# 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: 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: 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: - https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=[example_id] example_id: CASGEN:1040 example_url: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=1040 - database: CASREF name: Catalog of Fishes publications database generic_urls: - https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id] example_id: CASREF:2031 example_url: https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031 - database: CASSPC name: Catalog of Fishes species database synonyms: - CAS_SPC generic_urls: - https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=[example_id] example_url: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=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: DisProt name: DisProt description: Database of intrinsically disordered proteins generic_urls: - https://www.disprot.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://www.disprot.org/[example_id] example_id: DP00086 example_url: https://www.disprot.org/DP00086 - 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: Scientific database for the bacterium Escherichia coli K-12 MG1655 generic_urls: - https://ecocyc.org/ entity_types: - type_name: biological_process type_id: GO:0008150 id_syntax: ^[A-Za-z0-9+_.%-:]+$ url_syntax: https://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=[example_id] example_id: EcoCyc:P2-PWY example_url: https://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY - database: EcoCyc_REF name: Scientific database for the bacterium Escherichia coli K-12 MG1655 synonyms: - ECOCYC_REF generic_urls: - https://ecocyc.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://ecocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=[example_id] example_id: EcoCyc_REF:COLISALII example_url: https://ecocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=COLISALII - database: EcoCyc_GENE name: Scientific database for the bacterium Escherichia coli K-12 MG1655 generic_urls: - https://ecocyc.org/ entity_types: - type_name: protein type_id: PR:000000001 id_syntax: ^[A-Za-z0-9+_.%-:]+$ url_syntax: https://ecocyc.org/gene?orgid=ECOLI&id=[example_id] example_id: EcoCyc:RBSA-MONOMER example_url: https://ecocyc.org/gene?orgid=ECOLI&id=RBSA-MONOMER - type_name: ribonucleic acid type_id: CHEBI:33697 id_syntax: ^[A-Za-z0-9+_.%-:]+$ url_syntax: https://ecocyc.org/gene?orgid=ECOLI&id=[example_id] example_id: EcoCyc:EG30086 example_url: https://ecocyc.org/gene?orgid=ECOLI&id=EG30086 - type_name: protein-containing complex type_id: GO:0032991 id_syntax: ^[A-Za-z0-9+_.%-:]+$ url_syntax: https://ecocyc.org/ECOLI/NEW-IMAGE?id=[example_id] example_id: EcoCyc:ABC-28-CPLX example_url: https://ecocyc.org/ECOLI/NEW-IMAGE?id=ABC-28-CPLX - 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 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 id_syntax: '[0-9]{8}' 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 - type_name: cell type_id: GO:0005623 id_syntax: '[0-9]{8}' url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id] example_id: FBbt:00007002 example_url: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00007002 - type_name: metazoan anatomical entity type_id: UBERON:0001062 id_syntax: '[0-9]{8}' url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id] example_id: FBbt:10000000 example_url: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:10000000 - 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/ 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_Ensembl name: Gramene generic_urls: - http://www.gramene.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://gramene.org/?idList=[example_id] example_id: GR_Ensembl:At1g10040 example_url: http://gramene.org/?idList=At1g10040 - 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: GRIN name: Germplasm Resources Information Network synonyms: - grin generic_urls: - https://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: - https://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: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:[example_id] example_id: HGNC:29 example_url: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:29 - 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: IAO name: Information Artifact Ontology description: Ontology of information entities, including ontology metadata relations. rdf_uri_prefix: http://purl.obolibrary.org/obo/IAO_ generic_urls: - http://purl.obolibrary.org/obo/iao - database: iBB name: iBeetleBase description: RNAi phenotypes for beetle (Tribolium) genes generic_urls: - https://ibeetle-base.uni-goettingen.de/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://ibeetle-base.uni-goettingen.de/details|[example_id] example_id: TC006055 example_url: https://ibeetle-base.uni-goettingen.de/details/TC006055 - 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https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-2 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: https://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: https://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: 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: TriTrypDB name: TriTrypDB rdf_uri_prefix: https://identifiers.org/tritrypdb generic_urls: - https://tritrypdb.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: ((LmjF|LinJ|LmxM|LINF)\.[0-9]{2}\.[0-9]{4})|(Tb[0-9]+\.[A-Za-z0-9]+\.[0-9]+)|(Tb\.[0-9]{6}\.[0-9]+)| url_syntax: https://tritrypdb.org/tritrypdb/app/record/gene/[example_id] example_id: Tb927.1.630 example_url: https://tritrypdb.org/tritrypdb/app/record/gene/Tb927.1.630 - 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: 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: - https://www.uniprot.org/uniparc/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://www.uniprot.org/uniparc/[example_id] example_id: UniParc:UPI000000000A example_url: https://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 synonyms: - Swiss-Prot - SwissProt - TrEMBL - TR 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: https://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: https://www.uniprot.org/uniprot/[example_id] example_id: UniProtKB:P51587 example_url: https://www.uniprot.org/uniprot/ - 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: https://www.uniprot.org/keywords/[example_id] example_id: UniProtKB-KW:KW-0812 example_url: https://www.uniprot.org/keywords/KW-0812 - database: UniProtKB-SubCell name: UniProt Knowledgebase Subcellular Location vocabulary synonyms: - SP_SL generic_urls: - https://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: - https://www.uniprot.org/unirule/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://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: https://www.uniprot.org/unirule/UR000107224 - database: ARBA name: ARBA machine learning models for automatic annotation of UniProtKB unreviewed entries generic_urls: - https://www.uniprot.org/arba/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://www.uniprot.org/arba/[example_id] id_syntax: ARBA[0-9]{8} example_id: ARBA:ARBA00000001 example_url: https://www.uniprot.org/arba/ARBA00000001 - 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: https://identifiers.org/wb generic_urls: - http://www.wormbase.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: (CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WB:WBGene00003001 example_url: http://www.wormbase.org/get?name=WBGene00003001 - type_name: variation type_id: VariO:0001 id_syntax: (CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WB:WBVar00089843 example_url: http://www.wormbase.org/get?name=WBVar00089843 - type_name: RNAi type_id: topic:3523 id_syntax: (CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WB:WBRNAi00110325 example_url: http://www.wormbase.org/get?name=WBRNAi00110325 - type_name: Transgene type_id: SO:0000902 id_syntax: (CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WB:WBTransgene00000059 example_url: http://www.wormbase.org/get?name=WBTransgene00000059 - type_name: protein type_id: PR:000000001 id_syntax: (CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WB:CE00274 example_url: http://www.wormbase.org/get?name=CE00274 - 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/get?name=[example_id] example_id: WB_REF:WBPaper00004823 example_url: http://www.wormbase.org/get?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}' url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WBbt:0005792 example_url: http://www.wormbase.org/get?name=WBbt:0005792 - type_name: metazoan anatomical entity type_id: UBERON:0001062 id_syntax: '[0-9]{7}' url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WBbt:0005733 example_url: http://www.wormbase.org/get?name=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}' url_syntax: http://www.wormbase.org/get?name=[example_id] example_id: WBls:0000010 example_url: http://www.wormbase.org/get?name=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/get?name=[example_id] example_id: WBPhenotype:0002117 example_url: http://www.wormbase.org/get?name=WBPhenotype:0002117 - 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: WikipediaVersioned name: WikipediaVersioned generic_urls: - http://en.wikipedia.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://en.wikipedia.org/w/index.php?title=[example_id] example_id: WikipediaVersioned:Fallopian_tube&oldid=998395727 example_url: https://en.wikipedia.org/w/index.php?title=Fallopian_tube&oldid=998395727 - database: Xenbase name: Xenbase rdf_uri_prefix: https://identifiers.org/xenbase generic_urls: - http://www.xenbase.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+ url_syntax: http://www.xenbase.org/entry/[example_id] example_id: Xenbase:XB-GENE-6255962 example_url: http://www.xenbase.org/entry/XB-GENE-6255962 - type_name: morpholino oligo type_id: SO:0000034 id_syntax: XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+ url_syntax: http://www.xenbase.org/entry/[example_id] example_id: Xenbase:XB-MORPHOLINO-17250301 example_url: http://www.xenbase.org/entry/XB-MORPHOLINO-17250301 - type_name: transgene type_id: SO:0000902 id_syntax: XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+ url_syntax: http://www.xenbase.org/entry/[example_id] example_id: Xenbase:XB-TRANSGENE-17326811 example_url: http://www.xenbase.org/entry/XB-TRANSGENE-17326811 - type_name: strain type_id: EFO:0005135 id_syntax: XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+ url_syntax: http://www.xenbase.org/entry/[example_id] example_id: Xenbase:XB-LINE-1248 example_url: http://www.xenbase.org/entry/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: https://identifiers.org/zfin generic_urls: - http://zfin.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: ZDB-(TRNAG|LINCRNAG|MIRNAG|NCRNAG|SNORNAG|GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+ url_syntax: http://zfin.org/[example_id] example_id: ZDB-GENE-990415-103 example_url: http://zfin.org/ZDB-GENE-990415-103 - type_name: variation type_id: VariO:0001 id_syntax: ZDB-(TRNAG|LINCRNAG|MIRNAG|NCRNAG|SNORNAG|GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+ url_syntax: http://zfin.org/[example_id] example_id: ZDB-GENE-990415-103 example_url: http://zfin.org/ZDB-GENE-990415-103 - database: TFClass name: TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains generic_urls: - http://tfclass.bioinf.med.uni-goettingen.de/ synonyms: - TFCLASS_FAMILY - tfclass entity_types: - type_name: protein type_id: PR:000000001 url_syntax: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id] id_syntax: \d+(\.\d+){2,3} example_id: TFCLASS_FAMILY:2.1.1 example_url: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1 - database: HGNC-UCL name: UCL-based HGNC description: While based at UCL, HGNC provided GO annotations for proteins during the process of assigning approved gene names and symbols generic_urls: - https://www.ucl.ac.uk/cardiovascular/hgnc-gene-annotation entity_types: - type_name: entity type_id: BET:0000000 - database: Animal_QTLdb name: QTLdb generic_urls: - https://www.animalgenome.org/QTLdb description: A database with curated publicly available trait mapping data (QTL and SNP associations) in livestock animal species. The link ID is called QTL_ID on QTLdb data dpownloads. entity_types: - type_name: QTL type_id: QTL_ID:0000000 url_syntax: https://www.animalgenome.org/QTLdb/q?id=[example_id] id_syntax: \d+ example_id: Animal_QTLdb:23155 example_url: https://www.animalgenome.org/QTLdb/q?id=23155 - database: Animal_CorrDB name: CorrDB generic_urls: - https://www.animalgenome.org/CorrDB description: A database with curated publicly available trait correlation and inheritability data in livestock animal species. The link ID is called The link ID is called Corr_ID on CorrDB data downloads. entity_types: - type_name: Correlation type_id: CorrID:000000 url_syntax: https://www.animalgenome.org/CorrDB/q/?id=[example_id] id_syntax: \d+ example_id: Animal_CorrDB:37232 example_url: https://www.animalgenome.org/CorrDB/q/?id=37232 - database: AlphaFold name: AlphaFold Protein Structure Database generic_urls: - https://alphafold.ebi.ac.uk/ 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: https://alphafold.ebi.ac.uk/entry/[example_id] example_id: AlphaFold:Q5VSL9 example_url: https://alphafold.ebi.ac.uk/entry/Q5VSL9 - database: JaponicusDB name: JaponicusDB generic_urls: - https://www.japonicusdb.org/ entity_types: - type_name: gene type_id: SO:0000704 url_syntax: https://www.japonicusdb.org/gene/[example_id] example_id: JaponicusDB:SJAG_01143 example_url: https://www.japonicusdb.org/gene/SJAG_01143