro
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GR
name: Gramene
generic_urls:
- http://www.gramene.org/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Z][0-9][A-Z0-9]{3}[0-9]'
url_syntax: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=[example_id]
example_id: GR:sd1
example_url: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=sd1
- database: GR_GENE
name: Gramene
synonyms:
- GR_gene
rdf_uri_prefix: http://identifiers.org/gramene.gene/
generic_urls:
- http://www.gramene.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]
example_id: GR_GENE:GR:0060198
example_url: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198
- database: GR_MUT
name: A Comparative Mapping Resource for Grains
generic_urls:
- http://www.gramene.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]
example_id: GR_MUT:GR:0060198
example_url: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198
- database: GR_PROTEIN
name: Gramene
synonyms:
- GR_protein
rdf_uri_prefix: http://identifiers.org/gramene.protein/
generic_urls:
- http://www.gramene.org/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Z][0-9][A-Z0-9]{3}[0-9]'
url_syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id]
example_id: GR_PROTEIN:Q6VSV0
example_url: http://www.gramene.org/db/protein/protein_search?acc=Q6VSV0
- database: GR_QTL
name: Gramene
rdf_uri_prefix: http://identifiers.org/gramene.qtl/
generic_urls:
- http://www.gramene.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=[example_id]
example_id: GR_QTL:CQU7
example_url: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQU7
- database: GR_REF
name: Gramene
generic_urls:
- http://www.gramene.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.gramene.org/db/literature/pub_search?ref_id=[example_id]
example_id: GR_REF:659
example_url: http://www.gramene.org/db/literature/pub_search?ref_id=659
- database: GRIMS
name: IRRI Genetic Resources Information Management System
synonyms:
- irri
generic_urls:
- https://www.genesys-pgr.org
entity_types:
- type_name: germplasm
type_id: BET:0000000
url_syntax: https://www.genesys-pgr.org/acn/search2?q=IRGC+[example_id]
example_id: GRIMS:90637
example_url: https://www.genesys-pgr.org/acn/search2?q=IRGC+90637
- database: GRIN
name: Germplasm Resources Information Network
synonyms:
- grin
generic_urls:
- http://www.ars-grin.gov/
entity_types:
- type_name: germplasm
type_id: BET:0000000
url_syntax: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=[example_id]
example_id: GRIN:1882640
example_url: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=1882640
- database: GRINDesc
name: Germplasm Resources Information Network
generic_urls:
- http://www.ars-grin.gov/
entity_types:
- type_name: germplasm descriptors
type_id: BET:0000000
url_syntax: https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=[example_id]
example_id: GRINdesc:89033
example_url: https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=89033
- database: H-invDB
name: H-invitational Database
generic_urls:
- http://www.h-invitational.jp/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: H-invDB_cDNA
name: H-invitational Database
generic_urls:
- http://www.h-invitational.jp/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=[example_id]
example_id: H-invDB_cDNA:AK093148
example_url: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=AK093149
- database: H-invDB_locus
name: H-invitational Database
generic_urls:
- http://www.h-invitational.jp/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=[example_id]
example_id: H-invDB_locus:HIX0014446
example_url: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0014446
- database: HAMAP
name: High-quality Automated and Manual Annotation of microbial Proteomes
generic_urls:
- http://hamap.expasy.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://hamap.expasy.org/unirule/[example_id]
example_id: HAMAP:MF_00031
example_url: http://hamap.expasy.org/unirule/MF_00131
- database: HGNC
name: HUGO Gene Nomenclature Committee
rdf_uri_prefix: http://identifiers.org/hgnc/
generic_urls:
- http://www.genenames.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[0-9]+'
url_syntax: http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:[example_id]
example_id: HGNC:29
example_url: http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:29
- database: HGNC_gene
name: HUGO Gene Nomenclature Committee
generic_urls:
- http://www.genenames.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.genenames.org/data/hgnc_data.php?app_sym=[example_id]
example_id: HGNC_gene:ABCA1
example_url: http://www.genenames.org/data/hgnc_data.php?app_sym=ABCA1
- database: HPA
name: Human Protein Atlas tissue profile information
generic_urls:
- http://www.proteinatlas.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.proteinatlas.org/tissue_profile.php?antibody_id=[example_id]
example_id: HPA:HPA000237
example_url: http://www.proteinatlas.org/tissue_profile.php?antibody_id=HPA000237
- database: HPA_antibody
name: Human Protein Atlas antibody information
generic_urls:
- http://www.proteinatlas.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.proteinatlas.org/antibody_info.php?antibody_id=[example_id]
example_id: HPA_antibody:HPA000237
example_url: http://www.proteinatlas.org/antibody_info.php?antibody_id=HPA000237
- database: HUGO
name: Human Genome Organisation
generic_urls:
- http://www.hugo-international.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: IMG
name: Integrated Microbial Genomes; JGI web site for genome annotation
generic_urls:
- http://img.jgi.doe.gov
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=[example_id]
example_id: IMG:640008772
example_url: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772
- database: IMGT_HLA
name: IMGT/HLA human major histocompatibility complex sequence database
generic_urls:
- http://www.ebi.ac.uk/imgt/hla
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: IMGT_HLA:HLA00031
- database: IMGT_LIGM
name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
description: Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.
generic_urls:
- http://imgt.cines.fr
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: IMGT_LIGM:U03895
- database: IntAct
name: IntAct protein interaction database
rdf_uri_prefix: http://identifiers.org/intact/
generic_urls:
- http://www.ebi.ac.uk/intact/
entity_types:
- type_name: molecular interaction
type_id: BET:0000013
id_syntax: EBI-[0-9]+
url_syntax: http://www.ebi.ac.uk/intact/search/do/search?searchString=[example_id]
example_id: IntAct:EBI-17086
example_url: http://www.ebi.ac.uk/intact/search/do/search?searchString=EBI-17086
- type_name: protein-containing complex
type_id: GO:0032991
id_syntax: EBI-[0-9]+
url_syntax: http://www.ebi.ac.uk/complexportal/complex/[example_id]
example_id: IntAct:EBI-10205244
example_url: http://www.ebi.ac.uk/complexportal/complex/EBI-10205244
- database: InterPro
name: InterPro database of protein domains and motifs
rdf_uri_prefix: http://identifiers.org/interpro/
synonyms:
- INTERPRO
- IPR
generic_urls:
- http://www.ebi.ac.uk/interpro/
entity_types:
- type_name: polypeptide region
type_id: SO:0000839
id_syntax: IPR\d{6}
url_syntax: http://www.ebi.ac.uk/interpro/entry/[example_id]
example_id: InterPro:IPR000001
example_url: http://www.ebi.ac.uk/interpro/entry/IPR015421
- database: IPI
name: International Protein Index
generic_urls:
- http://www.ebi.ac.uk/IPI/IPIhelp.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: IPI:IPI00000005.1
- database: iPTMnet
name: iPTMnet protein post-translational modification database
generic_urls:
- http://annotation.dbi.udel.edu/iptmnet/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://annotation.dbi.udel.edu/iptmnet/entry/[example_id]/
example_id: iPTM:P06493
example_url: http://annotation.dbi.udel.edu/iptmnet/entry/P06493/
- database: IRIC
name: International Rice Research Institute
generic_urls:
- http://oryzasnp.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://oryzasnp.org/_variety.zul?irisid=[example_id]
example_id: IRIS_313-8922
example_url: http://oryzasnp.org/_variety.zul?irisid=IRIS_313-8922
- database: IRGC
name: International Rice Genebank Collection
generic_urls:
- https://www.genesys-pgr.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.genesys-pgr.org/acn/search?q=IRGC+[example_id]
example_id: IRGC:10012
example_url: https://www.genesys-pgr.org/acn/search?q=IRGC+10013
- database: ISBN
name: International Standard Book Number
generic_urls:
- https://www.worldcat.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.worldcat.org/search?q=bn%3A[example_id]
example_id: ISBN:0781702534
example_url: https://www.worldcat.org/search?q=bn%3A0781702534
- database: ISRR
name: International Society for Root Research
generic_urls:
- http://www.rootresearch.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://wiki.plantontology.org/index.php/ISRR_references
example_id: ISRR:Richard Zobel
example_url: http://wiki.plantontology.org/index.php/ISRR_references
- database: ISSN
name: International Standard Serial Number
generic_urls:
- http://www.issn.org/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: ISSN:1234-1231
- database: IUPHAR
name: International Union of Pharmacology
generic_urls:
- http://www.iuphar.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: IUPHAR_GPCR
name: International Union of Pharmacology
generic_urls:
- http://www.iuphar.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=[example_id]
example_id: IUPHAR_GPCR:1279
example_url: http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=13
- database: IUPHAR_RECEPTOR
name: International Union of Pharmacology
generic_urls:
- http://www.iuphar.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=[example_id]
example_id: IUPHAR_RECEPTOR:2205
example_url: http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=56
- database: Jaiswal_Lab
name: Jaiswal_Lab
generic_urls:
- http://wiki.plantontology.org/index.php/PO_REF:00008
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://wiki.plantontology.org/index.php/PO_REF:00008
example_id: Jaiswal_Lab:gene00002
example_url: http://wiki.plantontology.org/index.php/PO_REF:00008
- database: JCVI
name: J. Craig Venter Institute
synonyms:
- TIGR
generic_urls:
- http://www.jcvi.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: JCVI_CMR
name: EGAD database at the J. Craig Venter Institute
synonyms:
- TIGR_CMR
- TIGR_EGAD
generic_urls:
- http://cmr.jcvi.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[A-Z][A-Za-z0-9_]+(\.[0-9])?'
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=[example_id]
example_id: JCVI_CMR:VCA0557
example_url: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=VCA0557
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Z][A-Za-z0-9_]+(\.[0-9])?'
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=[example_id]
example_id: JCVI_CMR:VCA0557
example_url: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=VCA0557
- database: JCVI_EGAD
name: JCVI CMR Egad
generic_urls:
- http://cmr.jcvi.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=[example_id]
example_id: JCVI_EGAD:74462
example_url: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=74462
- database: JCVI_GenProp
name: Genome Properties database at the J. Craig Venter Institute
synonyms:
- TIGR_GenProp
generic_urls:
- http://cmr.jcvi.org/
entity_types:
- type_name: biological_process
type_id: GO:0008150
id_syntax: GenProp[0-9]{4}
url_syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=[example_id]
example_id: JCVI_GenProp:GenProp0120
example_url: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=GenProp0120
- database: JCVI_Medtr
name: Medicago truncatula genome database at the J. Craig Venter Institute
generic_urls:
- http://medicago.jcvi.org/cgi-bin/medicago/overview.cgi
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=[example_id]
example_id: JCVI_Medtr:Medtr5g024510
example_url: http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=Medtr5g024510
- database: JCVI_REF
name: J. Craig Venter Institute
synonyms:
- TIGR_REF
generic_urls:
- http://cmr.jcvi.org/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: JCVI_REF:GO_ref
example_url: http://cmr.jcvi.org/CMR/AnnotationSops.shtml
- database: JCVI_TIGRFAMS
name: TIGRFAMs HMM collection at the J. Craig Venter Institute
synonyms:
- TIGR_TIGRFAMS
generic_urls:
- http://search.jcvi.org/
entity_types:
- type_name: polypeptide region
type_id: SO:0000839
id_syntax: TIGR[0-9]{5}
url_syntax: http://search.jcvi.org/search?p&q=[example_id]
example_id: JCVI_TIGRFAMS:TIGR00254
example_url: http://search.jcvi.org/search?p&q=TIGR00254
- database: JSTOR
name: Digital archive of scholarly articles
generic_urls:
- http://www.jstor.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.jstor.org/stable/[example_id]
example_id: JSTOR:3093870
example_url: http://www.jstor.org/stable/3093870
- database: KEGG
name: Kyoto Encyclopedia of Genes and Genomes
generic_urls:
- http://www.genome.ad.jp/kegg/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: KEGG_ENZYME
name: KEGG Enzyme Database
rdf_uri_prefix: http://identifiers.org/kegg.enzyme/
generic_urls:
- http://www.genome.jp/dbget-bin/www_bfind?enzyme
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d(\.\d{1,2}){2}\.\d{1,3}
url_syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]
example_id: KEGG_ENZYME:2.1.1.4
example_url: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4
- database: KEGG_LIGAND
name: KEGG LIGAND Database
generic_urls:
- http://www.genome.ad.jp/kegg/docs/upd_ligand.html
entity_types:
- type_name: chemical entity
type_id: CHEBI:24431
id_syntax: C\d{5}
url_syntax: http://www.genome.jp/dbget-bin/www_bget?cpd:[example_id]
example_id: KEGG_LIGAND:C00577
example_url: http://www.genome.jp/dbget-bin/www_bget?cpd:C00577
- database: KEGG_PATHWAY
name: KEGG Pathways Database
rdf_uri_prefix: http://identifiers.org/kegg.pathway/
generic_urls:
- http://www.genome.jp/kegg/pathway.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.genome.jp/dbget-bin/www_bget?path:[example_id]
example_id: KEGG_PATHWAY:ot00020
example_url: http://www.genome.jp/dbget-bin/www_bget?path:ot00020
- database: KEGG_REACTION
name: KEGG Reaction Database
generic_urls:
- http://www.genome.jp/kegg/reaction/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: R\d+
url_syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]
example_id: KEGG:R02328
example_url: http://www.genome.jp/dbget-bin/www_bget?rn:R02328
- database: LIFEdb
name: LifeDB
description: LifeDB is a database for information on protein localization, interaction, functional assays and expression.
generic_urls:
- http://www.lifedb.de/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=[example_id]
example_id: LIFEdb:DKFZp564O1716
example_url: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=DKFZp564O1716
- database: LIS
name: Legume Information System
generic_urls:
- http://legumeinfo.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://legumeinfo.org/feature/Medicago/truncatula/gene/[example_id].JCVIMt4.0v1
example_id: LIS:Medtr5g030920
example_url: http://legumeinfo.org/feature/Medicago/truncatula/gene/Medtr5g030920.JCVIMt4.0v1
- database: LOCSVMpsi
name: LOCSVMPSI
description: Subcellular localization for eukayotic proteins based on SVM and PSI-BLAST
generic_urls:
- http://bioinformatics.ustc.edu.cn/locsvmpsi/locsvmpsi.php
entity_types:
- type_name: entity
type_id: BET:0000000
- database: MA
name: Adult Mouse Anatomical Dictionary
description: Adult Mouse Anatomical Dictionary; part of Gene Expression Database
rdf_uri_prefix: http://purl.obolibrary.org/obo/MA_
generic_urls:
- http://www.informatics.jax.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:[example_id]
example_id: MA:0000003
example_url: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003
- database: MACSC_REF
name: Maize Genetics and Genomics Database
generic_urls:
- http://www.maizegdb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=[example_id]
example_id: MACSC_REF:78112
example_url: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112
- database: MaizeGDB
name: MaizeGDB
generic_urls:
- http://www.maizegdb.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://maizegdb.org/gene_center/gene/[example_id]
example_id: MaizeGDB:12098
example_url: http://maizegdb.org/gene_center/gene/12098
- database: MaizeGDB_Locus
name: MaizeGDB
rdf_uri_prefix: http://identifiers.org/maizegdb.locus/
generic_urls:
- http://www.maizegdb.org
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[A-Za-z][A-Za-z0-9]*'
url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=[example_id]
example_id: MaizeGDB_Locus:ZmPK1
example_url: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=ZmPK1
- database: MaizeGDB_QTL
name: Maize Genetics and Genomics Database
generic_urls:
- http://www.maizegdb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.maizegdb.org/data_center/trait?id=[example_id]
example_id: MaizeGDB_QTL:78112
example_url: http://www.maizegdb.org/data_center/trait?id=78112
- database: MaizeGDB_REF
name: Maize Genetics and Genomics Database
generic_urls:
- http://www.maizegdb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://maizegdb.org/data_center/reference?id=[example_id]
example_id: MaizeGDB_REF:9021423
example_url: http://maizegdb.org/data_center/reference?id=9021423
- database: MaizeGDB_stock
name: Maize Genetics and Genomics Database
generic_urls:
- http://www.maizegdb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://maizegdb.org/data_center/stock?id=[example_id]
example_id: MaizeGDB_stock:12098
example_url: http://maizegdb.org/data_center/stock?id=12098
- database: MEDLINE
name: Medline literature database
generic_urls:
- http://www.nlm.nih.gov/databases/databases_medline.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: MEDLINE:20572430
- database: MENGO
name: Microbial ENergy processes Gene Ontology Project
generic_urls:
- http://mengo.vbi.vt.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: MEROPS
name: MEROPS peptidase database
generic_urls:
- http://merops.sanger.ac.uk/
entity_types:
- type_name: protein
type_id: PR:000000001
url_syntax: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=[example_id]
example_id: MEROPS:A08.001
example_url: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=A08.001
- database: MEROPS_fam
name: MEROPS peptidase database
generic_urls:
- http://merops.sanger.ac.uk/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://merops.sanger.ac.uk/cgi-bin/famsum?family=[example_id]
example_id: MEROPS_fam:M18
example_url: http://merops.sanger.ac.uk/cgi-bin/famsum?family=m18
- database: MeSH
synonyms:
- MESH
- MSH
name: Medical Subject Headings
generic_urls:
- https://www.nlm.nih.gov/mesh/MBrowser.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://n2t.net/MESH:[example_id]
example_id: MeSH:D017209
example_url: http://n2t.net/MESH:D017209
- database: MetaCyc
name: Metabolic Encyclopedia of metabolic and other pathways
synonyms:
- METACYC
rdf_uri_prefix: http://identifiers.org/metacyc/
generic_urls:
- http://metacyc.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=[example_id]
example_id: MetaCyc:GLUTDEG-PWY
example_url: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY
- database: MGCSC_GENETIC_STOCKS
name: Maize Genetics and Genomics Database
generic_urls:
- http://www.maizegdb.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=[example_id]
example_id: MGCSC_GENETIC_STOCKS:78112
example_url: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112
- database: MGD
name: Mouse Genome Database
generic_urls:
- http://www.informatics.jax.org/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: MGD:Adcy9
- database: MGI
name: Mouse Genome Informatics
rdf_uri_prefix: "http://identifiers.org/mgi/MGI:"
generic_urls:
- http://www.informatics.jax.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: MGI:[0-9]{5,}
url_syntax: http://www.informatics.jax.org/accession/[example_id]
example_id: MGI:MGI:80863
example_url: http://www.informatics.jax.org/accession/MGI:80863
- type_name: variation
type_id: VariO:0001
id_syntax: MGI:[0-9]{5,}
url_syntax: http://www.informatics.jax.org/accession/[example_id]
example_id: MGI:MGI:80863
example_url: http://www.informatics.jax.org/accession/MGI:80863
- database: MIPS_funcat
name: MIPS Functional Catalogue
generic_urls:
- http://mips.gsf.de/proj/funcatDB/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=[example_id]
example_id: MIPS_funcat:11.02
example_url: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02
- database: MITRE
name: The MITRE Corporation
generic_urls:
- http://www.mitre.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: MO
name: MGED Ontology
generic_urls:
- http://mged.sourceforge.net/ontologies/MGEDontology.php
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#[example_id]
example_id: MO:Action
example_url: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action
- database: ModBase
name: ModBase comprehensive Database of Comparative Protein Structure Models
generic_urls:
- http://modbase.compbio.ucsf.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://salilab.org/modbase/searchbyid?databaseID=[example_id]
example_id: ModBase:P10815
example_url: http://salilab.org/modbase/searchbyid?databaseID=P04848
- database: MTBBASE
name: Collection and Refinement of Physiological Data on Mycobacterium tuberculosis
generic_urls:
- http://www.ark.in-berlin.de/Site/MTBbase.html
entity_types:
- type_name: entity
type_id: BET:0000000
- database: MultiFun
name: MultiFun cell function assignment schema
generic_urls:
- http://genprotec.mbl.edu/files/MultiFun.html
entity_types:
- type_name: entity
type_id: BET:0000000
- database: NASC_code
name: Nottingham Arabidopsis Stock Centre Seeds Database
synonyms:
- NASC
generic_urls:
- http://arabidopsis.info
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]
example_id: NASC_code:N3371
example_url: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371
- database: NC-IUBMB
name: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
generic_urls:
- http://www.chem.qmw.ac.uk/iubmb/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: NCBI
name: National Center for Biotechnology Information
generic_urls:
- http://www.ncbi.nlm.nih.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: NCBIGene
name: NCBI Gene
synonyms:
- GeneID
- LocusID
- NCBI_Gene
rdf_uri_prefix: http://identifiers.org/ncbigene/
generic_urls:
- http://www.ncbi.nlm.nih.gov/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: \d+
url_syntax: http://www.ncbi.nlm.nih.gov/gene/[example_id]
example_id: NCBI_Gene:4771
example_url: http://www.ncbi.nlm.nih.gov/gene/4771
- database: NCBI_gi
name: NCBI databases
generic_urls:
- http://www.ncbi.nlm.nih.gov/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[0-9]{5,}'
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
example_id: NCBI_gi:113194944
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=113194944
- database: NCBI_GP
name: NCBI GenPept
generic_urls:
- http://www.ncbi.nlm.nih.gov/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Z]{3}[0-9]{5}(\.[0-9]+)?'
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=[example_id]
example_id: NCBI_GP:EAL72968
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=EAL72968
- database: NCBI_locus_tag
name: NCBI locus tag
generic_urls:
- http://www.ncbi.nlm.nih.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: NCBI_locus_tag:CTN_0547
- database: NIF_Subcellular
name: Neuroscience Information Framework standard ontology, subcellular hierarchy
generic_urls:
- http://www.neurolex.org/wiki
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.neurolex.org/wiki/[example_id]
example_id: NIF_Subcellular:sao1186862860
example_url: http://www.neurolex.org/wiki/sao1770195789
- database: NMPDR
name: National Microbial Pathogen Data Resource
generic_urls:
- http://www.nmpdr.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.nmpdr.org/linkin.cgi?id=[example_id]
example_id: NMPDR:fig|306254.1.peg.183
example_url: http://www.nmpdr.org/linkin.cgi?id=fig|306254.1.peg.183
- database: NTNU_SB
name: Norwegian University of Science and Technology, Systems Biology team
generic_urls:
- http://www.ntnu.edu/nt/systemsbiology
entity_types:
- type_name: entity
type_id: BET:0000000
- database: OBI
name: Ontology for Biomedical Investigations
generic_urls:
- http://obi-ontology.org/page/Main_Page
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
example_id: OBI:0000038
- database: OBO_REL
name: OBO relation ontology
generic_urls:
- http://www.obofoundry.org/ro/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: OBO_REL:part_of
- database: OBO_SF_PO
name: Source Forge OBO Plant Ontology (PO) term request tracker
generic_urls:
- http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555
example_id: OBO_SF_PO:3184921
example_url: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555
- database: OBO_SF2_PO
name: Source Forge OBO Plant Ontology (PO) term request tracker
generic_urls:
- https://sourceforge.net/p/obo/plant-ontology-po-term-requests/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/[example_id]
example_id: OBO_SF2_PO:500
example_url: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/500
- database: OBO_SF2_PECO
name: Source Forge OBO plant-experimental-conditions-ontology (PECO) term request tracker
generic_urls:
- https://sourceforge.net/p/obo/plant-environment-ontology-eo/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://sourceforge.net/p/obo/plant-environment-ontology-eo/[example_id]
example_id: OBO_SF2_PECO:89
example_url: https://sourceforge.net/p/obo/plant-environment-ontology-eo/89/
- database: OMIM
name: Mendelian Inheritance in Man
synonyms:
- MIM
generic_urls:
- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://omim.org/entry/[example_id]
example_id: OMIM:190198
example_url: http://omim.org/entry/190198
- database: OMSSA
name: Open Mass Spectrometry Search Algorithm
generic_urls:
- http://pubchem.ncbi.nlm.nih.gov/omssa/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PAINT_REF
name: Phylogenetic Annotation INference Tool References
generic_urls:
- http://www.pantherdb.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: '[0-9]{5}'
url_syntax: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR[example_id]
example_id: PAINT_REF:23266
example_url: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR23266
- database: PAMGO
name: Plant-Associated Microbe Gene Ontology Interest Group
generic_urls:
- http://pamgo.vbi.vt.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PAMGO_GAT
name: Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group
generic_urls:
- http://agro.vbi.vt.edu/public/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=[example_id]
example_id: PAMGO_GAT:Atu0001
example_url: http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=atu0001
- database: PAMGO_MGG
name: Magnaporthe grisea database
description: Magnaporthe grisea database at North Carolina State University; member of PAMGO Interest Group
generic_urls:
- http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html
entity_types:
- type_name: entity
type_id: BET:0000000
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]
example_id: PAMGO_MGG:MGG_05132
example_url: 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
- database: PAMGO_VMD
name: Virginia Bioinformatics Institute Microbial Database
description: Virginia Bioinformatics Institute Microbial Database; member of PAMGO Interest Group
generic_urls:
- http://phytophthora.vbi.vt.edu
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=[example_id]
example_id: PAMGO_VMD:109198
example_url: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=109198
- database: PANTHER
name: Protein ANalysis THrough Evolutionary Relationships Classification System
rdf_uri_prefix: http://identifiers.org/panther.family/
generic_urls:
- http://www.pantherdb.org/
entity_types:
- type_name: protein family
type_id: NCIT:C20130
id_syntax: PTN[0-9]{9}|PTHR[0-9]{5}_[A-Z0-9]+
url_syntax: http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]
example_id: PANTHER:PTHR11455
example_url: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000
- database: ParkinsonsUK-UCL
name: Parkinsons Disease Gene Ontology Initiative
generic_urls:
- http://www.ucl.ac.uk/functional-gene-annotation/neurological
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PATO
name: Phenotypic quality ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/PATO_
generic_urls:
- http://www.bioontology.org/wiki/index.php/PATO:Main_Page
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: PATO:0001420
- database: PATRIC
name: PathoSystems Resource Integration Center
description: PathoSystems Resource Integration Center at the Virginia Bioinformatics Institute
generic_urls:
- http://patric.vbi.vt.edu
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://patric.vbi.vt.edu/gene/overview.php?fid=[example_id]
example_id: PATRIC:cds.000002.436951
example_url: http://patric.vbi.vt.edu/gene/overview.php?fid=cds.000002.436951
- database: PDB
name: Protein Data Bank
generic_urls:
- http://www.rcsb.org/pdb/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Za-z0-9]{4}'
url_syntax: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=[example_id]
example_id: PDB:1A4U
example_url: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1A4U
- database: PECO_GIT
name: GitHub Issue Tracker for PECO
generic_urls:
- https://github.com/Planteome/plant-experimental-conditions-ontology
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
example_id: PECO_GIT:76
example_url: https://github.com/Planteome/plant-experimental-conditions-ontology/issues/76
- database: Pfam
name: Pfam database of protein families
description: Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs)
generic_urls:
- http://pfam.xfam.org
entity_types:
- type_name: sequence feature
type_id: SO:0000110
id_syntax: PF[0-9]{5}
url_syntax: http://pfam.xfam.org/family/[example_id]
example_id: Pfam:PF00046
example_url: http://pfam.xfam.org/family/PF00069
- type_name: polypeptide region
type_id: SO:0000839
id_syntax: PF[0-9]{5}
url_syntax: http://pfam.xfam.org/family/[example_id]
example_id: Pfam:PF00046
example_url: http://pfam.xfam.org/family/PF00069
- database: PfamB
name: Pfam-B supplement to Pfam
generic_urls:
- http://www.sanger.ac.uk/Software/Pfam/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: PfamB:PB014624
- database: PharmGKB
name: Pharmacogenetics and Pharmacogenomics Knowledge Base
generic_urls:
- http://www.pharmgkb.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.pharmgkb.org/do/serve?objId=[example_id]
example_id: PharmGKB:PA267
example_url: http://www.pharmgkb.org/do/serve?objId=PA267
- database: PhenoScape
name: PhenoScape Knowledgebase
generic_urls:
- http://phenoscape.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PHI
name: MeGO (Phage and Mobile Element Ontology)
generic_urls:
- http://aclame.ulb.ac.be/Classification/mego.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: PHI:0000055
- database: PINC
name: Proteome Inc.
description: represents GO annotations created in 2001 for NCBI and extracted into UniProtKB-GOA from EntrezGene
generic_urls:
- http://www.proteome.com/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PIR
name: Protein Information Resource
generic_urls:
- http://pir.georgetown.edu/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Z]{1}[0-9]{5}'
url_syntax: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=[example_id]
example_id: PIR:I49499
example_url: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=I49499
- database: PIRSF
name: PIR Superfamily Classification System
generic_urls:
- http://pir.georgetown.edu/pirsf/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]
example_id: PIRSF:SF002327
example_url: http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327
- database: Planteome_gene
name: Generic planteome genes without homes
generic_urls:
- http://www.google.com
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.google.com/search?q=[example_id]
example_id: Planteome_gene:AC148152.3_FGT008
example_url: https://www.google.com/search?q=AC148152.3_FGT008
- database: PlantSystematics_image_archive
name: PlantSystematics.org
generic_urls:
- http://plantsystematics.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.plantsystematics.org/imagebyid_[example_id].html
example_id: PlantSystematics_image_archivee:37658
example_url: http://www.plantsystematics.org/imagebyid_37658.html
- database: PMCID
name: Pubmed Central
generic_urls:
- http://www.pubmedcentral.nih.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=[example_id]
example_id: PMCID:PMC201377
example_url: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC201377
- database: PMID
name: PubMed
synonyms:
- PUBMED
- PubMed
generic_urls:
- http://www.ncbi.nlm.nih.gov/PubMed/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: '[0-9]+'
url_syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
example_id: PMID:4208797
example_url: http://www.ncbi.nlm.nih.gov/pubmed/4208797
- database: PO
name: Plant Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/PO_
generic_urls:
- http://www.planteome.org/
entity_types:
- type_name: plant anatomical entity
type_id: PO:0025131
id_syntax: '[0-9]{7}'
url_syntax: http://browser.planteome.org/amigo/term/PO:[example_id]
example_id: PO:0009004
example_url: http://browser.planteome.org/amigo/term/PO:0009004
- type_name: plant structure development stage
type_id: PO:0009012
id_syntax: '[0-9]{7}'
url_syntax: http://browser.planteome.org/amigo/term/PO:[example_id]
example_id: PO:0025131
example_url: http://browser.planteome.org/amigo/term/PO:0025131
- database: PO_GIT
name: GitHub Issue Tracker for PO
generic_urls:
- https://github.com/Planteome/plant-ontology
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://github.com/Planteome/plant-ontology/issues/[example_id]
example_id: PO_GIT:626
example_url: https://github.com/Planteome/plant-ontology/issues/626
- database: PO_REF
name: Plant Ontology custom references
generic_urls:
- http://planteome.org/po_ref
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://planteome.org/po_ref/[example_id]
example_id: PO_REF:00001
example_url: http://planteome.org/po_ref/00001
- database: POC
name: Plant Ontology Consortium
generic_urls:
- http://www.plantontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PomBase
name: PomBase
rdf_uri_prefix: http://identifiers.org/pombase/
generic_urls:
- http://www.pombase.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: S\w+(\.)?\w+(\.)?
url_syntax: http://www.pombase.org/spombe/result/[example_id]
example_id: PomBase:SPBC11B10.09
example_url: http://www.pombase.org/spombe/result/SPBC11B10.09
- database: Pompep
name: Schizosaccharomyces pombe protein data
generic_urls:
- ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: Pompep:SPAC890.04C
- database: PPI
name: Pseudomonas syringae community annotation project
generic_urls:
- http://genome.pseudomonas-syringae.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PR
name: Protein Ontology
synonyms:
- PRO
rdf_uri_prefix: http://purl.obolibrary.org/obo/PR_
generic_urls:
- http://www.proconsortium.org/pro/pro.shtml
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: ([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}){1}(-[0-9]+){0,1}|[0-9]{9}
url_syntax: http://purl.obolibrary.org/obo/PR_[example_id]
example_id: PR:000025380
example_url: http://purl.obolibrary.org/obo/PR_000025380
- database: PRINTS
name: PRINTS compendium of protein fingerprints
generic_urls:
- http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
entity_types:
- type_name: polypeptide region
type_id: SO:0000839
id_syntax: PR[0-9]{5}
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]
example_id: PRINTS:PR00025
example_url: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=PR00025
- database: ProDom
name: ProDom protein domain families
description: ProDom protein domain families automatically generated from UniProtKB
generic_urls:
- http://prodom.prabi.fr/prodom/current/html/home.php
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=[example_id]
example_id: ProDom:PD000001
example_url: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=PD000001
- database: Prosite
name: Prosite database of protein families and domains
generic_urls:
- http://www.expasy.ch/prosite/
entity_types:
- type_name: polypeptide region
type_id: SO:0000839
id_syntax: PS[0-9]{5}
url_syntax: http://www.expasy.ch/cgi-bin/prosite-search-ac?[example_id]
example_id: Prosite:PS00365
example_url: http://www.expasy.ch/cgi-bin/prosite-search-ac?PS00365
- database: protein_id
name: DDBJ / ENA / GenBank
description: protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases
generic_urls:
- http://www.ddbj.nig.ac.jp/
- http://www.ebi.ac.uk/ena/
- http://www.ncbi.nlm.nih.gov/Genbank/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[A-Z]{3}[0-9]{5}(\.[0-9]+)?'
example_id: protein_id:CAA71991
- database: PROW
name: Protein Reviews on the Web
generic_urls:
- http://www.ncbi.nlm.nih.gov/prow/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PseudoCAP
name: Pseudomonas Genome Project
generic_urls:
- http://v2.pseudomonas.com/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://v2.pseudomonas.com/getAnnotation.do?locusID=[example_id]
example_id: PseudoCAP:PA4756
example_url: http://v2.pseudomonas.com/getAnnotation.do?locusID=PA4756
- database: PSO_GIT
name: GitHub Issue Tracker for PSO
generic_urls:
- https://github.com/Planteome/plant-stress-ontology
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://github.com/Planteome/plant-stress-ontology/issues/[example_id]
example_id: PSO_GIT:169
example_url: https://github.com/Planteome/plant-stress-ontology/issues/169
- database: PSI-MI
name: Proteomic Standard Initiative for Molecular Interaction
synonyms:
- MI
generic_urls:
- http://psidev.sourceforge.net/mi/xml/doc/user/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: MI:0018
- database: PSI-MOD
name: Proteomics Standards Initiative protein modification ontology
synonyms:
- MOD
generic_urls:
- http://psidev.sourceforge.net/mod/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:[example_id]
example_id: MOD:00219
example_url: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:00219
- database: PSORT
name: PSORT protein subcellular localization databases and prediction tools for bacteria
generic_urls:
- http://www.psort.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: pTARGET
name: pTARGET Prediction server for protein subcellular localization
generic_urls:
- http://bioinformatics.albany.edu/~ptarget/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: PubChem_BioAssay
name: NCBI PubChem database of bioassay records
generic_urls:
- http://pubchem.ncbi.nlm.nih.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=[example_id]
example_id: PubChem_BioAssay:177
example_url: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=177
- database: PubChem_Compound
name: NCBI PubChem database of chemical structures
generic_urls:
- http://pubchem.ncbi.nlm.nih.gov/
entity_types:
- type_name: chemical entity
type_id: CHEBI:24431
id_syntax: '[0-9]+'
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=[example_id]
example_id: PubChem_Compound:2244
example_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=2244
- database: PubChem_Substance
name: NCBI PubChem database of chemical substances
generic_urls:
- http://pubchem.ncbi.nlm.nih.gov/
entity_types:
- type_name: chemical entity
type_id: CHEBI:24431
id_syntax: '[0-9]{4,}'
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=[example_id]
example_id: PubChem_Substance:4594
example_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=4594
- database: RAP-DB
name: Rice annotation Project database
generic_urls:
- http://rapdb.dna.affrc.go.jp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=[example_id]
example_id: RAP-DB:OS01T0100600-01
example_url: http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=Os01g0100200
- database: Reactome
name: Reactome - a curated knowledgebase of biological pathways
synonyms:
- REACTOME
- REAC
rdf_uri_prefix: http://identifiers.org/reactome/
generic_urls:
- http://www.reactome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: R-[A-Z]{3}-[0-9]+(-[0-9]+){0,1}(\.[0-9]+){0,1}
url_syntax: http://www.reactome.org/content/detail/[example_id]
example_id: Reactome:R-HSA-109582
example_url: http://www.reactome.org/content/detail/R-HSA-109582
- database: REBASE
name: REBASE restriction enzyme database
generic_urls:
- http://rebase.neb.com/rebase/rebase.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://rebase.neb.com/rebase/enz/[example_id].html
example_id: REBASE:EcoRI
example_url: http://rebase.neb.com/rebase/enz/EcoRI.html
- database: RefGenome
name: GO Reference Genomes
synonyms:
- REFGENOME
generic_urls:
- http://www.geneontology.org/GO.refgenome.shtml
entity_types:
- type_name: entity
type_id: BET:0000000
- database: RefSeq
name: RefSeq
generic_urls:
- http://www.ncbi.nlm.nih.gov/RefSeq/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+(\.[0-9]+){0,1}
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
example_id: RefSeq:XP_001068954
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954
- type_name: protein
type_id: PR:000000001
id_syntax: (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+(\.[0-9]+){0,1}
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
example_id: RefSeq:XP_001068954
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954
- database: RESID
name: RESID Database of Protein Modifications
generic_urls:
- ftp://ftp.ncifcrf.gov/pub/users/residues/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: RESID:AA0062
- database: Rfam
name: Rfam database of RNA families
generic_urls:
- http://rfam.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://rfam.org/family/[example_id]
example_id: Rfam:RF00012
example_url: http://rfam.org/family/RF00012
- database: RGD
name: Rat Genome Database
synonyms:
- RAD
- RGDID
rdf_uri_prefix: http://identifiers.org/rgd/
generic_urls:
- http://rgd.mcw.edu/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[0-9]{4,7}'
url_syntax: http://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]
example_id: RGD:2004
example_url: http://rgd.mcw.edu/rgdweb/search/search.html?term=2004
- database: RHEA
name: Rhea, the Annotated Reactions Database
description: Rhea is a manually annotated database of chemical reactions. All data in Rhea is freely accessible and available for anyone to use.
generic_urls:
- http://www.rhea-db.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.rhea-db.org/reaction.xhtml?id=[example_id]
example_id: RHEA:25811
example_url: http://www.rhea-db.org/reaction.xhtml?id=25811
- database: RiceSES
name: Rice Knowledge Bank
generic_urls:
- http://www.ncbi.nlm.nih.gov/PubMed/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/[example_id].html
example_id: RiceSES:bakanae-diseases-bak
example_url: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/bakanae-diseases-bak.html
- database: RNAcentral
name: RNAcentral
description: An international database of ncRNA sequences
generic_urls:
- http://rnacentral.org
entity_types:
- type_name: ribonucleic acid
type_id: CHEBI:33697
id_syntax: URS[0-9A-F]{10}([_\/][0-9]+){0,1}
url_syntax: http://rnacentral.org/rna/[example_id]
example_id: RNAcentral:URS000047C79B_9606
example_url: http://rnacentral.org/rna/URS000047C79B_9606
- database: RNAmods
name: RNA Modification Database
synonyms:
- RNAMDB
generic_urls:
- http://s59.cas.albany.edu/RNAmods/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?[example_id]
example_id: RNAmods:037
example_url: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?091
- database: RO
name: OBO Relation Ontology Ontology
description: A collection of relations used across OBO ontologies
rdf_uri_prefix: http://purl.obolibrary.org/obo/RO_
generic_urls:
- http://purl.obolibrary.org/obo/ro
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/RO_[example_id]
example_id: RO:0002211
example_url: http://purl.obolibrary.org/obo/RO_0002211
- database: Roslin_Institute
name: Roslin Institute
synonyms:
- RI
generic_urls:
- http://www.roslin.ac.uk/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: SABIO-RK
name: SABIO Reaction Kinetics
description: The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
generic_urls:
- http://sabio.villa-bosch.de/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=[example_id]
example_id: SABIO-RK:1858
example_url: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=1858
- database: Sanger
name: Wellcome Trust Sanger Institute
generic_urls:
- http://www.sanger.ac.uk/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: SEED
name: The SEED;
description: Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices
generic_urls:
- http://www.theseed.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.theseed.org/linkin.cgi?id=[example_id]
example_id: SEED:fig|83331.1.peg.1
example_url: http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1
- database: SFLD
name: Structure-Function Linkage Database
description: A hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities
generic_urls:
- http://sfld.rbvi.ucsf.edu/django/
- database: SGD
name: Saccharomyces Genome Database
synonyms:
- SGDID
rdf_uri_prefix: http://identifiers.org/sgd/
generic_urls:
- http://www.yeastgenome.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: S[0-9]{9}
url_syntax: http://www.yeastgenome.org/locus/[example_id]/overview
example_id: SGD:S000006169
example_url: http://www.yeastgenome.org/locus/S000006169/overview
- database: SGD_LOCUS
name: Saccharomyces Genome Database
generic_urls:
- http://www.yeastgenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.yeastgenome.org/locus/[example_id]/overview
example_id: SGD_LOCUS:GAL4
example_url: http://www.yeastgenome.org/locus/S000006169/overview
- database: SGD_REF
name: Saccharomyces Genome Database
generic_urls:
- http://www.yeastgenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.yeastgenome.org/reference/[example_id]/overview
example_id: SGD_REF:S000049602
example_url: http://www.yeastgenome.org/reference/S000049602/overview
- database: SGN
name: Sol Genomics Network
synonyms:
- SGN_gene
rdf_uri_prefix: http://identifiers.org/sgn/
generic_urls:
- http://www.sgn.cornell.edu/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=[example_id]
example_id: SGN_gene:7740
example_url: http://solgenomics.net/phenome/locus_display.pl?locus_id=7740
- database: SGN_ref
name: Sol Genomics Network
generic_urls:
- http://www.sgn.cornell.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]
example_id: SGN_ref:861
example_url: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=861
- database: SGN_germplasm
name: Sol Genomics Network
generic_urls:
- http://www.ncbi.nlm.nih.gov/PubMed/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://solgenomics.net/stock/[example_id]/view/
example_id: SGN_germplasm:6583
example_url: http://solgenomics.net/stock/6583/view/
- database: SMART
name: Simple Modular Architecture Research Tool
generic_urls:
- http://smart.embl-heidelberg.de/
entity_types:
- type_name: polypeptide region
type_id: SO:0000839
url_syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=[example_id]
example_id: SMART:SM00005
example_url: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005
- database: SMD
name: Stanford Microarray Database
generic_urls:
- http://genome-www.stanford.edu/microarray
entity_types:
- type_name: entity
type_id: BET:0000000
- database: SO
name: Sequence Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/SO_
generic_urls:
- http://sequenceontology.org/
entity_types:
- type_name: sequence attribute
type_id: SO:0000400
id_syntax: \d{7}
url_syntax: http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]
example_id: SO:0000195
example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0001850
- type_name: sequence feature
type_id: SO:0000110
id_syntax: \d{7}
url_syntax: http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]
example_id: SO:0000195
example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0001850
- database: Soy_gene
name: SoyBase
generic_urls:
- http://soybase.org/
entity_types:
- type_name: gene
type_id: BET:0000000
url_syntax: http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=[example_id]
example_id: Glyma18g02210
example_url: http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=Glyma18g02210
- database: SOY_QTL
name: SoyBase
generic_urls:
- http://soybase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=[example_id]
example_id: Seedling, abnormal+1-1
example_url: http://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Seedling,+abnormal+1-1
- database: SOY_ref
name: SoyBase
generic_urls:
- http://soybase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=[example_id]
example_id: SOY ref:SoyBase6597900
example_url: http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=SoyBase3142000126
- database: SPD
name: Schizosaccharomyces pombe Postgenome Database at RIKEN; includes Orfeome Localisation data
generic_urls:
- http://www.riken.jp/SPD/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: '[0-9]{2}/[0-9]{2}[A-Z][0-9]{2}'
url_syntax: http://www.riken.jp/SPD/[example_id].html
example_id: SPD:05/05F01
example_url: http://www.riken.jp/SPD/05/05F01.html
- database: SPTR
name: SRS database at EBI
synonyms:
- SP
generic_urls:
- http://srs.ebi.ac.uk
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]]
example_id: SPTR:12345
example_url: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:12345]
- database: SUBTILIST
name: Bacillus subtilis Genome Sequence Project
generic_urls:
- http://genolist.pasteur.fr/SubtiList/
entity_types:
- type_name: gene
type_id: SO:0000704
example_id: SUBTILISTG:BG11384
- type_name: protein
type_id: PR:000000001
example_id: SUBTILISTG:BG11384
- database: SUBTILISTG
name: Bacillus subtilis Genome Sequence Project
generic_urls:
- http://genolist.pasteur.fr/SubtiList/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: SUBTILISTG:accC
- database: SUPERFAMILY
name: SUPERFAMILY protein annotation database
description: A database of structural and functional protein annotations for completely sequenced genomes
generic_urls:
- http://supfam.cs.bris.ac.uk/SUPERFAMILY/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF[example_id]
example_id: SUPERFAMILY:51905
example_url: http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF51905
- database: SWALL
name: ExPASY Bioinformatics Resource Portal
generic_urls:
- http://ca.expasy.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=[example_id]
example_id: SWALL:12345
example_url: http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=12345
- database: Swiss-Prot
name: Swiss-Prot protein database.
generic_urls:
- http://ca.expasy.org/sprot/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=[example_id]
example_id: Swiss-Prot:P45867
example_url: http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=P45867
- database: SynGO
name: The Synapse Gene Ontology and Annotation Initiative
generic_urls:
- http://geneontology.org/page/syngo-synapse-biology
entity_types:
- type_name: entity
type_id: BET:0000000
- database: SynGO-UCL
name: The Synapse Gene Ontology and Annotation Initiative at UCL
generic_urls:
- http://geneontology.org/page/syngo-synapse-biology
entity_types:
- type_name: entity
type_id: BET:0000000
- database: SYSCILIA_CCNET
name: Syscilia
description: A systems biology approach to dissect cilia function and its disruption in human genetic disease
generic_urls:
- http://syscilia.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: TAIR
name: The Arabidopsis Information Resource
rdf_uri_prefix: http://identifiers.org/tair.locus/
generic_urls:
- http://www.arabidopsis.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: gene:[0-9]{7,12}
url_syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id]
example_id: TAIR:gene:2062713
example_url: http://arabidopsis.org/servlets/TairObject?accession=gene:2062713
- type_name: communication
type_id: BET:0000000
id_syntax: Communication:[0-9]{7,12}
url_syntax: http://arabidopsis.org/servlets/TairObject?type=communication&id=[example_id]
example_id: TAIR:Communication:1345790
example_url: http://arabidopsis.org/servlets/TairObject?type=communication&id=1345790
- type_name: primary transcript
type_id: SO:0000185
id_syntax: locus:[0-9]{7,12}
url_syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id]
example_id: TAIR:locus:2146653
example_url: http://arabidopsis.org/servlets/TairObject?accession=locus:2146653
- database: taxon
name: NCBI Taxonomy
synonyms:
- NCBITaxon
- ncbi_taxid
rdf_uri_prefix: http://purl.obolibrary.org/obo/NCBITaxon_
generic_urls:
- http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]
example_id: taxon:7227
example_url: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702
- database: TC
name: Transport Protein Database
generic_urls:
- http://www.tcdb.org/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: '[0-9]+\.[A-Z](\.[0-9]+)+'
url_syntax: http://www.tcdb.org/tcdb/index.php?tc=[example_id]
example_id: TC:9.A.4.1.1
example_url: http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1
- database: TGD
name: Tetrahymena Genome Database
rdf_uri_prefix: http://identifiers.org/tgd/
generic_urls:
- http://www.ciliate.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: TGD_LOCUS
name: Tetrahymena Genome Database
generic_urls:
- http://www.ciliate.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://db.ciliate.org/cgi-bin/locus.pl?locus=[example_id]
example_id: TGD_LOCUS:PDD1
example_url: http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1
- database: TGD_REF
name: Tetrahymena Genome Database
generic_urls:
- http://www.ciliate.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=[example_id]
example_id: TGD_REF:T000005818
example_url: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818
- database: TO_GIT
name: GitHub Issue Tracker for TO
generic_urls:
- https://github.com/Planteome/plant-trait-ontology
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://github.com/Planteome/plant-trait-ontology/issues/[example_id]
example_id: TO_GIT:381
example_url: https://github.com/Planteome/plant-trait-ontology/issues/381
- database: TR
name: TREMBL
synonyms:
- SPTREMBL
- TREMBL
- TrEMBL
generic_urls:
- http://www.ebi.ac.uk/swissprot/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]]
example_id: TrEMBL:Q00177
example_url: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:Q00177]
- database: TRAIT
name: TRAnscript Integrated Table
description: an integrated database of transcripts expressed in human skeletal muscle
synonyms:
- MuscleTRAIT
generic_urls:
- http://muscle.cribi.unipd.it/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: TRANSFAC
name: TRANSFAC database of eukaryotic transcription factors
generic_urls:
- http://www.gene-regulation.com/pub/databases.html#transfac
entity_types:
- type_name: entity
type_id: BET:0000000
- database: TreeGenes
name: Forest Tree Genome Database
generic_urls:
- http://dendrome.ucdavis.edu/treegenes/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=[example_id]
example_id: TreeGenes:254
example_url: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254
- database: UBERON
name: Uber-anatomy ontology
description: A multi-species anatomy ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/UBERON_
generic_urls:
- http://uberon.org
entity_types:
- type_name: anatomical entity
type_id: CARO:0000000
id_syntax: '[0-9]{7}'
url_syntax: http://purl.obolibrary.org/obo/UBERON_[example_id]
example_id: UBERON:0002398
example_url: http://purl.obolibrary.org/obo/UBERON_0002398
- type_name: life cycle stage
type_id: UBERON:0000105
id_syntax: '[0-9]{7}'
url_syntax: http://purl.obolibrary.org/obo/UBERON_[example_id]
example_id: UBERON:0000069
- database: UM-BBD
name: EAWAG Biocatalysis/Biodegradation Database
generic_urls:
- http://eawag-bbd.ethz.ch/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: UM-BBD_enzymeID
name: EAWAG Biocatalysis/Biodegradation Database
generic_urls:
- http://eawag-bbd.ethz.ch/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=[example_id]
example_id: UM-BBD_enzymeID:e0413
example_url: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=e0230
- database: UM-BBD_pathwayID
name: EAWAG Biocatalysis/Biodegradation Database
generic_urls:
- http://eawag-bbd.ethz.ch/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://eawag-bbd.ethz.ch/[example_id]/[example_id]_map.html
example_id: UM-BBD_pathwayID:acr
example_url: http://eawag-bbd.ethz.ch/acr/acr_map.html
- database: UM-BBD_reactionID
name: EAWAG Biocatalysis/Biodegradation Database
generic_urls:
- http://eawag-bbd.ethz.ch/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=[example_id]
example_id: UM-BBD_reactionID:r0129
example_url: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0129
- database: UM-BBD_ruleID
name: EAWAG Biocatalysis/Biodegradation Database
generic_urls:
- http://eawag-bbd.ethz.ch/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=[example_id]
example_id: UM-BBD_ruleID:bt0330
example_url: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=bt0330
- database: UniGene
name: UniGene
description: NCBI transcript cluster database, organized by transcriptome. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene).
generic_urls:
- http://www.ncbi.nlm.nih.gov/UniGene
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=[organism_abbreviation]&CID=[cluster_id]
example_id: UniGene:Hs.212293
example_url: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=212293
- database: UniMod
name: UniMod
description: protein modifications for mass spectrometry
generic_urls:
- http://www.unimod.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.unimod.org/modifications_view.php?editid1=[example_id]
example_id: UniMod:1287
example_url: http://www.unimod.org/modifications_view.php?editid1=1287
- database: UniParc
name: UniProt Archive
description: A non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office
generic_urls:
- http://www.uniprot.org/uniparc/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.uniprot.org/uniparc/[example_id]
example_id: UniParc:UPI000000000A
example_url: http://www.uniprot.org/uniparc/UPI000000000A
- database: UniPathway
name: UniPathway
description: UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.
generic_urls:
- http://www.grenoble.prabi.fr/obiwarehouse/unipathway
entity_types:
- type_name: biological_process
type_id: GO:0008150
url_syntax: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=[example_id]
example_id: UniPathway:UPA00155
example_url: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00155
- database: UniProt
name: Universal Protein Knowledgebase
description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database
generic_urls:
- http://www.uniprot.org
- database: UniProtKB
name: Universal Protein Knowledgebase
description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database
rdf_uri_prefix: http://identifiers.org/uniprot/
generic_urls:
- http://www.uniprot.org
entity_types:
- type_name: protein
type_id: PR:000000001
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}|:VAR_[0-9]{6}){0,1}
url_syntax: http://www.uniprot.org/uniprot/[example_id]
example_id: UniProtKB:P51587
example_url: http://www.uniprot.org/uniprot/P51587
- database: UniProtKB-KW
name: UniProt Knowledgebase keywords
synonyms:
- SP_KW
generic_urls:
- http://www.uniprot.org/keywords/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.uniprot.org/keywords/[example_id]
example_id: UniProtKB-KW:KW-0812
example_url: http://www.uniprot.org/keywords/KW-0812
- database: UniProtKB-SubCell
name: UniProt Knowledgebase Subcellular Location vocabulary
synonyms:
- SP_SL
generic_urls:
- http://www.uniprot.org/locations/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.uniprot.org/locations/[example_id]
example_id: UniProtKB-SubCell:SL-0012
example_url: http://www.uniprot.org/locations/SL-0012
- database: UniRule
name: Manually curated rules for automatic annotation of UniProtKB unreviewed entries
generic_urls:
- http://www.uniprot.org/unirule
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.uniprot.org/unirule/[example_id]
id_syntax: UR[0-9]{9}|MF_[0-9]{5}|PIRNR[0-9]{6}|PRU[0-9]{5}|RU[0-9]{6}
example_id: UniRule:UR000107224
example_url: http://www.uniprot.org/unirule/UR000107224
- database: VBRC
name: Viral Bioinformatics Resource Center
generic_urls:
- http://vbrc.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://vbrc.org/query.asp?web_id=VBRC:[example_id]
example_id: VBRC:F35742
example_url: http://vbrc.org/query.asp?web_id=VBRC:F35742
- database: VEGA
name: Vertebrate Genome Annotation database
generic_urls:
- http://vega.sanger.ac.uk/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://vega.sanger.ac.uk/id/[example_id]
example_id: VEGA:OTTHUMP00000000661
example_url: http://vega.sanger.ac.uk/id/OTTHUMP00000000661
- database: VIDA
name: Virus Database at University College London
generic_urls:
- http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
entity_types:
- type_name: entity
type_id: BET:0000000
- database: VMD
name: Virginia Bioinformatics Institute Microbial Database
generic_urls:
- http://phytophthora.vbi.vt.edu
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=[example_id]
example_id: VMD:109198
example_url: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=109198
- database: VZ
name: ViralZone
generic_urls:
- http://viralzone.expasy.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://viralzone.expasy.org/all_by_protein/[example_id].html
example_id: VZ:957
example_url: http://viralzone.expasy.org/all_by_protein/957.html
- database: WB
name: WormBase database of nematode biology
synonyms:
- WormBase
rdf_uri_prefix: http://identifiers.org/wormbase/
generic_urls:
- http://www.wormbase.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})
url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
example_id: WB:WBGene00003001
example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
- type_name: variation
type_id: VariO:0001
id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})
url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
example_id: WB:WBGene00003001
example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
- type_name: protein
type_id: PR:000000001
id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})
url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
example_id: WB:WBGene00003001
example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
- database: WB_REF
name: WormBase database of nematode biology
generic_urls:
- http://www.wormbase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.wormbase.org/db/misc/paper?name=[example_id]
example_id: WB_REF:WBPaper00004823
example_url: http://www.wormbase.org/db/misc/paper?name=WBPaper00004823
- database: WBbt
name: C. elegans gross anatomy
generic_urls:
- http://www.wormbase.org/
entity_types:
- type_name: cell
type_id: GO:0005623
id_syntax: '[0-9]{7}'
example_id: WBbt:0005733
- type_name: metazoan anatomical entity
type_id: UBERON:0001062
id_syntax: '[0-9]{7}'
example_id: WBbt:0005733
- database: WBls
name: C. elegans development
rdf_uri_prefix: http://purl.obolibrary.org/obo/WBls_
generic_urls:
- http://www.wormbase.org/
entity_types:
- type_name: nematoda life stage
type_id: WBls:0000075
id_syntax: '[0-9]{7}'
example_id: WBls:0000010
- database: WBPhenotype
name: WormBase phenotype ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/WBPhenotype_
generic_urls:
- http://www.wormbase.org/
entity_types:
- type_name: quality
type_id: PATO:0000001
id_syntax: '[0-9]{7}'
url_syntax: http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype:[example_id]
example_id: WBPhenotype:0002117
example_url: http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype:0000154
- database: Wikipedia
name: Wikipedia
generic_urls:
- http://en.wikipedia.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://en.wikipedia.org/wiki/[example_id]
example_id: Wikipedia:Endoplasmic_reticulum
example_url: http://en.wikipedia.org/wiki/Endoplasmic_reticulum
- database: Xenbase
name: Xenbase
rdf_uri_prefix: http://identifiers.org/xenbase/
generic_urls:
- http://www.xenbase.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: XB-GENE-[0-9]+
url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id]
example_id: Xenbase:XB-GENE-6255962
example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-GENE-6255962
- type_name: morpholino oligo
type_id: SO:0000034
id_syntax: XB-MORPHOLINO-[0-9]+
url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id]
example_id: Xenbase:XB-MORPHOLINO-17250301
example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-MORPHOLINO-17250301
- type_name: transgene
type_id: SO:0000902
id_syntax: XB-TRANSGENE-[0-9]+
url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id]
example_id: Xenbase:XB-TRANSGENE-17326811
example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-TRANSGENE-17326811
- type_name: strain
type_id: EFO:0005135
id_syntax: XB-LINE-[0-9]+
url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id]
example_id: Xenbase:XB-LINE-1248
example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-LINE-1248
- database: YeastFunc
name: Yeast Function
generic_urls:
- http://func.med.harvard.edu/yeast/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: YuBioLab
name: CITGeneDB
description: CITGeneDB is a comprehensive database of human and mouse genes enhancing or suppressing Cold-Induced Thermogenesis (CIT).
generic_urls:
- http://citgenedb.yubiolab.org
- database: ZFIN
name: Zebrafish Information Network
rdf_uri_prefix: http://identifiers.org/zfin/
generic_urls:
- http://zfin.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ZDB-(GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+
url_syntax: http://zfin.org/cgi-bin/ZFIN_jump?record=[example_id]
example_id: ZFIN:ZDB-GENE-990415-103
example_url: http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-990415-103
- type_name: variation
type_id: VariO:0001
id_syntax: ZDB-(GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+
url_syntax: http://zfin.org/cgi-bin/ZFIN_jump?record=[example_id]
example_id: ZFIN:ZDB-GENE-990415-103
example_url: http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-990415-103
- database: PLANA_REF
name: Planaria Ontology Database References
generic_urls:
- http://purl.obolibrary.org/obo/plana/references/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
url_syntax: http://purl.obolibrary.org/obo/plana/references/[example_id]
example_id: "0000001"
example_url: http://purl.obolibrary.org/obo/plana/references/0000001