# Metadata on databases and database prefixes of relevances to the GOC # See the README.md in this directory for more details. # - database: AgBase name: AgBase resource for functional analysis of agricultural plant and animal gene products generic_urls: - http://www.agbase.msstate.edu/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=[example_id] - database: AGI_LocusCode name: Arabidopsis Genome Initiative description: Comprises TAIR, TIGR and MIPS generic_urls: - http://www.arabidopsis.org entity_types: - type_name: gene type_id: SO:0000704 id_syntax: A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})? url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id] example_id: AGI_LocusCode:At2g17950 example_url: http://arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950 - database: AGRICOLA_ID name: AGRICultural OnLine Access generic_urls: - http://agricola.nal.usda.gov/ entity_types: - type_name: entity type_id: BET:0000000 example_id: AGRICOLA_NAL:TP248.2 P76 v.14 - database: AGRICOLA_IND name: AGRICultural OnLine Access generic_urls: - http://agricola.nal.usda.gov/ entity_types: - type_name: entity type_id: BET:0000000 example_id: AGRICOLA_IND:IND23252955 - database: Alzheimers_University_of_Toronto name: Alzheimers Project at University of Toronto generic_urls: - http://www.ims.utoronto.ca/ entity_types: - type_name: entity type_id: BET:0000000 - database: ApiDB_PlasmoDB name: PlasmoDB Plasmodium Genome Resource generic_urls: - http://plasmodb.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.plasmodb.org/gene/[example_id] example_id: ApiDB_PlasmoDB:PF11_0344 example_url: http://www.plasmodb.org/gene/PF11_0344 - database: APSNET name: APSNET Common Names of Plant Diseases generic_urls: - http://www.mobot.org/mobot/research/apweb/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.apsnet.org/publications/commonnames/Pages/[example_id].aspx example_id: APSNET:AfricanDaisy example_url: http://www.apsnet.org/publications/commonnames/Pages/AfricanDaisy.aspx - database: APweb name: Angiosperm Phylogeny Website generic_urls: - http://www.mobot.org/mobot/research/apweb/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html example_id: APweb:Glossary example_url: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html - database: AraCyc name: AraCyc metabolic pathway database for Arabidopsis thaliana generic_urls: - http://www.arabidopsis.org/biocyc/index.jsp entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=[example_id] example_id: AraCyc:PWYQT-62 example_url: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=PWYQT-62 - database: ARUK-UCL name: Alzheimers Research Gene Ontology Initiative generic_urls: - http://www.ucl.ac.uk/functional-gene-annotation/neurological entity_types: - type_name: entity type_id: BET:0000000 - database: ASAP name: A Systematic Annotation Package for Community Analysis of Genomes generic_urls: - https://asap.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: - http://www.ucl.ac.uk/cardiovasculargeneontology/ entity_types: - type_name: entity type_id: BET:0000000 - database: BioCyc name: BioCyc collection of metabolic pathway databases generic_urls: - http://biocyc.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id] example_id: BioCyc:PWY-5271 example_url: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271 - database: BIOMD name: BioModels Database synonyms: - BIOMDID generic_urls: - http://www.ebi.ac.uk/biomodels/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=[example_id] example_id: BIOMD:BIOMD0000000045 example_url: http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIOMD0000000045 - database: bioPIXIE_MEFIT name: biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology generic_urls: - http://avis.princeton.edu/mefit/ - http://pixie.princeton.edu/pixie/ entity_types: - type_name: entity type_id: BET:0000000 - database: 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: BIOSIS name: BIOSIS previews generic_urls: - http://www.biosis.org/ entity_types: - type_name: entity type_id: BET:0000000 example_id: BIOSIS:200200247281 - database: BRENDA name: BRENDA, The Comprehensive Enzyme Information System generic_urls: - http://www.brenda-enzymes.info entity_types: - type_name: catalytic activity type_id: GO:0003824 url_syntax: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=[example_id] example_id: BRENDA:4.2.1.3 example_url: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3 - database: BTO name: BRENDA tissue / enzyme ontology description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. rdf_uri_prefix: http://purl.obolibrary.org/obo/BTO_ generic_urls: - http://purl.obolibrary.org/obo/bto entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://purl.obolibrary.org/obo/BTO_[example_id] example_id: BTO_0002164 example_url: http://purl.obolibrary.org/obo/BTO_0002164 - database: Broad name: Broad Institute generic_urls: - http://www.broad.mit.edu/ entity_types: - type_name: entity type_id: BET:0000000 - database: Broad_MGG name: Magnaporthe grisea Database description: Magnaporthe grisea Database at the Broad Institute generic_urls: - http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S[example_id] example_id: Broad_MGG:MGG_05132.5 example_url: http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=SMGG_05132 - database: Broad_NEUROSPORA name: Neurospora crassa Database description: Neurospora crassa database at the Broad Institute generic_urls: - http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S[example_id] example_id: BROAD_NEUROSPORA:7000007580576824 example_url: http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000007580576824 - database: CACAO name: Community Assessment of Community Annotation with Ontologies description: The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition. generic_urls: - http://gowiki.tamu.edu/wiki/index.php/Category:CACAO entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://gowiki.tamu.edu/wiki/index.php/[example_id] example_id: MYCS2:A0QNF5 example_url: http://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5 - database: CAFA name: Critical Assessment of Protein Function Annotation generic_urls: - http://biofunctionprediction.org/cafa/ entity_types: - type_name: entity type_id: BET:0000000 - database: 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: CBS name: Center for Biological Sequence Analysis generic_urls: - http://www.cbs.dtu.dk/ entity_types: - type_name: entity type_id: BET:0000000 example_id: CBS:TMHMM example_url: http://www.cbs.dtu.dk/services/[example_id]/ - database: CDD name: Conserved Domain Database at NCBI generic_urls: - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id] example_id: CDD:34222 example_url: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222 - database: CGD name: Candida Genome Database synonyms: - CGDID rdf_uri_prefix: http://identifiers.org/cgd/ generic_urls: - http://www.candidagenome.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: (CAL|CAF)[0-9]{10} url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id] example_id: CGD:CAL0000179664 example_url: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664 - database: CGD_LOCUS name: Candida Genome Database generic_urls: - http://www.candidagenome.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id] example_id: CGD_LOCUS:HWP1 example_url: http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1 - database: CGD_REF name: Candida Genome Database generic_urls: - http://www.candidagenome.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id] example_id: CGD_REF:1490 example_url: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490 - database: CGEN name: Compugen Gene Ontology Gene Association Data generic_urls: - http://www.cgen.com/ entity_types: - type_name: entity type_id: BET:0000000 example_id: CGEN:PrID131022 - database: CGSC name: CGSC generic_urls: - http://cgsc.biology.yale.edu/ entity_types: - type_name: entity type_id: BET:0000000 example_id: CGSC:rbsK example_url: http://cgsc.biology.yale.edu/Site.php?ID=315 - database: CHEBI name: Chemical Entities of Biological Interest synonyms: - ChEBI rdf_uri_prefix: http://purl.obolibrary.org/obo/CHEBI_ generic_urls: - http://www.ebi.ac.uk/chebi/ entity_types: - type_name: chemical entity type_id: CHEBI:24431 id_syntax: '[0-9]{1,6}' url_syntax: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id] example_id: CHEBI:17234 example_url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234 - database: CL name: Cell Type Ontology rdf_uri_prefix: http://purl.obolibrary.org/obo/CL_ generic_urls: - http://cellontology.org entity_types: - type_name: cell type_id: GO:0005623 id_syntax: '[0-9]{7}' url_syntax: http://purl.obolibrary.org/obo/CL_[example_id] example_id: CL:0000041 example_url: http://purl.obolibrary.org/obo/CL_0000041 - database: CO_125 name: Crop Ontology CGIAR Musa Anatomy generic_urls: - http://www.cropontology.org/ontology/CO_125:0000000/CGIAR_Musa_anatomy entity_types: - type_name: entity type_id: BET:0000000 example_id: CO_125:0000002 example_url: http://www.cropontology.org/ontology/CO_125:0000000 - database: COG name: NCBI Clusters of Orthologous Groups generic_urls: - http://www.ncbi.nlm.nih.gov/COG/ entity_types: - type_name: entity type_id: BET:0000000 - database: COG_Cluster name: NCBI COG cluster generic_urls: - http://www.ncbi.nlm.nih.gov/COG/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id] example_id: COG_Cluster:COG0001 example_url: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001 - database: COG_Function name: NCBI COG function generic_urls: - http://www.ncbi.nlm.nih.gov/COG/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id] example_id: COG_Function:H example_url: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H - database: COG_Pathway name: NCBI COG pathway generic_urls: - http://www.ncbi.nlm.nih.gov/COG/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id] example_id: COG_Pathway:14 example_url: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14 - database: CollecTF name: Database of transcription factor binding sites (TFBS) in the Bacteria domain generic_urls: - http://www.collectf.org/ entity_types: - type_name: entity type_id: BET:0000000 - database: ComplexPortal name: Complex Portal database of macromolecular complexes generic_urls: - https://www.ebi.ac.uk/complexportal entity_types: - type_name: macromolecular complex type_id: GO:0032991 id_syntax: CPX-[0-9]+ url_syntax: https://www.ebi.ac.uk/complexportal/complex/[example_id] example_id: ComplexPortal:CPX-2158 example_url: https://www.ebi.ac.uk/complexportal/complex/CPX-2158 - database: CORIELL name: Coriell Institute for Medical Research description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. generic_urls: - http://ccr.coriell.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=[example_id] example_id: GM07892 example_url: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07892 - database: CORUM name: CORUM - the Comprehensive Resource of Mammalian protein complexes generic_urls: - http://mips.gsf.de/genre/proj/corum/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=[example_id] example_id: CORUM:837 example_url: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=837 - database: cosmoss_PpV1.2 name: plantco.de|cosmoss.org generic_urls: - https://www.cosmoss.org/annotation/genonaut entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://www.cosmoss.org/annotation/genonaut?accession=[example_id]&version=V1.2 example_id: cosmoss_PpV1.2:Pp1s47_77V2.1 example_url: https://www.cosmoss.org/annotation/genonaut?accession=Pp1s53_22V2.1&version=V1.2 - database: cribi_vitis name: Vitis CRIBI database generic_urls: - http://genomes.cribi.unipd.it entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=[example_id]&release=v1 example_id: VIT_00s0173g00270 example_url: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=VIT_00s0173g00270&release=v1 - database: dbSNP name: NCBI dbSNP rdf_uri_prefix: http://identifiers.org/dbsnp/ generic_urls: - http://www.ncbi.nlm.nih.gov/projects/SNP entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d+ url_syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id] example_id: dbSNP:rs3131969 example_url: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969 - database: DDANAT name: Dictyostelium discoideum anatomy rdf_uri_prefix: http://purl.obolibrary.org/obo/DDANAT_ generic_urls: - http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html entity_types: - type_name: anatomical entity type_id: CARO:0000000 id_syntax: '[0-9]{7}' example_id: DDANAT:0000068 - database: DDBJ name: DNA Databank of Japan generic_urls: - http://www.ddbj.nig.ac.jp/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=[example_id] example_id: DDBJ:AA816246 example_url: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=AA816246 - database: DFLAT name: Developmental FunctionaL Annotation at Tufts generic_urls: - http://bcb.cs.tufts.edu/dflat/ entity_types: - type_name: entity type_id: BET:0000000 - database: dictyBase name: dictyBase synonyms: - DDB - DictyBase rdf_uri_prefix: http://identifiers.org/dictybase.gene/ generic_urls: - http://dictybase.org entity_types: - type_name: gene type_id: SO:0000704 id_syntax: DDB_G[0-9]{7} url_syntax: http://dictybase.org/gene/[example_id] example_id: dictyBase:DDB_G0277859 example_url: http://dictybase.org/gene/DDB_G0277859 - database: dictyBase_gene_name name: dictyBase generic_urls: - http://dictybase.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://dictybase.org/gene/[example_id] example_id: dictyBase_gene_name:mlcE example_url: http://dictybase.org/gene/mlcE - database: dictyBase_REF name: dictyBase literature references synonyms: - DDB_REF generic_urls: - http://dictybase.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=[example_id] example_id: dictyBase_REF:10157 example_url: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=10157 - database: DOI name: Digital Object Identifier generic_urls: - http://dx.doi.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: 10\.[0-9]+\/.* url_syntax: http://dx.doi.org/[example_id] example_id: DOI:10.1016/S0963-9969(99)00021-6 example_url: http://dx.doi.org/10.1016/S0963-9969(99)00021-6 - database: EC name: Enzyme Commission generic_urls: - http://enzyme.expasy.org/ - http://www.chem.qmul.ac.uk/iubmb/enzyme/ entity_types: - type_name: catalytic activity type_id: GO:0003824 url_syntax: http://www.expasy.org/enzyme/[example_id] example_id: EC:1.4.3.6 example_url: http://www.expasy.org/enzyme/1.4.3.6 - database: EchoBASE name: EchoBASE post-genomic database for Escherichia coli generic_urls: - http://www.ecoli-york.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: EB[0-9]{4} url_syntax: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=[example_id] example_id: EchoBASE:EB0231 example_url: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=EB0231 - database: ECK name: EcoGene Database of Escherichia coli Sequence and Function generic_urls: - http://www.ecogene.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: ECK[0-9]{4} url_syntax: http://www.ecogene.org/geneInfo.php?eck_id=[example_id] example_id: ECK:ECK3746 example_url: http://www.ecogene.org/geneInfo.php?eck_id=ECK3746 - database: ECO name: Evidence Code ontology rdf_uri_prefix: http://purl.obolibrary.org/obo/ECO_ generic_urls: - http://www.geneontology.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} example_id: ECO:0000002 - database: EcoCyc name: Encyclopedia of E. coli metabolism generic_urls: - 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type_name: macromolecular complex type_id: GO:0032991 id_syntax: \d{7} url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id] example_id: GO:0004352 example_url: http://amigo.geneontology.org/amigo/term/GO:0004352 - database: GO_Central name: GO Central synonyms: - GO_CENTRAL description: Manual annotation from PAINT curators into the UniProt Protein2GO curation tool. generic_urls: - http://www.geneontology.org/GO.refgenome.shtml entity_types: - type_name: entity type_id: BET:0000000 - database: GO_Noctua name: GO Noctua description: Manual annotation derived from LEGO annotations generic_urls: - https://github.com/geneontology/noctua-models entity_types: - type_name: entity type_id: BET:0000000 - database: GO_REF name: Gene Ontology Database references generic_urls: - http://purl.obolibrary.org/obo/go/references/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} url_syntax: http://purl.obolibrary.org/obo/go/references/[example_id] example_id: "0000001" example_url: http://purl.obolibrary.org/obo/go/references/0000001 - 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database: GR_REF name: Gramene generic_urls: - http://www.gramene.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.gramene.org/db/literature/pub_search?ref_id=[example_id] example_id: GR_REF:659 example_url: http://www.gramene.org/db/literature/pub_search?ref_id=659 - database: GRIMS name: IRRI Genetic Resources Information Management System synonyms: - irri generic_urls: - https://www.genesys-pgr.org entity_types: - type_name: germplasm type_id: BET:0000000 url_syntax: https://www.genesys-pgr.org/acn/search2?q=IRGC+[example_id] example_id: GRIMS:90637 example_url: https://www.genesys-pgr.org/acn/search2?q=IRGC+90637 - database: GRIN name: Germplasm Resources Information Network synonyms: - grin generic_urls: - http://www.ars-grin.gov/ entity_types: - type_name: germplasm type_id: BET:0000000 url_syntax: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=[example_id] example_id: GRIN:1882640 example_url: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=1882640 - 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database: RAP-DB name: Rice annotation Project database generic_urls: - http://rapdb.dna.affrc.go.jp entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=[example_id] example_id: RAP-DB:OS01T0100600-01 example_url: http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=Os01g0100200 - database: Reactome name: Reactome - a curated knowledgebase of biological pathways synonyms: - REACTOME - REAC rdf_uri_prefix: http://identifiers.org/reactome/ generic_urls: - http://www.reactome.org/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: R-[A-Z]{3}-[0-9]+(-[0-9]+){0,1}(\.[0-9]+){0,1} url_syntax: http://www.reactome.org/content/detail/[example_id] example_id: Reactome:R-HSA-109582 example_url: http://www.reactome.org/content/detail/R-HSA-109582 - database: REBASE name: REBASE restriction enzyme database generic_urls: - http://rebase.neb.com/rebase/rebase.html entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://rebase.neb.com/rebase/enz/[example_id].html example_id: REBASE:EcoRI example_url: http://rebase.neb.com/rebase/enz/EcoRI.html - database: RefGenome name: GO Reference Genomes synonyms: - REFGENOME generic_urls: - http://www.geneontology.org/GO.refgenome.shtml entity_types: - type_name: entity type_id: BET:0000000 - database: RefSeq name: RefSeq generic_urls: - http://www.ncbi.nlm.nih.gov/RefSeq/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+(\.[0-9]+){0,1} url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id] example_id: RefSeq:XP_001068954 example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954 - type_name: protein type_id: PR:000000001 id_syntax: (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+(\.[0-9]+){0,1} url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id] example_id: RefSeq:XP_001068954 example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954 - database: RESID name: RESID Database of Protein Modifications generic_urls: - https://proteininformationresource.org/resid/resid.shtml entity_types: - type_name: entity type_id: BET:0000000 id_syntax: AA[0-9]{4} url_syntax: https://proteininformationresource.org/cgi-bin/resid?id=[example_id] example_id: RESID:AA0062 example_url: https://proteininformationresource.org/cgi-bin/resid?id=AA0062 - database: Rfam name: Rfam database of RNA families generic_urls: - http://rfam.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://rfam.org/family/[example_id] example_id: Rfam:RF00012 example_url: http://rfam.org/family/RF00012 - database: RGD name: Rat Genome Database synonyms: - RAD - RGDID rdf_uri_prefix: http://identifiers.org/rgd/ generic_urls: - http://rgd.mcw.edu/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: '[0-9]{4,7}' url_syntax: http://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id] example_id: RGD:2004 example_url: http://rgd.mcw.edu/rgdweb/search/search.html?term=2004 - database: RHEA name: Rhea, the Annotated Reactions Database description: Rhea is a manually annotated database of chemical reactions. All data in Rhea is freely accessible and available for anyone to use. generic_urls: - http://www.rhea-db.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.rhea-db.org/reaction.xhtml?id=[example_id] example_id: RHEA:25811 example_url: http://www.rhea-db.org/reaction.xhtml?id=25811 - database: RiceSES name: Rice Knowledge Bank generic_urls: - http://www.ncbi.nlm.nih.gov/PubMed/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/[example_id].html example_id: RiceSES:bakanae-diseases-bak example_url: http://www.knowledgebank.irri.org/extension/crop-damage-diseases/bakanae-diseases-bak.html - database: RNAcentral name: RNAcentral description: An international database of ncRNA sequences generic_urls: - http://rnacentral.org entity_types: - type_name: ribonucleic acid type_id: CHEBI:33697 id_syntax: URS[0-9A-F]{10}([_\/][0-9]+){0,1} url_syntax: http://rnacentral.org/rna/[example_id] example_id: RNAcentral:URS000047C79B_9606 example_url: http://rnacentral.org/rna/URS000047C79B_9606 - database: RNAmods name: RNA Modification Database synonyms: - RNAMDB generic_urls: - http://s59.cas.albany.edu/RNAmods/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?[example_id] example_id: RNAmods:037 example_url: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?091 - database: RO name: OBO Relation Ontology Ontology description: A collection of relations used across OBO ontologies rdf_uri_prefix: http://purl.obolibrary.org/obo/RO_ generic_urls: - http://purl.obolibrary.org/obo/ro entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://purl.obolibrary.org/obo/RO_[example_id] example_id: RO:0002211 example_url: http://purl.obolibrary.org/obo/RO_0002211 - database: Roslin_Institute name: Roslin Institute synonyms: - RI generic_urls: - http://www.roslin.ac.uk/ entity_types: - type_name: entity type_id: BET:0000000 - database: SABIO-RK name: SABIO Reaction Kinetics description: The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. generic_urls: - http://sabio.villa-bosch.de/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=[example_id] example_id: SABIO-RK:1858 example_url: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=1858 - database: Sanger name: Wellcome Trust Sanger Institute generic_urls: - http://www.sanger.ac.uk/ entity_types: - type_name: entity type_id: BET:0000000 - database: SEED name: The SEED; description: Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices generic_urls: - http://www.theseed.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.theseed.org/linkin.cgi?id=[example_id] example_id: SEED:fig|83331.1.peg.1 example_url: http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1 - database: SFLD name: Structure-Function Linkage Database description: A hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities generic_urls: - http://sfld.rbvi.ucsf.edu/django/ - database: SGD name: Saccharomyces Genome Database synonyms: - SGDID rdf_uri_prefix: http://identifiers.org/sgd/ generic_urls: - http://www.yeastgenome.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: S[0-9]{9} url_syntax: http://www.yeastgenome.org/locus/[example_id]/overview example_id: SGD:S000006169 example_url: http://www.yeastgenome.org/locus/S000006169/overview - database: SGD_LOCUS name: Saccharomyces Genome Database generic_urls: - http://www.yeastgenome.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.yeastgenome.org/locus/[example_id]/overview example_id: SGD_LOCUS:GAL4 example_url: http://www.yeastgenome.org/locus/S000006169/overview - database: SGD_REF name: Saccharomyces Genome Database generic_urls: - http://www.yeastgenome.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.yeastgenome.org/reference/[example_id]/overview example_id: SGD_REF:S000049602 example_url: http://www.yeastgenome.org/reference/S000049602/overview - database: SGN name: Sol Genomics Network synonyms: - SGN_gene rdf_uri_prefix: http://identifiers.org/sgn/ generic_urls: - http://www.sgn.cornell.edu/ entity_types: - type_name: gene type_id: SO:0000704 url_syntax: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=[example_id] example_id: SGN_gene:7740 example_url: http://solgenomics.net/phenome/locus_display.pl?locus_id=7740 - database: SGN_ref name: Sol Genomics Network generic_urls: - http://www.sgn.cornell.edu/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=[example_id] example_id: SGN_ref:861 example_url: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=861 - database: SGN_germplasm name: Sol Genomics Network generic_urls: - http://www.ncbi.nlm.nih.gov/PubMed/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://solgenomics.net/stock/[example_id]/view/ example_id: SGN_germplasm:6583 example_url: http://solgenomics.net/stock/6583/view/ - database: SMART name: Simple Modular Architecture Research Tool generic_urls: - http://smart.embl-heidelberg.de/ entity_types: - type_name: polypeptide region type_id: SO:0000839 url_syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=[example_id] example_id: SMART:SM00005 example_url: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005 - database: SMD name: Stanford Microarray Database generic_urls: - http://genome-www.stanford.edu/microarray entity_types: - type_name: entity type_id: BET:0000000 - database: SO name: Sequence Ontology rdf_uri_prefix: http://purl.obolibrary.org/obo/SO_ generic_urls: - http://sequenceontology.org/ entity_types: - type_name: sequence attribute type_id: SO:0000400 id_syntax: \d{7} url_syntax: http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id] example_id: SO:0000195 example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0001850 - type_name: sequence feature type_id: SO:0000110 id_syntax: \d{7} url_syntax: http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id] example_id: SO:0000195 example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0001850 - database: Soy_gene name: SoyBase generic_urls: - http://soybase.org/ entity_types: - type_name: gene type_id: BET:0000000 url_syntax: http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=[example_id] example_id: Glyma18g02210 example_url: http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=Glyma18g02210 - database: SOY_QTL name: SoyBase generic_urls: - http://soybase.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=[example_id] example_id: Seedling, abnormal+1-1 example_url: http://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Seedling,+abnormal+1-1 - database: SOY_ref name: SoyBase generic_urls: - http://soybase.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=[example_id] example_id: SOY ref:SoyBase6597900 example_url: http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=SoyBase3142000126 - database: SPD name: Schizosaccharomyces pombe Postgenome Database at RIKEN; includes Orfeome Localisation data generic_urls: - http://www.riken.jp/SPD/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: '[0-9]{2}/[0-9]{2}[A-Z][0-9]{2}' url_syntax: http://www.riken.jp/SPD/[example_id].html example_id: SPD:05/05F01 example_url: http://www.riken.jp/SPD/05/05F01.html - database: SPTR name: SRS database at EBI synonyms: - SP generic_urls: - http://srs.ebi.ac.uk entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]] example_id: SPTR:12345 example_url: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:12345] - database: SUBTILIST name: Bacillus subtilis Genome Sequence Project generic_urls: - http://genolist.pasteur.fr/SubtiList/ entity_types: - type_name: gene type_id: SO:0000704 example_id: SUBTILISTG:BG11384 - type_name: protein type_id: PR:000000001 example_id: SUBTILISTG:BG11384 - database: SUBTILISTG name: Bacillus subtilis Genome Sequence Project generic_urls: - http://genolist.pasteur.fr/SubtiList/ entity_types: - type_name: entity type_id: BET:0000000 example_id: SUBTILISTG:accC - database: SUPERFAMILY name: SUPERFAMILY protein annotation database description: A database of structural and functional protein annotations for completely sequenced genomes generic_urls: - http://supfam.cs.bris.ac.uk/SUPERFAMILY/index.html entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF[example_id] example_id: SUPERFAMILY:51905 example_url: http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF51905 - database: SWALL name: ExPASY Bioinformatics Resource Portal generic_urls: - http://ca.expasy.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=[example_id] example_id: SWALL:12345 example_url: http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=12345 - database: Swiss-Prot name: Swiss-Prot protein database. generic_urls: - http://ca.expasy.org/sprot/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=[example_id] example_id: Swiss-Prot:P45867 example_url: http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=P45867 - database: SynGO name: The Synapse Gene Ontology and Annotation Initiative generic_urls: - http://geneontology.org/page/syngo-synapse-biology entity_types: - type_name: entity type_id: BET:0000000 - database: SynGO-UCL name: The Synapse Gene Ontology and Annotation Initiative at UCL generic_urls: - http://geneontology.org/page/syngo-synapse-biology entity_types: - type_name: entity type_id: BET:0000000 - database: SYSCILIA_CCNET name: Syscilia description: A systems biology approach to dissect cilia function and its disruption in human genetic disease generic_urls: - http://syscilia.org/ entity_types: - type_name: entity type_id: BET:0000000 - database: TAIR name: The Arabidopsis Information Resource rdf_uri_prefix: http://identifiers.org/tair.locus/ generic_urls: - http://www.arabidopsis.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: gene:[0-9]{7,12} url_syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id] example_id: TAIR:gene:2062713 example_url: http://arabidopsis.org/servlets/TairObject?accession=gene:2062713 - type_name: communication type_id: BET:0000000 id_syntax: Communication:[0-9]{7,12} url_syntax: http://arabidopsis.org/servlets/TairObject?type=communication&id=[example_id] example_id: TAIR:Communication:1345790 example_url: http://arabidopsis.org/servlets/TairObject?type=communication&id=1345790 - type_name: primary transcript type_id: SO:0000185 id_syntax: locus:[0-9]{7,12} url_syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id] example_id: TAIR:locus:2146653 example_url: http://arabidopsis.org/servlets/TairObject?accession=locus:2146653 - database: taxon name: NCBI Taxonomy synonyms: - NCBITaxon - ncbi_taxid rdf_uri_prefix: http://purl.obolibrary.org/obo/NCBITaxon_ generic_urls: - http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id] example_id: taxon:7227 example_url: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702 - database: TC name: Transport Protein Database generic_urls: - http://www.tcdb.org/ entity_types: - type_name: protein type_id: PR:000000001 id_syntax: '[0-9]+\.[A-Z](\.[0-9]+)+' url_syntax: http://www.tcdb.org/tcdb/index.php?tc=[example_id] example_id: TC:9.A.4.1.1 example_url: http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1 - database: TGD name: Tetrahymena Genome Database rdf_uri_prefix: http://identifiers.org/tgd/ generic_urls: - http://www.ciliate.org/ entity_types: - type_name: entity type_id: BET:0000000 - database: TGD_LOCUS name: Tetrahymena Genome Database generic_urls: - http://www.ciliate.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://db.ciliate.org/cgi-bin/locus.pl?locus=[example_id] example_id: TGD_LOCUS:PDD1 example_url: http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1 - database: TGD_REF name: Tetrahymena Genome Database generic_urls: - http://www.ciliate.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=[example_id] example_id: TGD_REF:T000005818 example_url: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818 - database: TO_GIT name: GitHub Issue Tracker for TO generic_urls: - https://github.com/Planteome/plant-trait-ontology entity_types: - type_name: entity type_id: BET:0000000 url_syntax: https://github.com/Planteome/plant-trait-ontology/issues/[example_id] example_id: TO_GIT:381 example_url: https://github.com/Planteome/plant-trait-ontology/issues/381 - database: TR name: TREMBL synonyms: - SPTREMBL - TREMBL - TrEMBL generic_urls: - http://www.ebi.ac.uk/swissprot/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:[example_id]] example_id: TrEMBL:Q00177 example_url: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:Q00177] - database: TRAIT name: TRAnscript Integrated Table description: an integrated database of transcripts expressed in human skeletal muscle synonyms: - MuscleTRAIT generic_urls: - http://muscle.cribi.unipd.it/ entity_types: - type_name: entity type_id: BET:0000000 - database: TRANSFAC name: TRANSFAC database of eukaryotic transcription factors generic_urls: - http://www.gene-regulation.com/pub/databases.html#transfac entity_types: - type_name: entity type_id: BET:0000000 - database: TreeGenes name: Forest Tree Genome Database generic_urls: - http://dendrome.ucdavis.edu/treegenes/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=[example_id] example_id: TreeGenes:254 example_url: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254 - database: UBERON name: Uber-anatomy ontology description: A multi-species anatomy ontology rdf_uri_prefix: http://purl.obolibrary.org/obo/UBERON_ generic_urls: - http://uberon.org entity_types: - type_name: anatomical entity type_id: CARO:0000000 id_syntax: '[0-9]{7}' url_syntax: http://purl.obolibrary.org/obo/UBERON_[example_id] example_id: UBERON:0002398 example_url: http://purl.obolibrary.org/obo/UBERON_0002398 - type_name: life cycle stage type_id: UBERON:0000105 id_syntax: '[0-9]{7}' url_syntax: http://purl.obolibrary.org/obo/UBERON_[example_id] example_id: UBERON:0000069 - database: UM-BBD name: EAWAG Biocatalysis/Biodegradation Database generic_urls: - http://eawag-bbd.ethz.ch/ entity_types: - type_name: entity type_id: BET:0000000 - database: UM-BBD_enzymeID name: EAWAG Biocatalysis/Biodegradation Database generic_urls: - http://eawag-bbd.ethz.ch/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=[example_id] example_id: UM-BBD_enzymeID:e0413 example_url: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=e0230 - database: UM-BBD_pathwayID name: EAWAG Biocatalysis/Biodegradation Database generic_urls: - http://eawag-bbd.ethz.ch/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://eawag-bbd.ethz.ch/[example_id]/[example_id]_map.html example_id: UM-BBD_pathwayID:acr example_url: http://eawag-bbd.ethz.ch/acr/acr_map.html - database: UM-BBD_reactionID name: EAWAG Biocatalysis/Biodegradation Database generic_urls: - http://eawag-bbd.ethz.ch/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=[example_id] example_id: UM-BBD_reactionID:r0129 example_url: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0129 - database: UM-BBD_ruleID name: EAWAG Biocatalysis/Biodegradation Database generic_urls: - http://eawag-bbd.ethz.ch/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=[example_id] example_id: UM-BBD_ruleID:bt0330 example_url: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=bt0330 - database: UniGene name: UniGene description: NCBI transcript cluster database, organized by transcriptome. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene). generic_urls: - http://www.ncbi.nlm.nih.gov/UniGene entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=[organism_abbreviation]&CID=[cluster_id] example_id: UniGene:Hs.212293 example_url: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=212293 - database: UniMod name: UniMod description: protein modifications for mass spectrometry generic_urls: - http://www.unimod.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.unimod.org/modifications_view.php?editid1=[example_id] example_id: UniMod:1287 example_url: http://www.unimod.org/modifications_view.php?editid1=1287 - database: UniParc name: UniProt Archive description: A non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office generic_urls: - http://www.uniprot.org/uniparc/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.uniprot.org/uniparc/[example_id] example_id: UniParc:UPI000000000A example_url: http://www.uniprot.org/uniparc/UPI000000000A - database: UniPathway name: UniPathway description: UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. generic_urls: - http://www.grenoble.prabi.fr/obiwarehouse/unipathway entity_types: - type_name: biological_process type_id: GO:0008150 url_syntax: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=[example_id] example_id: UniPathway:UPA00155 example_url: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00155 - database: UniProt name: Universal Protein Knowledgebase description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database generic_urls: - http://www.uniprot.org - database: UniProtKB name: Universal Protein Knowledgebase description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database rdf_uri_prefix: http://identifiers.org/uniprot/ generic_urls: - http://www.uniprot.org entity_types: - type_name: protein type_id: PR:000000001 id_syntax: ([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z]([0-9][A-Z][A-Z0-9]{2}){1,2}[0-9])((-[0-9]+)|:PRO_[0-9]{10}|:VAR_[0-9]{6}){0,1} url_syntax: http://www.uniprot.org/uniprot/[example_id] example_id: UniProtKB:P51587 example_url: http://www.uniprot.org/uniprot/P51587 - database: UniProtKB-KW name: UniProt Knowledgebase keywords synonyms: - SP_KW generic_urls: - http://www.uniprot.org/keywords/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.uniprot.org/keywords/[example_id] example_id: UniProtKB-KW:KW-0812 example_url: http://www.uniprot.org/keywords/KW-0812 - database: UniProtKB-SubCell name: UniProt Knowledgebase Subcellular Location vocabulary synonyms: - SP_SL generic_urls: - http://www.uniprot.org/locations/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.uniprot.org/locations/[example_id] example_id: UniProtKB-SubCell:SL-0012 example_url: http://www.uniprot.org/locations/SL-0012 - database: UniRule name: Manually curated rules for automatic annotation of UniProtKB unreviewed entries generic_urls: - http://www.uniprot.org/unirule entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.uniprot.org/unirule/[example_id] id_syntax: UR[0-9]{9}|MF_[0-9]{5}|PIRNR[0-9]{6}|PRU[0-9]{5}|RU[0-9]{6} example_id: UniRule:UR000107224 example_url: http://www.uniprot.org/unirule/UR000107224 - database: VBRC name: Viral Bioinformatics Resource Center generic_urls: - http://vbrc.org entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://vbrc.org/query.asp?web_id=VBRC:[example_id] example_id: VBRC:F35742 example_url: http://vbrc.org/query.asp?web_id=VBRC:F35742 - database: VEGA name: Vertebrate Genome Annotation database generic_urls: - http://vega.sanger.ac.uk/index.html entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://vega.sanger.ac.uk/id/[example_id] example_id: VEGA:OTTHUMP00000000661 example_url: http://vega.sanger.ac.uk/id/OTTHUMP00000000661 - database: VIDA name: Virus Database at University College London generic_urls: - http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html entity_types: - type_name: entity type_id: BET:0000000 - database: VMD name: Virginia Bioinformatics Institute Microbial Database generic_urls: - http://phytophthora.vbi.vt.edu entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=[example_id] example_id: VMD:109198 example_url: http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=109198 - database: VZ name: ViralZone generic_urls: - http://viralzone.expasy.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://viralzone.expasy.org/all_by_protein/[example_id].html example_id: VZ:957 example_url: http://viralzone.expasy.org/all_by_protein/957.html - database: WB name: WormBase database of nematode biology synonyms: - WormBase rdf_uri_prefix: http://identifiers.org/wormbase/ generic_urls: - http://www.wormbase.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id] example_id: WB:WBGene00003001 example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001 - type_name: variation type_id: VariO:0001 id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id] example_id: WB:WBGene00003001 example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001 - type_name: protein type_id: PR:000000001 id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8}) url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id] example_id: WB:WBGene00003001 example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001 - database: WB_REF name: WormBase database of nematode biology generic_urls: - http://www.wormbase.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://www.wormbase.org/db/misc/paper?name=[example_id] example_id: WB_REF:WBPaper00004823 example_url: http://www.wormbase.org/db/misc/paper?name=WBPaper00004823 - database: WBbt name: C. elegans gross anatomy generic_urls: - http://www.wormbase.org/ entity_types: - type_name: cell type_id: GO:0005623 id_syntax: '[0-9]{7}' example_id: WBbt:0005733 - type_name: metazoan anatomical entity type_id: UBERON:0001062 id_syntax: '[0-9]{7}' example_id: WBbt:0005733 - database: WBls name: C. elegans development rdf_uri_prefix: http://purl.obolibrary.org/obo/WBls_ generic_urls: - http://www.wormbase.org/ entity_types: - type_name: nematoda life stage type_id: WBls:0000075 id_syntax: '[0-9]{7}' example_id: WBls:0000010 - database: WBPhenotype name: WormBase phenotype ontology rdf_uri_prefix: http://purl.obolibrary.org/obo/WBPhenotype_ generic_urls: - http://www.wormbase.org/ entity_types: - type_name: quality type_id: PATO:0000001 id_syntax: '[0-9]{7}' url_syntax: http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype:[example_id] example_id: WBPhenotype:0002117 example_url: http://www.wormbase.org/species/c_elegans/phenotype/WBPhenotype:0000154 - database: Wikipedia name: Wikipedia generic_urls: - http://en.wikipedia.org/ entity_types: - type_name: entity type_id: BET:0000000 url_syntax: http://en.wikipedia.org/wiki/[example_id] example_id: Wikipedia:Endoplasmic_reticulum example_url: http://en.wikipedia.org/wiki/Endoplasmic_reticulum - database: Xenbase name: Xenbase rdf_uri_prefix: http://identifiers.org/xenbase/ generic_urls: - http://www.xenbase.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: XB-GENE-[0-9]+ url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id] example_id: Xenbase:XB-GENE-6255962 example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-GENE-6255962 - type_name: morpholino oligo type_id: SO:0000034 id_syntax: XB-MORPHOLINO-[0-9]+ url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id] example_id: Xenbase:XB-MORPHOLINO-17250301 example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-MORPHOLINO-17250301 - type_name: transgene type_id: SO:0000902 id_syntax: XB-TRANSGENE-[0-9]+ url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id] example_id: Xenbase:XB-TRANSGENE-17326811 example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-TRANSGENE-17326811 - type_name: strain type_id: EFO:0005135 id_syntax: XB-LINE-[0-9]+ url_syntax: http://www.xenbase.org/common/xsearch.do?searchValue=[example_id] example_id: Xenbase:XB-LINE-1248 example_url: http://www.xenbase.org/common/xsearch.do?searchValue=XB-LINE-1248 - database: YeastFunc name: Yeast Function generic_urls: - http://func.med.harvard.edu/yeast/ entity_types: - type_name: entity type_id: BET:0000000 - database: YuBioLab name: CITGeneDB description: CITGeneDB is a comprehensive database of human and mouse genes enhancing or suppressing Cold-Induced Thermogenesis (CIT). generic_urls: - http://citgenedb.yubiolab.org - database: ZFIN name: Zebrafish Information Network rdf_uri_prefix: http://identifiers.org/zfin/ generic_urls: - http://zfin.org/ entity_types: - type_name: gene type_id: SO:0000704 id_syntax: ZDB-(GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+ url_syntax: http://zfin.org/[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-(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: PLANA_REF name: Planaria Ontology Database References generic_urls: - http://purl.obolibrary.org/obo/plana/references/ entity_types: - type_name: entity type_id: BET:0000000 id_syntax: \d{7} url_syntax: http://purl.obolibrary.org/obo/plana/references/[example_id] example_id: "0000001" example_url: http://purl.obolibrary.org/obo/plana/references/0000001 - 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: BET:0000000 url_syntax: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=[example_id] id_syntax: \d+\.\d+\.\d+ example_id: TFCLASS_FAMILY:2.1.1 example_url: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=2.1.1