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db-xrefs.yaml
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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
example_id: P02264
url_syntax: https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=[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: https://www.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: https://plasmodb.org/plasmo/app/record/gene/PF11_0344
- 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: ARUK-UCL
name: Alzheimers Research Gene Ontology Initiative
generic_urls:
- https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-0
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.genetics.wisc.edu/asap/ASAP1.htm
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=[example_id]
example_id: ASAP:ABF-0014586
example_url: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=ABF-0014586
- 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:
- https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/cardiovascular-gene
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:
- https://www.ebi.ac.uk/biomodels/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.ebi.ac.uk/biomodels/[example_id]
example_id: BIOMD:BIOMD0000000045
example_url: https://www.ebi.ac.uk/biomodels/BIOMD0000000045
- database: bioRxiv
name: bioRxiv
synonyms:
- BIORXIV
generic_urls:
- https://www.biorxiv.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: '[0-9]+'
url_syntax: https://www.biorxiv.org/content/[example_id]
example_id: bioRxiv:10.1101/530881v2
example_url: https://www.biorxiv.org/content/10.1101/530881v2
- 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: https://www.brenda-enzymes.info/enzyme.php?ecno=[example_id]
example_id: BRENDA:4.2.1.3
example_url: https://www.brenda-enzymes.info/enzyme.php?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: 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: https://gowiki.tamu.edu/wiki/index.php/[example_id]
example_id: MYCS2:A0QNF5
example_url: https://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: CARO
name: Common Anatomy Reference Ontology
description: An upper ontology for anatomy used by OBO Foundry ontologies. Used to facilitate interoperability between existing anatomy ontologies for different species
rdf_uri_prefix: http://purl.obolibrary.org/obo/CARO_
generic_urls:
- http://purl.obolibrary.org/obo/caro
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/CARO_[example_id]
example_id: CARO:0020003
example_url: http://purl.obolibrary.org/obo/CARO_0020003
- 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: DTU
name: DTU Health Tech Services
description: Formerly CBS (Center for Biological Sequence Analysis)
generic_urls:
- http://www.cbs.dtu.dk/services
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CBS:TMHMM
example_url: http://www.cbs.dtu.dk/services/TMHMM/
- database: CDD
name: Conserved Domain Database at NCBI
generic_urls:
- https://www.ncbi.nlm.nih.gov/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: 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:
- https://mips.helmholtz-muenchen.de/corum/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://mips.helmholtz-muenchen.de/corum/?id=[example_id]
example_id: CORUM:837
example_url: https://mips.helmholtz-muenchen.de/corum/?id=837
- 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:
- https://www.ddbj.nig.ac.jp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://getentry.ddbj.nig.ac.jp/getentry/na/[example_id]
example_id: DDBJ:AA816246
example_url: http://getentry.ddbj.nig.ac.jp/getentry/na/AA816246
- 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/publication/[example_id]
example_id: dictyBase_REF:10157
example_url: http://dictybase.org/publication/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/
entity_types:
- type_name: catalytic activity
type_id: GO:0003824
url_syntax: https://enzyme.expasy.org/EC/[example_id]
example_id: EC:1.1.1.1
example_url: https://enzyme.expasy.org/EC/1.1.1.1
- database: EchoBASE
name: EchoBASE post-genomic database for Escherichia coli
generic_urls:
- https://www.york.ac.uk/res/thomas/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: EB[0-9]{4}
url_syntax: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=[example_id]
example_id: EchoBASE:EB0231
example_url: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=EB0231
- database: ECO
name: Evidence Code Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/ECO_
generic_urls:
- http://www.evidenceontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
url_syntax: http://www.evidenceontology.org/browse/#ECO_[example_id]
example_id: ECO:0000315
example_url: http://www.evidenceontology.org/browse/#ECO_0000315
- 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: 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:
- https://enzyme.expasy.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://enzyme.expasy.org/EC/[example_id]
example_id: 1.1.1.1
example_url: https://enzyme.expasy.org/EC/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: 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: 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: 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:0044767
example_url: http://amigo.geneontology.org/amigo/term/GO:0044767
- 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:0005634
example_url: http://amigo.geneontology.org/amigo/term/GO:0005634
- 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:0044776
example_url: http://amigo.geneontology.org/amigo/term/GO:0044776
- 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://current.geneontology.org/metadata/gorefs/index.html
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: https://gowiki.tamu.edu/wiki/index.php/[example_id]
example_id: GONUTS:MOUSE:CD28
example_url: https://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/