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resourceDescriptors.yaml
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resourceDescriptors.yaml
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# AGR Schema Resource Descriptors YAML.
# When submitting identifiers, please use the appropriate example_id/gid field listed below.
#
# AGR
#
- db_prefix: Alliance of Genome Resources
name: Alliance of Genome Resources
default_url: https://www.alliancegenome.org/
pages:
- name: homepage
url: https://www.alliancegenome.org/
#
# MGI
#
- db_prefix: MGI
name: MGI
example_id: MGI:80863
gid_pattern: "^MGI:\\d+$"
default_url: http://www.informatics.jax.org/
pages:
- name: gene
url: http://www.informatics.jax.org/marker/MGI:[%s]
- name: gene/expression
url: http://www.informatics.jax.org/gxd/marker/MGI:[%s]
- name: gene/expression_images
url: http://www.informatics.jax.org/gxd/marker/MGI:[%s]?tab=imagestab
- name: gene/references
url: http://www.informatics.jax.org/reference/marker/MGI:[%s]
- name: gene/phenotypes
url: http://www.informatics.jax.org/marker/phenotypes/MGI:[%s]
- name: gene/phenotypes_impc
url: https://www.mousephenotype.org/data/genes/MGI:[%s]
- name: allele
url: http://www.informatics.jax.org/allele/MGI:[%s]
- name: allele/references
url: http://www.informatics.jax.org/reference/allele/MGI:[%s]?typeFilter=Literature
- name: genotype
url: http://www.informatics.jax.org/allele/genoview/MGI:[%s]
- name: homepage
url: http://www.informatics.jax.org/
- name: disease
url: http://www.informatics.jax.org/disease/MGI:[%s]
- name: gene/expression/annotation/detail
url: http://www.informatics.jax.org/assay/MGI:[%s]
- name: gene/MODinteractions_molecular
url: http://www.informatics.jax.org/interaction/explorer?markerIDs=MGI:[%s]
- name: gene/MODinteractions_genetic
url: http://www.informatics.jax.org/interaction/explorer?markerIDs=MGI:[%s]
- name: gene/MODinteractions
url: http://www.informatics.jax.org/interaction/explorer?markerIDs=MGI:[%s]
- name: reference
url: http://www.informatics.jax.org/reference/MGI:[%s]
- name: htp/dataset
url: http://www.informatics.jax.org/gxd/htexp_index/summary?arrayExpressID=[%s]
#
# MGI - old style IDs
#
- db_prefix: MGD_old
name: MGD_old
example_id: MGD_old:MGD-MRK-11588
gid_pattern: "^MGD_old:MGD-[A-Z]+-\\d+$"
default_url:
pages:
- name: gene
url: http://www.informatics.jax.org/accession/[%s]
#
# RGD
#
- db_prefix: RGD
name: RGD
example_gid: RGD:1311419
gid_pattern: "^RGD:\\d+$"
default_url: https://rgd.mcw.edu/rgdweb/elasticResults.html?term=RGD:[%s]
pages:
- name: gene
url: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=RGD:[%s]
- name: homepage
url: https://rgd.mcw.edu/
- name: allele
url: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=RGD:[%s]
- name: allele/references
url: https://rgd.mcw.edu/rgdweb/report/gene/main.html?view=5&id=[%s]
- name: gene/references
url: https://rgd.mcw.edu/rgdweb/report/gene/main.html?view=5&id=[%s]
- name: gene/phenotypes
url: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=RGD:[%s]
- name: disease/rat
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=Rat&x=1&acc_id=[%s]#annot
- name: disease/human
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=Human&x=1&acc_id=[%s]#annot
- name: disease/all
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=All&x=1&acc_id=[%s]#annot
- name: gene/MODinteractions
url: https://rgd.mcw.edu/rgdweb/cytoscape/cy.html?species=3&identifiers=[%s]
- name: gene/MODinteractions_molecular
url: https://rgd.mcw.edu/rgdweb/cytoscape/cy.html?species=3&identifiers=[%s]
- name: gene/MODinteractions_genetic
url: https://rgd.mcw.edu/rgdweb/cytoscape/cy.html?species=3&identifiers=[%s]
- name: reference
url: https://rgd.mcw.edu/rgdweb/report/reference/main.html?id=RGD:[%s]
- name: strain
url: https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=[%s]
- name: pub
url: http://rgd.mcw.edu/rgdweb/search/search.html?term=[%s]
#
# Xenbase
#
- db_prefix: Xenbase
name: Xenbase
aliases: ['XENBASE']
example_gid: Xenbase:XB-GENE-922462
gid_pattern: "^Xenbase:\\S+$"
default_url: https://www.xenbase.org/entry/[%s]
pages:
- name: gene
url: https://www.xenbase.org/entry/[%s]
- name: gene/expression
url: https://www.xenbase.org/entry/[%s]
- name: gene/references
url: https://www.xenbase.org/entry/[%s]
- name: gene/phenotypes
url: https://www.xenbase.org/entry/[%s]
- name: Xenopus
url: https://www.xenbase.org/entry/[%s]
- name: homepage
url: https://www.xenbase.org/entry/
- name: disease
url: https://www.xenbase.org/entry/[%s]
- name: figure
url: https://www.xenbase.org/entry/[%s]
- name: reference
url: https://www.xenbase.org/entry/[%s]
- name: gene/expression_images
url: https://www.xenbase.org/entry/[%s]
- name: htp/dataset
url: https://www.xenbase.org/entry/[%s]
- name: gene/MODinteractions
url: https://www.xenbase.org/entry/[%s]
- name: gene/MODinteractions_molecular
url: https://www.xenbase.org/entry/[%s]
- name: gene/MODinteractions_genetic
url: https://www.xenbase.org/entry/[%s]
#
# ZFIN
#
- db_prefix: ZFIN
name: ZFIN
example_gid: ZFIN:ZDB-GENE-030131-9438
gid_pattern: "^ZFIN:\\S+$"
default_url: https://zfin.org/[%s]
pages:
- name: gene
url: https://zfin.org/[%s]
- name: gene/expression
url: https://zfin.org/action/marker/[%s]/expression
- name: gene/wild_type_expression
description: "Wild type expression data"
url: https://zfin.org/[%s]/wt-expression
- name: gene/references
url: https://zfin.org/action/marker/citation-list/[%s]
- name: gene/phenotypes
url: https://zfin.org/action/marker/[%s]/phenotype-summary
- name: allele
url: https://zfin.org/[%s]
- name: variation
url: https://zfin.org/[%s]
- name: genotype
url: https://zfin.org/[%s]
- name: construct
url: https://zfin.org/[%s]
- name: fish
url: https://zfin.org/[%s]
- name: homepage
url: https://zfin.org/
- name: disease
url: https://zfin.org/[%s]
- name: figure
url: https://zfin.org/[%s]
- name: gene/expression/annotation/detail
url: https://zfin.org/[%s]
- name: reference
url: https://zfin.org/[%s]
- name: gene/expression_images
url: https://zfin.org/[%s]/wt-expression/images
- name: allele/references
url: https://zfin.org/action/publication/list/[%s]
- name: htp/dataset
url: https://zfin.org/[%s]
- name: journal
url: https://zfin.org/[%s]
- name: journal/references
url: https://zfin.org/[%s]
#
# FlyBase
#
- db_prefix: FB
name: FlyBase
aliases: ['FLYBASE']
example_gid: FB:FBgn0000490
gid_pattern: "^FB:FB.+$"
default_url: https://flybase.org/reports/[%s].html
pages:
- name: gene
url: https://flybase.org/reports/[%s].html
- name: gene/expression
url: https://flybase.org/reports/[%s].html#expression
- name: gene/expression_images
url: https://flybase.org/reports/[%s].html#expression
- name: gene/references
url: https://flybase.org/reports/[%s].html#pubs
- name: gene/phenotypes
url: https://flybase.org/reports/[%s].html#phenotypes
- name: gene/disease
url: https://flybase.org/reports/[%s].html#hdm_sub
- name: allele
url: https://flybase.org/reports/[%s].html
- name: allele/disease
url: https://flybase.org/reports/[%s].html#human_disease_models
- name: allele/references
url: https://flybase.org/reports/[%s].html#pubs
- name: construct
url: https://flybase.org/reports/[%s].html
- name: strain
url: https://flybase.org/reports/[%s].html
- name: homepage
url: https://flybase.org/
- name: gene/interactions
url: https://flybase.org/reports/[%s].html
- name: gene/MODinteractions
url: https://flybase.org/reports/[%s]#summary_physical_interactions_sub
- name: gene/MODinteractions_molecular
url: https://flybase.org/reports/[%s]#summary_physical_interactions_sub
- name: gene/MODinteractions_genetic
url: https://flybase.org/reports/[%s]#summary_genetic_interactions_sub
- name: reference
url: https://flybase.org/reports/[%s].html
- name: htp/dataset
url: https://flybase.org/reports/[%s].html
- name: expression_atlas
url: http://www.ebi.ac.uk/gxa/genes/[%s]
#
# WormBase
#
- db_prefix: WB
name: WormBase genes
aliases: ['WORMBASE']
example_gid: WB:WBGene00000064
gid_pattern: "^WB:\\w+$"
default_url: https://www.wormbase.org/get?name=[%s]
pages:
- name: gene
url: https://www.wormbase.org/db/get?name=[%s];class=Gene
- name: gene/phenotypes
url: https://www.wormbase.org/db/get?name=[%s];class=Gene;widget=phenotypes
- name: gene/expression
url: https://www.wormbase.org/db/get?name=[%s];class=Gene;widget=expression
- name: gene/expression_images
url: https://www.wormbase.org/db/get?name=[%s];class=Gene;widget=expression
- name: gene/interactions
url: http://www.wormbase.org/db/get?name=[%s];class=interaction
- name: gene/references
url: https://www.wormbase.org/db/get?name=[%s];class=Gene;widget=references
- name: gene/phenotypes
url: https://www.wormbase.org/db/get?name=[%s];class=Gene;widget=phenotype
- name: gene/spell
url: http://spell.wormbase.org/search/show_results?search_string=[%s]
- name: gene/expression/annotation/detail
url: https://www.wormbase.org/species/all/expr_pattern/[%s]
- name: strain
url: http://www.wormbase.org/db/get?name=[%s];class=Strain
- name: reference
url: https://www.wormbase.org/db/get?name=[%s];class=Paper
- name: transgene
url: https://www.wormbase.org/db/get?name=[%s];class=Transgene
- name: transgene/references
url: https://www.wormbase.org/db/get?name=[%s];class=Transgene;widget=references
- name: allele
url: https://www.wormbase.org/db/get?name=[%s];class=Variation
- name: allele/references
url: https://www.wormbase.org/db/get?name=[%s];class=Variation;widget=references
- name: homepage
url: https://www.wormbase.org/
- name: disease
url: https://www.wormbase.org/resources/disease/[%s]
- name: gene/MODinteractions
url: http://www.wormbase.org/db/get?name=[%s];class=Gene;widget=interactions
- name: gene/MODinteractions_molecular
url: http://www.wormbase.org/db/get?name=[%s];class=Gene;widget=interactions
- name: gene/MODinteractions_genetic
url: http://www.wormbase.org/db/get?name=[%s];class=Gene;widget=interactions
- name: construct
url: https://www.wormbase.org/db/get?name=[%s];class=Construct
- name: pub
url: http://www.wormbase.org/db/misc/paper?name=[%s]
- name: htp/dataset
url: https://www.wormbase.org/resources/analysis/[%s]
- name: genotype
url: https://wormbase.org/species/all/genotype/[%s]
- name: molecule
url: https://wormbase.org/resources/molecule/[%s]
#
# SGD
#
- db_prefix: SGD
name: SGD genes
example_gid: SGD:S000001855
gid_pattern: "^SGD:\\w+$"
default_url: https://www.yeastgenome.org/
pages:
- name: gene
url: https://www.yeastgenome.org/locus/[%s]
- name: gene/expression
url: https://www.yeastgenome.org/locus/[%s]/expression
- name: gene/interactions
url: https://www.yeastgenome.org/locus/[%s]/interaction
- name: homepage
url: https://www.yeastgenome.org/
- name: gene/spell
url: https://spell.yeastgenome.org/search/show_results?search_string=[%s]
- name: gene/references
url: https://www.yeastgenome.org/locus/[%s]/literature
- name: gene/disease
url: https://www.yeastgenome.org/locus/[%s]/disease
- name: gene/phenotypes
url: https://www.yeastgenome.org/locus/[%s]/phenotype
- name: gene/MODinteractions
url: https://www.yeastgenome.org/locus/[%s]/interaction#physical_interaction
- name: gene/MODinteractions_molecular
url: https://www.yeastgenome.org/locus/[%s]/interaction#physical_interaction
- name: gene/MODinteractions_genetic
url: https://www.yeastgenome.org/locus/[%s]/interaction#genetic_interaction
- name: htp/dataset
url: https://www.yeastgenome.org/dataset/[%s]
- name: reference
url: https://www.yeastgenome.org/reference/[%s]
- name: strain
url: https://www.yeastgenome.org/strain/[%s]
- name: allele
url: https://www.yeastgenome.org/allele/[%s]
- name: allele/references
url: https://www.yeastgenome.org/allele/[%s]/literature
- name: expression_atlas
url: http://www.ebi.ac.uk/gxa/genes/[%s]
#
# GO
#
- db_prefix: GO
name: Gene Ontology
example_gid: GO:0045860
gid_pattern: "^(go:)?GO:\\d+$"
default_url: http://amigo.geneontology.org/amigo/term/GO:[%s]
pages:
- name: gene/interactions
url: http://amigo.geneontology.org/amigo/term/[%s]
#
# External resources
# Ordered to make finding easier. Please add new ones in proper place.
#
- db_prefix: ArrayExpress
name: ArrayExpress
example_id: ArrayExpress:E-MEXP-31
gid_pattern: "^ArrayExpress:\\w+$"
default_url: https://www.ebi.ac.uk/arrayexpress/experiments/[%s]
pages:
- name: htp/dataset
url: https://www.ebi.ac.uk/arrayexpress/experiments/[%s]
- db_prefix: BIOGRID
name: Biological General Repository for Interaction Datasets
example_id: BIOGRID:1276808
gid_pattern: "^BIOGRID:\\d+$"
default_url: https://thebiogrid.org/interaction/[%s]
pages:
- name: gene/interactions
url: https://thebiogrid.org/interaction/[%s]
- db_prefix: bmrb
name: Biological Magnetic Resonance Data Bank
example_id: bmrb:4899
gid_pattern: "^bmrb:\\d+$"
default_url: https://bmrb.io/data_library/summary/index.php?bmrbId=[%s]
pages:
- name: gene/interactions
url: https://bmrb.io/data_library/summary/index.php?bmrbId=[%s]
- db_prefix: CHEBI
aliases: ['chebi']
name: Chemical Entities of Biological Interest Ontology
example_gid: CHEBI:53438
gid_pattern: "^(CHEBI|chebi):\\d+$"
default_url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=[%s]
pages:
- name: gene/interactions
url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=[%s]
- db_prefix: DIP
name: Database of Interacting Proteins
example_id: DIP:DIP-88423E
gid_pattern: "^DIP:DIP(\\:)?\\-\\d{1,}[ENXS]$"
default_url: http://dip.mbi.ucla.edu/dip/record?ac=[%s]
pages:
- name: gene/interactions
url: http://dip.mbi.ucla.edu/dip/record?ac=[%s]
- db_prefix: DOI
name: DOI
example_gid: DOI:10.3389/fcimb.2016.00052
gid_pattern: "^DOI:\\S+$"
default_url: https://doi.org/doi:[%s]
pages:
- name: reference
url: https://doi.org/doi:[%s]
- db_prefix: DOID
name: Disease Ontology
example_gid: DOID:820
gid_pattern: "^DOID:\\d+$"
default_url: http://www.disease-ontology.org/?id=[%s]
pages:
- name: disease/rat
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=Rat&x=1&acc_id=DOID:[%s]#annot
- name: disease/human
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=Human&x=1&acc_id=DOID:[%s]#annot
- name: disease/all
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=All&x=1&acc_id=DOID:[%s]#annot
- name: disease/zfin
url: https://zfin.org/[%s]
- name: disease/wb
url: https://www.wormbase.org/resources/disease/[%s]
- name: disease/fb
url: https://flybase.org/cgi-bin/cvreport.html?id=[%s]
- name: disease/sgd
url: https://www.yeastgenome.org/disease/[%s]
- db_prefix: DRSC
name: DRSC
example_gid: DRSC:FBgn0000490
gid_pattern: "^DRSC:\\S+$"
default_url:
- db_prefix: ECO
name: Evidence and Conclusion Ontology
example_gid: ECO:0000000
gid_pattern: "^ECO:\\d+$"
default_url: http://www.evidenceontology.org/browse/#ECO:[%s]
- db_prefix: EFO
name: Experimental Factor Ontology
example_gid: EFO:EFO_0000000
gid_pattern: "^(efo:)?EFO(:EFO_)?\\d+$"
default_url: http://www.ebi.ac.uk/efo/EFO_[%s]
pages:
- name: ontology_provided_cross_references
url: http://www.ebi.ac.uk/efo/EFO_[%s]
- name: gene/interactions
url: https://www.ebi.ac.uk/ols/search?q=[%s]&exact=on
# Note: The code has been modified to handle EFO identifiers in two configurations: "EFO:12345" and "EFO:EFO_12345".
# This normalization is done within the return_url_from_identifier method in the resource_descriptor_helper_2.py file.
- db_prefix: EMDB
name: Electron Microscopy Data Bank
example_id: EMDB:EMD-1191
gid_pattern: "^(EMDB:EMDB?-\\d{4})|(EMDB:\\d{4})$"
default_url: http://www.ebi.ac.uk/pdbe/entry/emdb/[%s]
pages:
- name: gene/interactions
url: http://www.ebi.ac.uk/pdbe/entry/emdb/[%s]
- db_prefix: empiar
name: EMPIAR
example_id: empiar:EMPIAR-10357
gid_pattern: "^empiar:EMPIAR\\-\\d{5}$"
default_url: https://www.ebi.ac.uk/pdbe/emdb/empiar/[%s]
pages:
- name: gene/interactions
url: https://www.ebi.ac.uk/pdbe/emdb/empiar/[%s]
- db_prefix: ENSEMBL
name: Ensembl
example_id: ENSEMBL:FBgn0000490
gid_pattern: "^ENSEMBL:\\w+$"
default_url: http://www.ensembl.org/id/[%s]
pages:
- name: expression_atlas
url: http://www.ebi.ac.uk/gxa/genes/[%s]
- db_prefix: flannotator
name: The FlAnnotator
example_id: flannotator:CPTI-002267
gid_pattern: "^flannotator:[A-Z]+\\-\\d+$"
default_url: http://www.flannotator.org.uk
pages:
- name: gene/interactions
url: http://www.flannotator.org.uk
- db_prefix: GARD
name: GARD
example_id: GARD:262
gid_pattern: "^GARD:\\d+$"
default_url: https://rarediseases.info.nih.gov/diseases/[%s]/index
pages:
- name: ontology_provided_cross_reference
url: https://rarediseases.info.nih.gov/diseases/[%s]/index
- db_prefix: GEO
name: Gene Expression Omnibus
example_id: GEO:GSE59105
gid_pattern: "^GEO:GS[EM]\\d+$"
default_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=[%s]
pages:
- name: htp/dataset
url: https://www.ncbi.nlm.nih.gov/gds/?term=[%s]
- name: htp/datasetsample
url: https://www.ncbi.nlm.nih.gov/gds/?term=[%s]
- name: entrezgene
url: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=geoprofiles&DbFrom=gene&Cmd=Link&LinkName=gene_geoprofiles&LinkReadableName=GEO%20Profiles&IdsFromResult=[%s]
- db_prefix: GXA
name: ExpressionAtlas
example_id: GXA:E-MTAB-8344
gid_pattern: "^GXA:\\w+$"
default_url: https://www.ebi.ac.uk/gxa/experiments/[%s]/Results
pages:
- name: htp/dataset
url: https://www.ebi.ac.uk/gxa/experiments/[%s]/Results
- db_prefix: HGNC
name: HGNC
example_gid: HGNC:33510
gid_pattern: "^HGNC:\\d+$"
default_url: https://bioregistry.io/hgnc:[%s]
pages:
- name: gene
url: https://bioregistry.io/hgnc:[%s]
- name: gene/MODinteractions
url: https://rgd.mcw.edu/rgdweb/cytoscape/cy.html?species=1&identifiers=HGNC:[%s]
- name: gene/MODinteractions_genetic
url: https://rgd.mcw.edu/rgdweb/cytoscape/cy.html?species=1&identifiers=HGNC:[%s]
- name: gene/MODinteractions_molecular
url: https://rgd.mcw.edu/rgdweb/cytoscape/cy.html?species=1&identifiers=HGNC:[%s]
- name: disease/human
url: https://rgd.mcw.edu/rgdweb/ontology/annot.html?species=Human&x=1&acc_id=[%s]#annot
- db_prefix: ICD9CM
name: ICD9CM
example_gid: ICD9CM:237.7
gid_pattern: "^ICD9CM:[EV]?\\d+(\\.[\\dA-z]+)?(\\-[EV]?\\d+(\\.[\\dA-z]+)?)?$"
default_url: http://www.icd9data.com/Search/?q=[%s]
pages:
- name: gene/MODinteractions_genetic
url: http://www.icd9data.com/Search/?q=[%s]
- name: ontology_provided_cross_reference
url: http://www.icd9data.com/Search/?q=[%s]
- db_prefix: ICD10
name: ICD10
example_gid: ICD10:H00.019
gid_pattern: "^ICD10:.+$"
default_url: http://www.icd10data.com/search?s=[%s]
pages:
- name: ontology_provided_cross_reference
url: http://www.icd10data.com/search?s=[%s]
- db_prefix: ICD10CM
name: ICD10CM
example_gid: ICD10CM:L89
gid_pattern: "^ICD10CM:[A-Z]\\d(\\d|[A-Z])(\\.[\\d|[A-Z]+)?(\\-[A-Z]\\d(\\d|[A-Z])(\\.[\\d|[A-Z]+)?)?$"
default_url: http://www.icd10data.com/search?s=[%s]
pages:
- name: gene/MODinteractions_genetic
url: http://www.icd10data.com/search?s=[%s]
- name: ontology_provided_cross_reference
url: http://www.icd10data.com/search?s=[%s]
- db_prefix: ICD11
name: ICD11
example_gid: ICD11:4B24
gid_pattern: "^ICD11:.+$"
default_url: https://icd.who.int/en
pages:
- name: ontology_provided_cross_reference
url: https://icd.who.int/en
- db_prefix: ICDO
name: ICDO
example_gid: ICDO:M8174/3
gid_pattern: "^ICDO:.+$"
default_url: https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology
pages:
- name: ontology_provided_cross_reference
url: https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology
- db_prefix: IMEX
name: The International Molecular Exchange Consortium
example_id: IMEX:IM-10766-6
gid_pattern: "^IMEX:IM-\\d+(-?)(\\d+?)$"
default_url: https://www.ebi.ac.uk/intact/search?query=[%s]
pages:
- name: gene/interactions
url: https://www.ebi.ac.uk/intact/search?query=[%s]
- db_prefix: INTACT
name: IntAct Molecular Interaction Database
example_id: INTACT:EBI-1000008
gid_pattern: "^INTACT:EBI\\-[0-9]+$"
default_url: https://www.ebi.ac.uk/intact/details/interaction/[%s]
pages:
- name: gene/interactions
url: https://www.ebi.ac.uk/intact/details/interaction/[%s]
- db_prefix: interpro
name: InterPro
example_id: interpro:IPR000048
gid_pattern: "^interpro:IPR\\d{6}$"
default_url: https://www.ebi.ac.uk/interpro/entry/InterPro/[%s]
pages:
- name: gene/interactions
url: https://www.ebi.ac.uk/interpro/entry/InterPro/[%s]
- db_prefix: KEGG
name: Kyoto Encyclopedia of Genes and Genomes
example_id: KEGG:05220
gid_pattern: "^KEGG:\\w*:*\\d+$"
default_url: http://www.genome.jp/dbget-bin/www_bget?map[%s]
pages:
- name: ontology_provided_cross_reference
url: http://www.genome.jp/dbget-bin/www_bget?map[%s]
- db_prefix: MEDDRA
name: MEDDRA
example_id: MEDDRA:10071135
gid_pattern: "^MEDDRA:\\d+$"
default_url: https://www.meddra.org/
pages:
- name: ontology_provided_cross_reference
url: https://www.meddra.org/
- db_prefix: MESH
name: Medical Subject Headings
example_gid: MESH:D020516
gid_pattern: "^MESH:[CD]+\\d+$"
default_url: https://www.ncbi.nlm.nih.gov/mesh/[%s]
pages:
- name: ontology_provided_cross_reference
url: https://www.ncbi.nlm.nih.gov/mesh/[%s]
- db_prefix: MINT
name: The Molecular INTeraction database
example_id: MINT:MINT-1954459
gid_pattern: "^MINT:MINT\\-\\d{1,7}$"
default_url: https://mint.bio.uniroma2.it/index.php/results-interactions/?id=[%s]
pages:
- name: gene/interactions
url: https://mint.bio.uniroma2.it/index.php/results-interactions/?id=[%s]
- db_prefix: mpidb
name: The Microbial Protein Interaction Database
example_id: mpidb:MPIDB-INT-1044
gid_pattern: "^mpidb:MPIDB\\-INT\\-\\d+$"
default_url: https://www.ebi.ac.uk/intact/interactions?query=[%s]
pages:
- name: gene/interactions
url: https://www.ebi.ac.uk/intact/interactions?query=[%s]
- db_prefix: NCBITaxon
name: NCBI Taxonomy
example_gid: NCBITaxon:7227
gid_pattern: "^NCBITaxon:\\d+$"
default_url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[%s]
- db_prefix: NCBI_Gene
name: NCBI Gene
example_gid: NCBI_Gene:33432
gid_pattern: "^NCBI_Gene:\\d+$"
default_url: https://www.ncbi.nlm.nih.gov/gene/[%s]
pages:
- name: gene/interactions
url: https://www.ncbi.nlm.nih.gov/gene/[%s]
- name: biogrid/orcs
url: https://orcs.thebiogrid.org/Gene/[%s]
- name: gene/other_expression
url: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=geoprofiles&DbFrom=gene&Cmd=Link&LinkName=gene_geoprofiles&LinkReadableName=GEO%20Profiles&IdsFromResult=[%s]
- db_prefix: SRA
name: SRA
example_gid: SRA:SRA044886
gid_pattern: "^SRA:SRA.+$"
default_url: https://www.ncbi.nlm.nih.gov/sra/?term=[%s]
pages:
- name: htp/dataset
url: https://www.ncbi.nlm.nih.gov/sra/?term=[%s]
- db_prefix: NCI
name: NCI Thesaurus
aliases: ['NCI_Thesaurus', 'NCI']
example_gid: NCI:C7646
gid_pattern: "^NCI:C\\d+$"
default_url : https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=[%s]
pages:
- name: pub
url: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=[%s]
- name: ontology_provided_cross_references
url: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=[%s]
- db_prefix: MIM
name: MIM
aliases: ['mim', 'omim', 'MIM', 'OMIM']
example_id: MIM:600483, MIM:PS203655
gid_pattern: "^(OMIM|omim|MIM|mim):[PS]*\\d+$"
default_url: https://www.omim.org/MIM:[%s]
pages:
- name: homepage
url: https://www.omim.org/
- name: gene
url: https://www.omim.org/MIM:[%s]
- name: gene/interactions
url: https://www.omim.org/MIM:[%s]
- name: disease
url: https://www.omim.org/MIM:[%s]
- name: ont
url: https://www.omim.org/MIM:[%s]
- db_prefix: ORCID
name: ORCID
example_id: ORCID:0000-0002-3843-3472
gid_pattern: "^ORCID:\\d{4}\\-\\d{4}\\-\\d{4}\\-(\\d{3}X|\\d{4})$"
default_url: https://orcid.org/[%s]
# maybe make this an alias of Orphanet instead.
- db_prefix: ORDO
name: ORDO
example_id: ORDO:600483, ORDO:644:GARD:262
gid_pattern: "^ORDO:\\d+:*[GARD]*:*\\d*$"
default_url: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=[%s]
pages:
- name: ontology_provided_cross_references
url: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=[%s]
- db_prefix: Orphanet
name: Orphanet
aliases: ['ORPHA']
example_id: ORPHA:600483
gid_pattern: "^ORPHA:\\d+$"
default_url: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=[%s]
- db_prefix: PANTHER
name: PANTHER
example_id: PANTHER:PTHR11662
gid_pattern: "^PANTHER:PTHR\\d+$"
default_url: http://pantherdb.org/panther/family.do?clsAccession=[%s]
pages:
- name: MGI
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=MGI=MGI=[%s]
- name: FB
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=FlyBase=[%s]
- name: RGD
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=RGD=[%s]
- name: ZFIN
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=ZFIN=[%s]
- name: WB
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=WormBase=[%s]
- name: HGNC
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=HGNC=[%s]
- name: SGD
url: http://pantherdb.org/treeViewer/treeViewer.jsp?book=PAN_BOOK&species=agr&seq=SGD=[%s]
- db_prefix: PDBE
name: Protein Data Bank in Europe
example_id: PDBE:1FHI
gid_pattern: "^PDBE:\\w+$"
default_url: https://www.ebi.ac.uk/pdbe/entry/pdb/[%s]
pages:
- name: gene/interactions
url: https://www.ebi.ac.uk/pdbe/entry/pdb/[%s]
- db_prefix: pdbj
name: Protein Data Bank Japan
example_id: pdbj:1FHI
gid_pattern: "^pdbj:\\w+$"
default_url: https://pdbj.org/mine/summary/[%s]
pages:
- name: gene/interactions
url: https://pdbj.org/mine/summary/[%s]
- db_prefix: PMID
name: PubMed
aliases: ['pubmed', 'PubMed']
example_gid: PMID:26447131
gid_pattern: "^(PMID|pubmed|PubMed):\\d+$"
default_url: https://www.ncbi.nlm.nih.gov/pubmed/[%s]
- db_prefix: PMCID
name: PubMed Central
aliases: ['PMC']
example_gid: PMCID:PMC7519054
gid_pattern: "^(PMCID|PMC):PMC\\d+$"
default_url: https://www.ncbi.nlm.nih.gov/pmc/[%s]
pages:
- name: gene/interactions
url: https://www.ncbi.nlm.nih.gov/pubmed/[%s]
- db_prefix: ISSN
name: International Standard Serial Number
example_gid: ISSN:0092-8674
gid_pattern: "^ISSN:[0-9]{4}-[0-9]{3}[0-9xX]$"
default_url: https://portal.issn.org/resource/ISSN/[%s]
- db_prefix: ISBN
name: International Standard Book Number
example_gid: ISBN:9780879697068
gid_pattern: "^ISBN:[0-9]+(-| )?[0-9]+(-| )?[0-9]+(-| )?[0-9]+(-| )?[0-9]+$"
default_url: https://isbnsearch.org/isbn/[%s]
- db_prefix: psi-mi
name: HUPO Protein Standards Initiative Molecular Interactions
example_gid: psi-mi:MI:0465
gid_pattern: "^psi\\-mi:MI:\\d+$"
default_url: http://identifiers.org/[%s]
pages:
- name: gene/interactions
url: http://identifiers.org/[%s]
- db_prefix: RCSB_PDB
name: RCSB Protein Data Bank
aliases: ['RCSB PDB']
example_id: RCSB_PDB:1AGR
gid_pattern: "^RCSB_PDB:\\w+$"
default_url: https://www.rcsb.org/structure/[%s]
pages:
- name: gene/interactions
url: https://www.rcsb.org/structure/[%s]
- db_prefix: RNAcentral
name: RNAcentral
example_gid: RNAcentral:URS000075C808
gid_pattern: "^RNAcentral:\\w+$"
default_url: http://rnacentral.org/rna/[%s]
- db_prefix: RefSeq
name: RefSeq
aliases: ['refseq']
example_gid: RefSeq:NT_033778
gid_pattern: "^(RefSeq|refseq):\\w+$"
default_url: https://www.ncbi.nlm.nih.gov/nuccore/[%s]
pages:
- name: gene/interactions
url: https://www.ncbi.nlm.nih.gov/nuccore/[%s]
- db_prefix: SO
name: Sequence Ontology
example_gid: SO:0001217
gid_pattern: "^SO:\\d+$"
default_url: http://www.sequenceontology.org/browser/current_svn/term/SO:[%s]
- db_prefix: SNOMED
name: SNOMED
aliases: ['SNOMEDCT_US_2019_09_01', 'SNOMEDCT_US_2020_03_01', 'SNOMED_CT_US_2018_03_01',
'SNOMEDCT_US_2020_09_01', 'SNOMEDCT_2020_03_01', 'SNOMEDCT_US_2018_03_01',
'SNOMEDCT_US_2021_09_01', 'SNOMEDCT_US_2021_07_31', 'SNOMEDCT_US_2023_11_01',
'SNOMEDCT_US_2023_09_01', 'SNOMEDCT_US_2022_03_01', 'SNOMEDCT_US_2022_07_31',
'SNOMEDCT_US_2023_10_01', 'SNOMEDCT_US_2023_03_01']
example_gid: SNOMEDCT_US_2019_09_01:785879009
gid_pattern: "^SNOMEDCT(_US)?(_\\d{4}_\\d{2}_\\d{2})?:\\d+$"
default_url: https://browser.ihtsdotools.org/?perspective=full&conceptId1=[%s]
pages:
- name: ontology_provided_cross_reference
url: https://browser.ihtsdotools.org/?perspective=full&conceptId1=[%s]
- db_prefix: UMLS_CUI
name: UMLS_CUI
example_gid: UMLS_CUI:C0011127
gid_pattern: "^UMLS_CUI:C\\d+$"
default_url: https://identifiers.org/umls:[%s]
pages:
- name: ontology_provided_cross_reference
url: https://identifiers.org/umls:[%s]
- db_prefix: UniProtKB
name: UniProtKB
aliases: ['uniprotkb']
example_gid: UniProtKB:P07713
gid_pattern: "^(UniProtKB|uniprotkb):\\w+$"
default_url: http://www.uniprot.org/uniprot/[%s]
- db_prefix: WBbt
name: WormBase anatomy Ontology
example_gid: WBbt:0008611
gid_pattern: "^WBbt:\\d+$"
default_url: https://www.wormbase.org/db/get?name=WBbt:[%s];class=Anatomy
- db_prefix: WBls
name: WormBase life-stage Ontology
example_gid: WBls:0000001
gid_pattern: "^WBls:\\d+$"
default_url: https://www.wormbase.org/db/get?name=WBls:[%s];class=Life_stage
- db_prefix: WBPhenotype
name: WormBase Phenotype Ontology
example_gid: WBPhenotype:0000517
gid_pattern: "^WBPhenotype:\\d+$"
default_url: https://www.wormbase.org/db/get?name=WBPhenotype:[%s];class=Phenotype
- db_prefix: WIKIP
name: Wikipedia
example_id: WIKIP:BRCA2
gid_pattern: "^WIKIP:\\S+$"
default_url: https://en.wikipedia.org/wiki/[%s]
- db_prefix: WWPDB
name: Worldwide Protein Data Bank
example_id: WWPDB:1AUI
gid_pattern: "^WWPDB:\\w+$"
default_url: https://www.rcsb.org/structure/[%s]
pages:
- name: gene/interactions
url: https://www.rcsb.org/structure/[%s]
- db_prefix: ZECO
name: Zebrafish Environment Condition Ontology
example_gid: ZECO:0000103
gid_pattern: "^ZECO:\\d+$"
default_url: https://zfin.org/action/ontology/term-detail/ZECO:[%s]
- db_prefix: ZFA
name: Zebrafish Anatomy Ontology
example_id: ZFA:0001327
gid_pattern: "^ZFA:\\d+$"
default_url: http://zfin.org/action/ontology/term-detail/ZFA:[%s]