metadata/db-xrefs.yaml

# 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: https://www.ncbi.nlm.nih.gov/research/cog/cog/[example_id]
      example_id: COG_Cluster:COG0001
      example_url: https://www.ncbi.nlm.nih.gov/research/cog/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
    - 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: 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: 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
    - type_name: reference
      type_id: BET:0000000
      id_syntax: FBrf[0-9]{7}
      url_syntax: http://flybase.org/reports/[example_id].htm
      example_id: FBrf0193169
      example_url: https://flybase.org/reports/FBrf0193169.htm      
- database: FBbt
  name: Drosophila gross anatomy
  rdf_uri_prefix: http://purl.obolibrary.org/obo/FBbt_
  generic_urls:
    - http://flybase.org/
  entity_types:
    - 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: 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: FBdv
  name: Drosophila development
  rdf_uri_prefix: http://purl.obolibrary.org/obo/FBdv_
  generic_urls:
    - http://flybase.org/
  entity_types:
    - type_name: life cycle stage
      type_id: UBERON:0000105
      id_syntax: '[0-9]{8}'
      url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:[example_id]
      example_id: FBdv:00007012
      example_url: http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:00007012
- 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
  rdf_uri_prefix: http://purl.obolibrary.org/obo/go/references/
  generic_urls:
    - http://geneontology.org/gorefs
  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 (GO-CAM)
  rdf_uri_prefix: http://model.geneontology.org/
  generic_urls:
    - https://geneontology.org/go-cam
  entity_types:
    - type_name: model
      type_id: BET:0000000
      url_syntax: https://model.geneontology.org/[example_id]
      example_id: gomodel:5ae3b0f600001522
      example_url: https://model.geneontology.org/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
- database: IMG
  name: Integrated Microbial Genomes; JGI web site for genome annotation
  generic_urls:
    - http://img.jgi.doe.gov
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=[example_id]
      example_id: IMG:640008772
      example_url: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772
- database: IMGT_HLA
  name: IMGT/HLA human major histocompatibility complex sequence database
  generic_urls:
    - http://www.ebi.ac.uk/imgt/hla
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: IMGT_HLA:HLA00031
- database: IMGT_LIGM
  name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
  description: Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.
  generic_urls:
    - http://www.imgt.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: IMGT_LIGM:U03895
- database: IntAct
  name: IntAct protein interaction database
  rdf_uri_prefix: http://identifiers.org/intact/
  generic_urls:
    - https://www.ebi.ac.uk/intact/
  entity_types:
    - type_name: molecular interaction
      type_id: BET:0000013
      id_syntax: EBI-[0-9]+
      url_syntax: https://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=[example_id]
      example_id: IntAct:EBI-17086
      example_url: https://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=EBI-17086
    - type_name: protein-containing complex
      type_id: GO:0032991
      id_syntax: EBI-[0-9]+
      url_syntax: http://www.ebi.ac.uk/complexportal/complex/[example_id]
      example_id: IntAct:EBI-10205244
      example_url: http://www.ebi.ac.uk/complexportal/complex/EBI-10205244
- database: InterPro
  name: InterPro database of protein domains and motifs
  rdf_uri_prefix: http://identifiers.org/interpro/
  synonyms:
    - INTERPRO
    - IPR
  generic_urls:
    - http://www.ebi.ac.uk/interpro/
  entity_types:
    - type_name: polypeptide region
      type_id: SO:0000839
      id_syntax: IPR\d{6}
      url_syntax: http://www.ebi.ac.uk/interpro/entry/[example_id]
      example_id: InterPro:IPR000001
      example_url: http://www.ebi.ac.uk/interpro/entry/IPR015421
- database: iPTMnet
  name: iPTMnet protein post-translational modification database
  generic_urls:
    - https://research.bioinformatics.udel.edu/iptmnet/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://research.bioinformatics.udel.edu/iptmnet/entry/[example_id]/
      example_id: iPTM:P06493
      example_url: https://research.bioinformatics.udel.edu/iptmnet/entry/P06493/
- database: IRIC
  name: International Rice Research Institute
  generic_urls:
    - https://oryzasnp.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://oryzasnp.org/_variety.zul?irisid=[example_id]
      example_id: IRIS_313-8922
      example_url: https://oryzasnp.org/_variety.zul?irisid=IRIS_313-8922
- database: IRGC
  name: International Rice Genebank Collection
  generic_urls:
    - https://www.genesys-pgr.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.genesys-pgr.org/acn/search?q=IRGC+[example_id]
      example_id: IRGC:10012
      example_url: https://www.genesys-pgr.org/acn/search?q=IRGC+10013
- database: ISBN
  name: International Standard Book Number
  generic_urls:
    - https://www.worldcat.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.worldcat.org/search?q=bn%3A[example_id]
      example_id: ISBN:0781702534
      example_url: https://www.worldcat.org/search?q=bn%3A0781702534
- database: ISSN
  name: International Standard Serial Number
  generic_urls:
    - http://www.issn.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: ISSN:1234-1231
- database: IUPHAR/BPS
  name: IUPHAR/BPS Guide to Pharmacology
  generic_urls:
    - https://www.guidetopharmacology.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: IUPHAR_GPCR
  name: International Union of Pharmacology
  generic_urls:
    - http://www.iuphar.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=[example_id]
      example_id: IUPHAR_GPCR:13
      example_url: https://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=13
- database: IUPHAR_RECEPTOR
  name: International Union of Pharmacology
  generic_urls:
    - http://www.iuphar.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=[example_id]
      example_id: IUPHAR_RECEPTOR:56
      example_url: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=56
- database: Jaiswal_Lab
  name: Jaiswal_Lab
  generic_urls:
    - http://wiki.plantontology.org/index.php/PO_REF:00008
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://wiki.plantontology.org/index.php/PO_REF:00008
      example_id: Jaiswal_Lab:gene00002
      example_url: http://wiki.plantontology.org/index.php/PO_REF:00008
- database: TIGRFAMS
  name: TIGRFAMs HMM collection at the J. Craig Venter Institute
  synonyms:
    - TIGR_TIGRFAMS
  generic_urls:
    - http://tigrfams.jcvi.org/cgi-bin/index.cgi
  entity_types:
    - type_name: polypeptide region
      type_id: SO:0000839
      id_syntax: TIGR[0-9]{5}
      url_syntax: http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=[example_id]
      example_id: TIGRFAMS:TIGR00254
      example_url: http://tigrfams.jcvi.org/cgi-bin/HmmReportPage.cgi?acc=TIGR00254
- database: JSTOR
  name: Digital archive of scholarly articles
  generic_urls:
    - https://www.jstor.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.jstor.org/stable/[example_id]
      example_id: JSTOR:3093870
      example_url: https://www.jstor.org/stable/3093870
- database: KEGG
  name: Kyoto Encyclopedia of Genes and Genomes
  generic_urls:
    - http://www.genome.ad.jp/kegg/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: KEGG_ENZYME
  name: KEGG Enzyme Database
  rdf_uri_prefix: http://identifiers.org/kegg.enzyme/
  generic_urls:
    - http://www.genome.jp/dbget-bin/www_bfind?enzyme
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: \d(\.\d{1,2}){2}\.\d{1,3}
      url_syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]
      example_id: KEGG_ENZYME:2.1.1.4
      example_url: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4
- database: KEGG_LIGAND
  name: KEGG LIGAND Database
  generic_urls:
    - http://www.genome.ad.jp/kegg/docs/upd_ligand.html
  entity_types:
    - type_name: chemical entity
      type_id: CHEBI:24431
      id_syntax: C\d{5}
      url_syntax: http://www.genome.jp/dbget-bin/www_bget?cpd:[example_id]
      example_id: KEGG_LIGAND:C00577
      example_url: http://www.genome.jp/dbget-bin/www_bget?cpd:C00577
- database: KEGG_PATHWAY
  name: KEGG Pathways Database
  rdf_uri_prefix: http://identifiers.org/kegg.pathway/
  generic_urls:
    - http://www.genome.jp/kegg/pathway.html
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.genome.jp/dbget-bin/www_bget?path:[example_id]
      example_id: KEGG_PATHWAY:ot00020
      example_url: http://www.genome.jp/dbget-bin/www_bget?path:ot00020
- database: KEGG_REACTION
  name: KEGG Reaction Database
  generic_urls:
    - http://www.genome.jp/kegg/reaction/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: R\d+
      url_syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]
      example_id: KEGG:R02328
      example_url: http://www.genome.jp/dbget-bin/www_bget?rn:R02328
- database: LIFEdb
  name: LifeDB
  description: LifeDB is a database for information on protein localization, interaction, functional assays and expression.
  generic_urls:
    - http://www.lifedb.de/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=[example_id]
      example_id: LIFEdb:DKFZp564O1716
      example_url: https://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html?ID=DKFZp564O1716
- database: MA
  name: Adult Mouse Anatomical Dictionary
  description: Adult Mouse Anatomical Dictionary; part of Gene Expression Database
  rdf_uri_prefix: http://purl.obolibrary.org/obo/MA_
  generic_urls:
    - http://www.informatics.jax.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:[example_id]
      example_id: MA:0000003
      example_url: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003
- database: MACSC_REF
  name: Maize Genetics and Genomics Database
  generic_urls:
    - http://www.maizegdb.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=[example_id]
      example_id: MACSC_REF:78112
      example_url: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112
- database: MaizeGDB
  name: MaizeGDB
  generic_urls:
    - https://www.maizegdb.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://maizegdb.org/gene_center/gene/[example_id]
      example_id: MaizeGDB:12098
      example_url: https://maizegdb.org/gene_center/gene/12098
- database: MaizeGDB_Locus
  name: MaizeGDB
  rdf_uri_prefix: http://identifiers.org/maizegdb.locus/
  generic_urls:
    - https://www.maizegdb.org/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: '[A-Za-z][A-Za-z0-9]*'
      url_syntax: https://www.maizegdb.org/gene_center/gene/[example_id]
      example_id: MaizeGDB_Locus:25011
      example_url: https://www.maizegdb.org/gene_center/gene/25011
- database: MaizeGDB_QTL
  name: Maize Genetics and Genomics Database
  generic_urls:
    - https://www.maizegdb.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.maizegdb.org/data_center/trait?id=[example_id]
      example_id: MaizeGDB_QTL:78112
      example_url: https://www.maizegdb.org/data_center/trait?id=78112
- database: MaizeGDB_REF
  name: Maize Genetics and Genomics Database
  generic_urls:
    - https://www.maizegdb.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://maizegdb.org/data_center/reference?id=[example_id]
      example_id: MaizeGDB_REF:9021423
      example_url: http://maizegdb.org/data_center/reference?id=9021423
- database: MaizeGDB_stock
  name: Maize Genetics and Genomics Database
  generic_urls:
    - https://www.maizegdb.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://maizegdb.org/data_center/stock?id=[example_id]
      example_id: MaizeGDB_stock:282110
      example_url: https://maizegdb.org/data_center/stock?id=282110
- database: MEDLINE
  name: Medline literature database
  generic_urls:
    - http://www.nlm.nih.gov/databases/databases_medline.html
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: MEDLINE:20572430
- database: MEROPS
  name: MEROPS peptidase database
  generic_urls:
    - https://www.ebi.ac.uk/merops/
  entity_types:
    - type_name: protein
      type_id: PR:000000001
      id_syntax: '^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3}|[A-Z]{3})$'
      url_syntax: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=[example_id]
      example_id: MEROPS:A08.001
      example_url: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=A08.001
- database: MEROPS_fam
  name: MEROPS peptidase database
  generic_urls:
    - https://www.ebi.ac.uk/merops
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: '^[SCTAGMNU]\d+$'
      url_syntax: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=[example_id]
      example_id: MEROPS_fam:M18
      example_url: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=M18
    - type_name: protein family
      type_id: NCIT:C20130
      id_syntax: '^[SCTAGMNU]\d+$'
      url_syntax: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=[example_id]
      example_id: MEROPS_fam:M18
      example_url: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=M18
- database: MeSH
  synonyms:
    - MESH
    - MSH
  name: Medical Subject Headings
  generic_urls:
    - https://meshb.nlm.nih.gov
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://id.nlm.nih.gov/mesh/[example_id]
      example_id: MeSH:D017209
      example_url: http://id.nlm.nih.gov/mesh/D017209
- database: MetaCyc
  name: Metabolic Encyclopedia of metabolic and other pathways
  synonyms:
    - METACYC
  rdf_uri_prefix: http://identifiers.org/metacyc.reaction/
  generic_urls:
    - https://metacyc.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: ^[A-Za-z0-9+_.%-:]+$
      url_syntax: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=[example_id]
      example_id: MetaCyc:GLUTDEG-PWY
      example_url: https://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY
- database: MGCSC_GENETIC_STOCKS
  name: Maize Genetics and Genomics Database
  generic_urls:
    - http://www.maizegdb.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=[example_id]
      example_id: MGCSC_GENETIC_STOCKS:78112
      example_url: http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=78112
- database: MGD
  name: Mouse Genome Database
  generic_urls:
    - http://www.informatics.jax.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: MGD:Adcy9
- database: MGI
  name: Mouse Genome Informatics
  rdf_uri_prefix: http://identifiers.org/MGI/
  generic_urls:
    - http://www.informatics.jax.org/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: MGI:[0-9]{5,}
      url_syntax: http://www.informatics.jax.org/accession/[example_id]
      example_id: MGI:MGI:1345277
      example_url: http://www.informatics.jax.org/accession/MGI:1345277
    - type_name: variation
      type_id: VariO:0001
      id_syntax: MGI:[0-9]{5,}
      url_syntax: http://www.informatics.jax.org/accession/[example_id]
      example_id: MGI:MGI:3590672
      example_url: http://www.informatics.jax.org/accession/MGI:3590672
- database: MIPS_funcat
  name: MIPS Functional Catalogue
  generic_urls:
    - http://mips.gsf.de/proj/funcatDB/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=[example_id]
      example_id: MIPS_funcat:11.02
      example_url: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02
- database: MITRE
  name: The MITRE Corporation
  generic_urls:
    - http://www.mitre.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: ModBase
  name: ModBase comprehensive Database of Comparative Protein Structure Models
  generic_urls:
    - http://modbase.compbio.ucsf.edu/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://salilab.org/modbase/searchbyid?databaseID=[example_id]
      example_id: ModBase:P10815
      example_url: http://salilab.org/modbase/searchbyid?databaseID=P04848
- database: NASC_code
  name: Nottingham Arabidopsis Stock Centre Seeds Database
  synonyms:
    - NASC
  generic_urls:
    - http://arabidopsis.info
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]
      example_id: NASC_code:N3371
      example_url: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371
- database: NC-IUBMB
  name: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
  generic_urls:
    - http://www.chem.qmw.ac.uk/iubmb/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: NCBI
  name: National Center for Biotechnology Information
  generic_urls:
    - http://www.ncbi.nlm.nih.gov/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: NCBIGene
  name: NCBI Gene
  synonyms:
    - GeneID
    - LocusID
    - NCBI_Gene
  rdf_uri_prefix: http://identifiers.org/ncbigene/
  generic_urls:
    - http://www.ncbi.nlm.nih.gov/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: \d+
      url_syntax: https://www.ncbi.nlm.nih.gov/gene/[example_id]
      example_id: NCBI_Gene:4771
      example_url: https://www.ncbi.nlm.nih.gov/gene/4771
- database: NCBI_gi
  name: NCBI databases
  generic_urls:
    - http://www.ncbi.nlm.nih.gov/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: '[0-9]{5,}'
      url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
      example_id: NCBI_gi:113194944
      example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=113194944
- database: NCBI_GP
  name: NCBI GenPept
  generic_urls:
    - http://www.ncbi.nlm.nih.gov/
  entity_types:
    - type_name: protein
      type_id: PR:000000001
      id_syntax: '[A-Z]{3}[0-9]{5}(\.[0-9]+)?'
      url_syntax: https://www.ncbi.nlm.nih.gov/protein/[example_id]
      example_id: NCBI_GP:EAL72968
      example_url: https://www.ncbi.nlm.nih.gov/protein/EAL72968
- database: NCBI_locus_tag
  name: NCBI locus tag
  generic_urls:
    - http://www.ncbi.nlm.nih.gov/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: NCBI_locus_tag:CTN_0547
- database: NCBI_NP
  name: NCBI Protein
  generic_urls:
    - https://www.ncbi.nlm.nih.gov/protein
- database: NIF_Subcellular
  name: Neuroscience Information Framework standard ontology, subcellular hierarchy
  generic_urls:
    - http://www.neurolex.org/wiki
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.neurolex.org/wiki/[example_id]
      example_id: NIF_Subcellular:sao1186862860
      example_url: http://www.neurolex.org/wiki/sao1770195789
- database: NTNU_SB
  name: Norwegian University of Science and Technology, Systems Biology team
  generic_urls:
    - http://www.ntnu.edu/nt/systemsbiology
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: OBI
  name: Ontology for Biomedical Investigations
  generic_urls:
    - http://obi-ontology.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: \d{7}
      example_id: OBI:0000038
      example_url: http://purl.obolibrary.org/obo/OBI_0000038
- database: OBO_SF_PO
  name: Source Forge OBO Plant Ontology (PO) term request tracker
  generic_urls:
    - http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555
      example_id: OBO_SF_PO:3184921
      example_url: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555
- database: OBO_SF2_PO
  name: Source Forge OBO Plant Ontology (PO) term request tracker
  generic_urls:
    - https://sourceforge.net/p/obo/plant-ontology-po-term-requests/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/[example_id]
      example_id: OBO_SF2_PO:500
      example_url: http://sourceforge.net/p/obo/plant-ontology-po-term-requests/500
- database: OBO_SF2_PECO
  name: Source Forge OBO plant-experimental-conditions-ontology (PECO) term request tracker
  generic_urls:
    - https://sourceforge.net/p/obo/plant-environment-ontology-eo/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://sourceforge.net/p/obo/plant-environment-ontology-eo/[example_id]
      example_id: OBO_SF2_PECO:89
      example_url: https://sourceforge.net/p/obo/plant-environment-ontology-eo/89/
- database: OMIM
  name: Mendelian Inheritance in Man
  synonyms:
    - MIM
  generic_urls:
    - https://omim.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax:  https://omim.org/entry/[example_id]
      example_id: OMIM:190198
      example_url: https://omim.org/entry/190198
- database: OMSSA
  name: Open Mass Spectrometry Search Algorithm
  generic_urls:
    - http://pubchem.ncbi.nlm.nih.gov/omssa/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: PANTHER
  name: Protein ANalysis THrough Evolutionary Relationships Classification System
  rdf_uri_prefix: http://identifiers.org/panther.family/
  generic_urls:
    - http://www.pantherdb.org/
  entity_types:
    - type_name: protein family
      type_id: NCIT:C20130
      id_syntax: PTN[0-9]{9}|PTHR[0-9]{5}|PTHR[0-9]{5}:SF[0-9]+
      url_syntax: http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]
      example_id: PANTHER:PTHR11455
      example_url: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000
- database: orcid
  name: Open Researcher and Contributor
  description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers.
  generic_urls:
    - https://orcid.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
      url_syntax: https://orcid.org/[example_id]
      example_id: orcid:0000-0003-4423-4370
      example_url: https://orcid.org/0000-0003-4423-4370
- database: ParkinsonsUK-UCL
  name: Parkinsons Disease Gene Ontology Initiative
  generic_urls:
    - https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: PATO
  name: Phenotypic quality ontology
  rdf_uri_prefix: http://purl.obolibrary.org/obo/PATO_
  generic_urls:
    - http://www.obofoundry.org/ontology/pato.html
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: PATO:0001420
      example_url: http://purl.obolibrary.org/obo/PATO_0001420
- database: PATRIC
  name: PathoSystems Resource Integration Center
  description: PathoSystems Resource Integration Center at the Virginia Bioinformatics Institute
  generic_urls:
    - https://www.patricbrc.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.patricbrc.org/view/Feature/[example_id]
      example_id: PATRIC:fig%7C83332.12.peg.11
      example_url: https://www.patricbrc.org/view/Feature/fig%7C83332.12.peg.1
- database: PDB
  name: Protein Data Bank
  generic_urls:
    - https://www.rcsb.org/pdb/
  entity_types:
    - type_name: protein
      type_id: PR:000000001
      id_syntax: '[A-Za-z0-9]{4}'
      url_syntax: https://www.rcsb.org/structure/[example_id]
      example_id: PDB:1A4U
      example_url: https://www.rcsb.org/structure/1A4U
- database: PECO_GIT
  name: GitHub Issue Tracker for PECO
  generic_urls:
    - https://github.com/Planteome/plant-experimental-conditions-ontology
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
      example_id: PECO_GIT:76
      example_url: https://github.com/Planteome/plant-experimental-conditions-ontology/issues/76
- database: Pfam
  name: Pfam database of protein families
  description: Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs)
  generic_urls:
    - https://www.ebi.ac.uk/interpro/entry/pfam
  entity_types:
    - type_name: sequence feature
      type_id: SO:0000110
      id_syntax: PF[0-9]{5}
      url_syntax: https://www.ebi.ac.uk/interpro/entry/pfam/[example_id]
      example_id: Pfam:PF00046
      example_url: https://www.ebi.ac.uk/interpro/entry/pfam/PF00069
    - type_name: polypeptide region
      type_id: SO:0000839
      id_syntax: PF[0-9]{5}
      url_syntax: https://www.ebi.ac.uk/interpro/entry/pfam/[example_id]
      example_id: Pfam:PF00046
      example_url: https://www.ebi.ac.uk/interpro/entry/pfam/PF00069
- database: PharmGKB
  name: Pharmacogenetics and Pharmacogenomics Knowledge Base
  generic_urls:
    - https://www.pharmgkb.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.pharmgkb.org/do/serve?objId=[example_id]
      example_id: PharmGKB:PA267
      example_url: https://www.pharmgkb.org/do/serve?objId=PA267
- database: PhenoScape
  name: PhenoScape Knowledgebase
  generic_urls:
    - http://phenoscape.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: PHI-base
  name: Pathogen-Host Interactions Database
  description: PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts.
  generic_urls:
    - http://www.phi-base.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: 'PHI:[0-9]+'
      url_syntax: http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:[example_id]
      example_id: PHI:3
      example_url: http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:3
- database: PIR
  name: Protein Information Resource
  generic_urls:
    - https://proteininformationresource.org/
  entity_types:
    - type_name: protein
      type_id: PR:000000001
      id_syntax: '[A-Z]{1}[0-9]{5}'
      url_syntax: https://proteininformationresource.org/cgi-bin/nbrfget?uid=[example_id]
      example_id: PIR:I49499
      example_url: https://proteininformationresource.org/cgi-bin/nbrfget?uid=I49499
- database: PIRSF
  name: PIR Superfamily Classification System
  generic_urls:
    - http://pir.georgetown.edu/pirsf/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]
      example_id: PIRSF:SF002327
      example_url: http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327
- database: PlantSystematics_image_archive
  name: PlantSystematics.org
  generic_urls:
    - http://plantsystematics.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.plantsystematics.org/imagebyid_[example_id].html
      example_id: PlantSystematics_image_archivee:37658
      example_url: http://www.plantsystematics.org/imagebyid_37658.html
- database: PMCID
  name: Pubmed Central
  synonyms:
    - PMC
  generic_urls:
    - https://www.ncbi.nlm.nih.gov/pmc/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.ncbi.nlm.nih.gov/pmc/articles/[example_id]
      example_id: PMCID:PMC201377
      example_url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC201377/
- database: PMID
  name: PubMed
  synonyms:
    - PUBMED
  rdf_uri_prefix: http://identifiers.org/pubmed/
  generic_urls:
    - https://www.ncbi.nlm.nih.gov/pubmed
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      id_syntax: '[0-9]+'
      url_syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
      example_id: PMID:31931324
      example_url: https://www.ncbi.nlm.nih.gov/pubmed/31931324
- database: PO
  name: Plant Ontology
  rdf_uri_prefix: http://purl.obolibrary.org/obo/PO_
  generic_urls:
    - http://www.planteome.org/
  entity_types:
    - type_name: plant anatomical entity
      type_id: PO:0025131
      id_syntax: '[0-9]{7}'
      url_syntax: http://browser.planteome.org/amigo/term/PO:[example_id]
      example_id: PO:0009004
      example_url: http://browser.planteome.org/amigo/term/PO:0009004
    - type_name: plant structure development stage
      type_id: PO:0009012
      id_syntax: '[0-9]{7}'
      url_syntax: http://browser.planteome.org/amigo/term/PO:[example_id]
      example_id: PO:0025131
      example_url: http://browser.planteome.org/amigo/term/PO:0025131
- database: PO_GIT
  name: GitHub Issue Tracker for PO
  generic_urls:
    - https://github.com/Planteome/plant-ontology
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://github.com/Planteome/plant-ontology/issues/[example_id]
      example_id: PO_GIT:626
      example_url: https://github.com/Planteome/plant-ontology/issues/626
- database: PO_REF
  name: Plant Ontology custom references
  generic_urls:
    - http://planteome.org/po_ref
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://planteome.org/po_ref/[example_id]
      example_id: PO_REF:00001
      example_url: http://planteome.org/po_ref/00001
- database: PlasmoDB
  name: PlasmoDB
  rdf_uri_prefix: http://identifiers.org/plasmodb/
  generic_urls:
    - https://plasmodb.org
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: PF3D7_[0-9]{7}
      url_syntax: https://plasmodb.org/plasmo/app/record/gene/[example_id]
      example_id: PF3D7_1467300
      example_url: https://plasmodb.org/plasmo/app/record/gene/PF3D7_1467300
- database: POC
  name: Plant Ontology Consortium
  generic_urls:
    - http://www.plantontology.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: PomBase
  name: PomBase
  rdf_uri_prefix: http://identifiers.org/pombase/
  generic_urls:
    - https://www.pombase.org/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: S\w+(\.)?\w+(\.)?
      url_syntax: https://www.pombase.org/gene/[example_id]
      example_id: PomBase:SPBC11B10.09
      example_url: https://www.pombase.org/gene/SPBC11B10.09
    - type_name: transcript
      type_id: SO:0000673
      id_syntax: S\w+(\.)?\w+(\.)?\d+
      url_syntax: https://www.pombase.org/gene/[example_id]
      example_id: PomBase:SPCC548.03c.2
      example_url: https://www.pombase.org/gene/SPCC548.03c.2
- database: Pompep
  name: Schizosaccharomyces pombe protein data
  generic_urls:
    - https://www.pombase.org/downloads/protein-datasets
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      example_id: Pompep:SPAC890.04C
- database: PPI
  name: Pseudomonas syringae community annotation project
  generic_urls:
    - http://www.pseudomonas-syringae.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: PR
  name: Protein Ontology
  synonyms:
    - PRO
  rdf_uri_prefix: http://purl.obolibrary.org/obo/PR_
  generic_urls:
    - https://proconsortium.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}[0-9]){1,2}){1}(-[0-9]+){0,1}|[0-9]{9}
      url_syntax: https://purl.obolibrary.org/obo/PR_[example_id]
      example_id: PR:Q64445
      example_url: https://purl.obolibrary.org/obo/PR_000060258
- database: PRINTS
  name: PRINTS compendium of protein fingerprints
  generic_urls:
    - http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
  entity_types:
    - type_name: polypeptide region
      type_id: SO:0000839
      id_syntax: PR[0-9]{5}
      url_syntax: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=[example_id]
      example_id: PRINTS:PR00025
      example_url: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=PR00025
- database: Prosite
  name: Prosite database of protein families and domains
  generic_urls:
    - https://prosite.expasy.org/
  entity_types:
    - type_name: polypeptide region
      type_id: SO:0000839
      id_syntax: PDOC[0-9]{5}
      url_syntax: https://prosite.expasy.org/[example_id]
      example_id: PDOC00314
      example_url: https://prosite.expasy.org/PDOC00314
- database: protein_id
  name: DDBJ / ENA / GenBank
  description: protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases
  generic_urls:
    - http://www.ddbj.nig.ac.jp/
    - http://www.ebi.ac.uk/ena/
    - http://www.ncbi.nlm.nih.gov/Genbank/
  entity_types:
    - type_name: protein
      type_id: PR:000000001
      id_syntax: '[A-Z]{3}[0-9]{5}(\.[0-9]+)?'
      example_id: protein_id:CAA71991
- database: PseudoCAP
  name: Pseudomonas Genome Project
  generic_urls:
    - http://www.pseudomonas.com
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://www.pseudomonas.com/feature/show?locus_tag=[example_id]
      example_id: PseudoCAP:PA4756
      example_url: http://www.pseudomonas.com/feature/show?locus_tag=PA4756
- database: PSO_GIT
  name: GitHub Issue Tracker for PSO
  generic_urls:
    - https://github.com/Planteome/plant-stress-ontology
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://github.com/Planteome/plant-stress-ontology/issues/[example_id]
      example_id: PSO_GIT:169
      example_url: https://github.com/Planteome/plant-stress-ontology/issues/169
- database: PSI-MI
  name: Proteomic Standard Initiative for Molecular Interaction
  synonyms:
    - MI
  generic_urls:
    - http://www.psidev.info/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://purl.obolibrary.org/obo/
      example_id: MI_0018
      example_url: http://purl.obolibrary.org/obo/MI_0018
- database: PSI-MOD
  name: Proteomics Standards Initiative protein modification ontology
  synonyms:
    - MOD
  generic_urls:
    - http://www.psidev.info/groups/protein-modifications
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://purl.obolibrary.org/obo/[example_id]
      example_id: MOD_00219
      example_url: http://purl.obolibrary.org/obo/MOD_00219
- database: PSORT
  name: PSORT protein subcellular localization databases and prediction tools for bacteria
  generic_urls:
    - https://www.psort.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: PubChem_BioAssay
  name: NCBI PubChem database of bioassay records
  generic_urls:
    - https://pubchem.ncbi.nlm.nih.gov
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://pubchem.ncbi.nlm.nih.gov/bioassay/[example_id]
      example_id: PubChem_BioAssay:177
      example_url: https://pubchem.ncbi.nlm.nih.gov/bioassay/177
- database: PubChem_Compound
  name: NCBI PubChem database of chemical structures
  generic_urls:
    - https://pubchem.ncbi.nlm.nih.gov
  entity_types:
    - type_name: chemical entity
      type_id: CHEBI:24431
      id_syntax: '[0-9]+'
      url_syntax: https://pubchem.ncbi.nlm.nih.gov/compound/[example_id]
      example_id: PubChem_Compound:159296
      example_url: https://pubchem.ncbi.nlm.nih.gov/compound/159296
- database: PubChem_Substance
  name: NCBI PubChem database of chemical substances
  generic_urls:
    - https://pubchem.ncbi.nlm.nih.gov
  entity_types:
    - type_name: chemical entity
      type_id: CHEBI:24431
      id_syntax: '[0-9]{4,}'
      url_syntax: https://pubchem.ncbi.nlm.nih.gov/substance/[example_id]
      example_id: PubChem_Substance:4594
      example_url: https://pubchem.ncbi.nlm.nih.gov/substance/4594
- database: RAP-DB
  name: Rice annotation Project database
  generic_urls:
    - https://rapdb.dna.affrc.go.jp
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=[example_id]
      example_id: RAP-DB:Os01t0100600-01
      example_url: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=Os01t0100600-01
- database: Reactome
  name: Reactome - a curated knowledgebase of biological pathways
  synonyms:
    - REACTOME
    - REAC
  rdf_uri_prefix: http://identifiers.org/reactome/
  generic_urls:
    - https://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: https://www.reactome.org/content/detail/[example_id]
      example_id: Reactome:R-HSA-109582
      example_url: https://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: https://www.ncbi.nlm.nih.gov/protein/[example_id]
      example_id: RefSeq:XP_001068954
      example_url: https://www.ncbi.nlm.nih.gov/protein/NP_001121125
- 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:
    - https://rfam.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://rfam.org/family/[example_id]
      example_id: Rfam:RF00012
      example_url: https://rfam.org/family/RF00012
- database: RGD
  name: Rat Genome Database
  synonyms:
    - RAD
    - RGDID
  rdf_uri_prefix: http://identifiers.org/rgd/
  generic_urls:
    - https://rgd.mcw.edu/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      id_syntax: '[0-9]{4,7}'
      url_syntax: https://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]
      example_id: RGD:2004
      example_url: https://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:
    - https://www.rhea-db.org
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.rhea-db.org/rhea/[example_id]
      example_id: RHEA:25811
      example_url: https://www.rhea-db.org/rhea/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:
    - https://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: https://rnacentral.org/rna/[example_id]
      example_id: RNAcentral:URS000047C79B_9606
      example_url: https://rnacentral.org/rna/URS000047C79B_9606
- database: RNAmods
  name: RNA Modification Database
  synonyms:
    - RNAMDB
  generic_urls:
    - https://mods.rna.albany.edu/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://mods.rna.albany.edu/mods/modifications/view/[example_id]
      example_id: RNAmods:20
      example_url: https://mods.rna.albany.edu/mods/modifications/view/20
- 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: 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: 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:  https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
      example_id: SGD:S000006169
      example_url: https://www.yeastgenome.org/search?q=S000006169&is_quick=true
- database: SGD_LOCUS
  name: Saccharomyces Genome Database
  generic_urls:
    - http://www.yeastgenome.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
      example_id: SGD_LOCUS:GAL4
      example_url: https://www.yeastgenome.org/search?q=S000006169&is_quick=true
- 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: SGD_PWY
  name: Saccharomyces Genome Database YeastPathways
  generic_urls:
    - https://pathway.yeastgenome.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax:  https://www.yeastgenome.org/locus/[example_id]
      example_id: SGD_PWY:CYSTEINE-SYN2-PWY
      example_url: https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=NIL&object=SERSYN-PWY
- database: SGN
  name: Sol Genomics Network
  synonyms:
    - SGN_gene
  rdf_uri_prefix: http://identifiers.org/sgn/
  generic_urls:
    - https://www.sgn.cornell.edu/
  entity_types:
    - type_name: gene
      type_id: SO:0000704
      url_syntax: http://solgenomics.net/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:
    - https://www.sgn.cornell.edu/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]
      example_id: SGN_ref:861
      example_url: https://sgn.cornell.edu/chado/publication.pl?pub_id=861
- database: SGN_germplasm
  name: Sol Genomics Network
  generic_urls:
    - https://solgenomics.net/
  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: SO
  name: Sequence Ontology
  rdf_uri_prefix: http://purl.obolibrary.org/obo/SO_
  generic_urls:
    - http://www.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:0000400
      example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0000400
    - 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:0000307
      example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0000307
    - type_name: sequence motif
      type_id: SO:0001683
      id_syntax: \d{7}
      url_syntax: http://www.sequenceontology.org/browser/current_svn/term/SO:[example_id]
      example_id: SO:0001166
      example_url: http://www.sequenceontology.org/browser/current_svn/term/SO:0001166
- database: Soy_gene
  name: SoyBase
  generic_urls:
    - https://soybase.org/
  entity_types:
    - type_name: gene
      type_id: BET:0000000
      url_syntax: https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=[example_id]
      example_id: Glyma18g02210
      example_url: https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=Glyma18g02210
- database: SOY_QTL
  name: SoyBase
  generic_urls:
    - https://soybase.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=[example_id]
      example_id: Seedling, abnormal+1-1
      example_url: https://www.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=Seedling,+abnormal+1-1
- database: SOY_ref
  name: SoyBase
  generic_urls:
    - https://soybase.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=[example_id]
      example_id: SOY ref:SoyBase6597900
      example_url: https://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=SoyBase3142000126
- database: SUPERFAMILY
  name: SUPERFAMILY protein annotation database
  description: A database of structural and functional protein annotations for completely sequenced genomes
  generic_urls:
    - http://supfam.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
      url_syntax: http://supfam.org/scop/[example_id]
      example_id: SUPERFAMILY:56994
      example_url: http://supfam.org/scop/56994
- database: SynGO
  name: The Synapse Gene Ontology and Annotation Initiative
  generic_urls:
    - https://www.syngoportal.org/
  entity_types:
    - type_name: entity
      type_id: BET:0000000
- database: SynGO-UCL
  name: The Synapse Gene Ontology and Annotation Initiative at UCL
  generic_urls:
    - 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: 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: NCBITaxon
  name: NCBI Taxonomy
  synonyms:
    - taxon
    - 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: NCBITaxon: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: 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: http://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: 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: 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: http://identifiers.org/wormbase/
  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: 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: http://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: http://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
- database: TreeGrafter
  name: TreeGrafter-generated GO annotations
  rdf_uri_prefix: http://identifiers.org/panther.family/
  generic_urls:
    - http://www.pantherdb.org/
  entity_types:
    - type_name: protein family
      type_id: NCIT:C20130
      id_syntax: PTN[0-9]{9}|PTHR[0-9]{5}|PTHR[0-9]{5}:SF[0-9]+
      url_syntax: http://www.pantherdb.org/panther/lookupId.jsp?id=[example_id]
      example_id: PANTHER:PTHR11455
      example_url: http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10000