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references/source-links.json
26.9 KB · Sep 30, 2026 · 23:00 UTC
{
"schema_version": 2,
"fallback_order": [
"canonical_record_url",
"sanitized_request_url",
"authoritative_homepage_without_linking_the_identifier"
],
"skills": {
"alphafold-skill": {
"source_name": "AlphaFold Protein Structure Database",
"homepage_url": "https://alphafold.ebi.ac.uk/",
"request_url_prefixes": [
"https://alphafold.ebi.ac.uk/"
],
"record_url_templates": [
{
"identifier_type": "UniProt accession",
"identifier_fields": [
"uniprot_accession",
"uniprotAccession",
"primaryAccession",
"accession",
"id"
],
"template": "https://alphafold.ebi.ac.uk/entry/{id}"
}
]
},
"bgee-skill": {
"source_name": "Bgee",
"homepage_url": "https://www.bgee.org/",
"record_url_templates": []
},
"bindingdb-skill": {
"source_name": "BindingDB",
"homepage_url": "https://www.bindingdb.org/",
"request_url_prefixes": [
"https://bindingdb.org/"
],
"record_url_templates": []
},
"biobankjapan-phewas-skill": {
"source_name": "BioBank Japan PheWeb",
"homepage_url": "https://pheweb.jp/",
"record_url_templates": [
{
"identifier_type": "variant",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"variant_name",
"canonical",
"variant_identifier",
"rsid"
],
"template": "https://pheweb.jp/variant/{id}"
},
{
"identifier_type": "phenotype",
"identifier_fields": [
"phenotype_id",
"phenotypeId",
"phenotype",
"phenocode",
"pheno"
],
"template": "https://pheweb.jp/pheno/{id}"
}
]
},
"biostudies-arrayexpress-skill": {
"source_name": "BioStudies and ArrayExpress",
"homepage_url": "https://www.ebi.ac.uk/biostudies/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/biostudies/api/v1"
],
"record_url_templates": [
{
"identifier_type": "study accession",
"identifier_fields": [
"study_accession",
"studyAccession",
"study_id",
"studyId",
"accession",
"id"
],
"template": "https://www.ebi.ac.uk/biostudies/studies/{id}"
}
]
},
"cbioportal-skill": {
"source_name": "cBioPortal",
"homepage_url": "https://www.cbioportal.org/",
"request_url_prefixes": [
"https://www.cbioportal.org/"
],
"record_url_templates": []
},
"cellxgene-skill": {
"source_name": "CZ CELLxGENE Discover",
"homepage_url": "https://cellxgene.cziscience.com/",
"request_url_prefixes": [
"https://api.cellxgene.cziscience.com/"
],
"record_url_templates": [
{
"identifier_type": "collection ID",
"identifier_fields": [
"collection_id",
"collectionId",
"collection_uuid",
"uuid",
"id"
],
"template": "https://cellxgene.cziscience.com/collections/{id}"
}
]
},
"chebi-skill": {
"source_name": "ChEBI",
"homepage_url": "https://www.ebi.ac.uk/chebi/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/chebi"
],
"request_base_urls": [
"https://www.ebi.ac.uk"
],
"record_url_templates": [
{
"identifier_type": "ChEBI ID",
"identifier_fields": [
"chebi_id",
"chebiId",
"CHEBI",
"accession",
"id"
],
"template": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId={id}"
}
]
},
"chembl-skill": {
"source_name": "ChEMBL",
"homepage_url": "https://www.ebi.ac.uk/chembl/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/chembl/api/data"
],
"record_url_templates": [
{
"identifier_type": "compound ID",
"identifier_fields": [
"molecule_chembl_id",
"compound_chembl_id",
"compound_id",
"molecule_id"
],
"template": "https://www.ebi.ac.uk/chembl/explore/compound/{id}"
},
{
"identifier_type": "target ID",
"identifier_fields": [
"target_chembl_id",
"target_id",
"targetId",
"target_ensembl_id",
"target"
],
"template": "https://www.ebi.ac.uk/chembl/explore/target/{id}"
}
]
},
"civic-skill": {
"source_name": "CIViC",
"homepage_url": "https://civicdb.org/",
"record_url_templates": [
{
"identifier_type": "variant ID",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"rsid"
],
"template": "https://civicdb.org/variants/{id}/summary"
},
{
"identifier_type": "evidence ID",
"identifier_fields": [
"evidence_id",
"evidenceId"
],
"template": "https://civicdb.org/evidence/{id}/summary"
}
]
},
"clinicaltrials-skill": {
"source_name": "ClinicalTrials.gov",
"homepage_url": "https://clinicaltrials.gov/",
"record_url_templates": [
{
"identifier_type": "NCT ID",
"identifier_fields": [
"nctId",
"nct_id",
"NCTId",
"nctid",
"id"
],
"template": "https://clinicaltrials.gov/study/{id}"
}
]
},
"clinvar-variation-skill": {
"source_name": "ClinVar and NCBI Variation",
"homepage_url": "https://www.ncbi.nlm.nih.gov/clinvar/",
"record_url_templates": [
{
"identifier_type": "numeric ClinVar Variation ID",
"identifier_fields": [
"variation_id",
"variationId",
"variationID",
"vcv",
"accession"
],
"template": "https://www.ncbi.nlm.nih.gov/clinvar/variation/{id}/",
"transform": "strip_clinvar_vcv"
},
{
"identifier_type": "RefSNP ID",
"identifier_fields": [
"rsid",
"rs_id",
"refsnp_id",
"rs"
],
"template": "https://www.ncbi.nlm.nih.gov/snp/{id}"
}
]
},
"efo-ontology-skill": {
"source_name": "Experimental Factor Ontology via OLS",
"homepage_url": "https://www.ebi.ac.uk/ols4/ontologies/efo",
"request_url_prefixes": [
"https://www.ebi.ac.uk/ols4/api"
],
"record_url_templates": []
},
"encode-skill": {
"source_name": "ENCODE",
"homepage_url": "https://www.encodeproject.org/",
"request_url_prefixes": [
"https://www.encodeproject.org/"
],
"record_url_templates": [
{
"identifier_type": "ENCODE accession",
"identifier_fields": [
"accession",
"encode_accession",
"id"
],
"template": "https://www.encodeproject.org/{id}/"
}
]
},
"ensembl-skill": {
"source_name": "Ensembl",
"homepage_url": "https://www.ensembl.org/",
"request_url_prefixes": [
"https://rest.ensembl.org/"
],
"record_url_templates": [
{
"identifier_type": "stable Ensembl ID",
"identifier_fields": [
"ensembl_id",
"ensemblId",
"ensembl_gene_id",
"stable_id",
"gene_id",
"transcript_id",
"id"
],
"template": "https://www.ensembl.org/id/{id}"
}
]
},
"epigraphdb-skill": {
"source_name": "EpiGraphDB",
"homepage_url": "https://epigraphdb.org/",
"request_url_prefixes": [
"https://api.epigraphdb.org/"
],
"record_url_templates": []
},
"eqtl-catalogue-skill": {
"source_name": "eQTL Catalogue",
"homepage_url": "https://www.ebi.ac.uk/eqtl/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/eqtl/api"
],
"record_url_templates": []
},
"eva-skill": {
"source_name": "European Variation Archive",
"homepage_url": "https://www.ebi.ac.uk/eva/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/eva/webservices"
],
"record_url_templates": []
},
"finngen-phewas-skill": {
"source_name": "FinnGen PheWeb",
"homepage_url": "https://r12.finngen.fi/",
"record_url_templates": [
{
"identifier_type": "variant",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"variant_name",
"canonical",
"variant_identifier",
"rsid"
],
"template": "https://r12.finngen.fi/variant/{id}"
},
{
"identifier_type": "phenotype",
"identifier_fields": [
"phenotype_id",
"phenotypeId",
"phenotype",
"phenocode",
"pheno"
],
"template": "https://r12.finngen.fi/pheno/{id}"
}
]
},
"genebass-gene-burden-skill": {
"source_name": "Genebass",
"homepage_url": "https://app.genebass.org/",
"record_url_templates": []
},
"gnomad-graphql-skill": {
"source_name": "gnomAD",
"homepage_url": "https://gnomad.broadinstitute.org/",
"record_url_templates": [
{
"identifier_type": "variant",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"variant_name",
"canonical",
"variant_identifier",
"rsid",
"id"
],
"template": "https://gnomad.broadinstitute.org/variant/{id}"
},
{
"identifier_type": "gene ID",
"identifier_fields": [
"gene_id",
"geneId",
"gene",
"gene_symbol",
"ensembl_id",
"id"
],
"template": "https://gnomad.broadinstitute.org/gene/{id}"
}
]
},
"gtex-eqtl-skill": {
"source_name": "GTEx Portal",
"homepage_url": "https://gtexportal.org/",
"record_url_templates": [
{
"identifier_type": "gene ID",
"identifier_fields": [
"gene_id",
"geneId",
"gene",
"gene_symbol",
"ensembl_id",
"id"
],
"template": "https://gtexportal.org/home/gene/{id}"
}
]
},
"gwas-catalog-skill": {
"source_name": "NHGRI-EBI GWAS Catalog",
"homepage_url": "https://www.ebi.ac.uk/gwas/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/gwas/rest/api"
],
"record_url_templates": [
{
"identifier_type": "study accession",
"identifier_fields": [
"study_accession",
"studyAccession",
"study_id",
"studyId",
"accession"
],
"template": "https://www.ebi.ac.uk/gwas/studies/{id}"
},
{
"identifier_type": "association accession",
"identifier_fields": [
"association_accession",
"association_id",
"associationId"
],
"template": "https://www.ebi.ac.uk/gwas/associations/{id}"
},
{
"identifier_type": "variant",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"variant_name",
"canonical",
"variant_identifier",
"rsid"
],
"template": "https://www.ebi.ac.uk/gwas/variants/{id}"
}
]
},
"human-protein-atlas-skill": {
"source_name": "Human Protein Atlas",
"homepage_url": "https://www.proteinatlas.org/",
"request_url_prefixes": [
"https://www.proteinatlas.org/"
],
"record_url_templates": [
{
"identifier_type": "gene symbol or Ensembl gene ID",
"identifier_fields": [
"gene_symbol",
"geneSymbol",
"ensembl_id",
"gene",
"id"
],
"template": "https://www.proteinatlas.org/{id}"
}
]
},
"ipd-skill": {
"source_name": "IPD-IMGT/HLA",
"homepage_url": "https://www.ebi.ac.uk/ipd/imgt/hla/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/cgi-bin/ipd/api"
],
"record_url_templates": []
},
"metabolights-skill": {
"source_name": "MetaboLights",
"homepage_url": "https://www.ebi.ac.uk/metabolights/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/metabolights/ws"
],
"record_url_templates": [
{
"identifier_type": "MetaboLights study accession",
"identifier_fields": [
"study_id",
"studyId",
"accession",
"id",
"identifier"
],
"template": "https://www.ebi.ac.uk/metabolights/{id}"
}
]
},
"mgnify-skill": {
"source_name": "MGnify",
"homepage_url": "https://www.ebi.ac.uk/metagenomics/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/metagenomics/api/v1"
],
"record_url_templates": [
{
"identifier_type": "study accession",
"identifier_fields": [
"study_accession",
"studyAccession",
"study_id",
"studyId",
"accession"
],
"template": "https://www.ebi.ac.uk/metagenomics/studies/{id}"
},
{
"identifier_type": "analysis accession",
"identifier_fields": [
"analysis_accession",
"analysis_id",
"analysisId"
],
"template": "https://www.ebi.ac.uk/metagenomics/analyses/{id}"
},
{
"identifier_type": "sample accession",
"identifier_fields": [
"sample_accession",
"sample_id",
"sampleId"
],
"template": "https://www.ebi.ac.uk/metagenomics/samples/{id}"
}
]
},
"ncbi-clinicaltables-skill": {
"source_name": "NCBI Gene via Clinical Tables",
"homepage_url": "https://clinicaltables.nlm.nih.gov/",
"record_url_templates": [
{
"identifier_type": "NCBI Gene ID",
"identifier_fields": [
"gene_id",
"geneId",
"GeneID",
"geneid",
"id"
],
"template": "https://www.ncbi.nlm.nih.gov/gene/{id}"
}
]
},
"ncbi-datasets-skill": {
"source_name": "NCBI Datasets",
"homepage_url": "https://www.ncbi.nlm.nih.gov/datasets/",
"record_url_templates": [
{
"identifier_type": "genome accession",
"identifier_fields": [
"assembly_accession",
"genome_accession",
"accession"
],
"template": "https://www.ncbi.nlm.nih.gov/datasets/genome/{id}/"
},
{
"identifier_type": "NCBI Gene ID",
"identifier_fields": [
"gene_id",
"geneId",
"GeneID",
"geneid"
],
"template": "https://www.ncbi.nlm.nih.gov/gene/{id}"
}
]
},
"ncbi-entrez-skill": {
"source_name": "NCBI Entrez",
"homepage_url": "https://www.ncbi.nlm.nih.gov/search/",
"record_url_templates": [
{
"identifier_type": "PMID",
"identifier_fields": [
"pmid",
"PMID",
"pubmed_id",
"pubmedId"
],
"template": "https://pubmed.ncbi.nlm.nih.gov/{id}/"
},
{
"identifier_type": "PMCID",
"identifier_fields": [
"pmcid",
"pmc_id",
"article_id"
],
"template": "https://pmc.ncbi.nlm.nih.gov/articles/{id}/"
},
{
"identifier_type": "DOI",
"identifier_fields": [
"doi",
"DOI",
"article_doi",
"articleDoi"
],
"template": "https://doi.org/{id}"
},
{
"identifier_type": "NCBI Gene ID",
"identifier_fields": [
"gene_id",
"geneId",
"GeneID",
"geneid"
],
"template": "https://www.ncbi.nlm.nih.gov/gene/{id}"
},
{
"identifier_type": "GEO accession",
"identifier_fields": [
"geo_accession",
"accession",
"gse",
"gsm",
"gpl"
],
"template": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={id}"
}
]
},
"opentargets-skill": {
"source_name": "Open Targets Platform",
"homepage_url": "https://platform.opentargets.org/",
"record_url_templates": [
{
"identifier_type": "target ID",
"identifier_fields": [
"target_chembl_id",
"target_id",
"targetId",
"target_ensembl_id",
"target",
"id"
],
"template": "https://platform.opentargets.org/target/{id}"
},
{
"identifier_type": "disease ID",
"identifier_fields": [
"disease_id",
"diseaseId",
"efo_id",
"disease",
"id"
],
"template": "https://platform.opentargets.org/disease/{id}"
}
]
},
"pharmgkb-skill": {
"source_name": "PharmGKB",
"homepage_url": "https://www.clinpgx.org/",
"request_url_prefixes": [
"https://api.clinpgx.org/"
],
"record_url_templates": [
{
"identifier_type": "chemical ID",
"identifier_fields": [
"chemical_id",
"chemicalId",
"drug_id"
],
"template": "https://www.clinpgx.org/chemical/{id}"
},
{
"identifier_type": "gene ID",
"identifier_fields": [
"gene_id",
"geneId",
"gene",
"gene_symbol",
"ensembl_id"
],
"template": "https://www.clinpgx.org/gene/{id}"
},
{
"identifier_type": "variant ID",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"rsid"
],
"template": "https://www.clinpgx.org/variant/{id}"
}
]
},
"pride-skill": {
"source_name": "PRIDE Archive",
"homepage_url": "https://www.ebi.ac.uk/pride/archive/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/pride/ws/archive/v2"
],
"record_url_templates": [
{
"identifier_type": "PRIDE project accession",
"identifier_fields": [
"accession",
"project_accession",
"projectAccession",
"id"
],
"template": "https://www.ebi.ac.uk/pride/archive/projects/{id}"
}
]
},
"proteomexchange-skill": {
"source_name": "ProteomeXchange",
"homepage_url": "https://www.proteomexchange.org/",
"request_url_prefixes": [
"https://proteomecentral.proteomexchange.org/"
],
"record_url_templates": [
{
"identifier_type": "ProteomeXchange accession",
"identifier_fields": [
"accession",
"dataset_id",
"datasetId",
"id"
],
"template": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID={id}"
}
]
},
"pubchem-pug-skill": {
"source_name": "PubChem",
"homepage_url": "https://pubchem.ncbi.nlm.nih.gov/",
"request_url_prefixes": [
"https://pubchem.ncbi.nlm.nih.gov/"
],
"record_url_templates": [
{
"identifier_type": "compound CID",
"identifier_fields": [
"cid",
"CID",
"compound_cid",
"compoundId"
],
"template": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}"
},
{
"identifier_type": "substance SID",
"identifier_fields": [
"sid",
"SID",
"substance_sid",
"substanceId"
],
"template": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}"
},
{
"identifier_type": "assay AID",
"identifier_fields": [
"aid",
"AID",
"assay_aid",
"assayId"
],
"template": "https://pubchem.ncbi.nlm.nih.gov/bioassay/{id}"
}
]
},
"quickgo-skill": {
"source_name": "QuickGO",
"homepage_url": "https://www.ebi.ac.uk/QuickGO/",
"request_url_prefixes": [
"https://www.ebi.ac.uk/QuickGO/services"
],
"record_url_templates": [
{
"identifier_type": "GO term",
"identifier_fields": [
"go_id",
"goId",
"go_term",
"goTerm",
"accession",
"id"
],
"template": "https://www.ebi.ac.uk/QuickGO/term/{id}"
}
]
},
"rcsb-pdb-skill": {
"source_name": "RCSB Protein Data Bank",
"homepage_url": "https://www.rcsb.org/",
"request_url_prefixes": [
"https://data.rcsb.org/",
"https://search.rcsb.org/",
"https://www.rcsb.org/"
],
"record_url_templates": [
{
"identifier_type": "PDB ID",
"identifier_fields": [
"pdb_id",
"pdbId",
"structure_id",
"entry_id",
"rcsb_id",
"id"
],
"template": "https://www.rcsb.org/structure/{id}"
}
]
},
"reactome-skill": {
"source_name": "Reactome",
"homepage_url": "https://reactome.org/",
"request_url_prefixes": [
"https://reactome.org/"
],
"record_url_templates": [
{
"identifier_type": "Reactome stable ID",
"identifier_fields": [
"stId",
"stable_id",
"reactome_id",
"pathway_id",
"id"
],
"template": "https://reactome.org/content/detail/{id}"
}
]
},
"rhea-skill": {
"source_name": "Rhea",
"homepage_url": "https://www.rhea-db.org/",
"request_url_prefixes": [
"https://sparql.rhea-db.org/"
],
"record_url_templates": [
{
"identifier_type": "Rhea numeric ID",
"identifier_fields": [
"rhea_id",
"rheaId",
"rhea",
"accession",
"id"
],
"template": "https://www.rhea-db.org/rhea/{id}",
"transform": "strip_rhea_prefix"
}
]
},
"rnacentral-skill": {
"source_name": "RNAcentral",
"homepage_url": "https://rnacentral.org/",
"request_url_prefixes": [
"https://rnacentral.org/"
],
"record_url_templates": [
{
"identifier_type": "RNAcentral ID",
"identifier_fields": [
"rnacentral_id",
"rnacentralId",
"accession",
"id"
],
"template": "https://rnacentral.org/rna/{id}"
}
]
},
"string-skill": {
"source_name": "STRING",
"homepage_url": "https://string-db.org/",
"request_url_prefixes": [
"https://string-db.org/"
],
"record_url_templates": [
{
"identifier_type": "STRING protein identifier",
"identifier_fields": [
"string_id",
"stringId",
"preferredName",
"protein_id",
"id"
],
"template": "https://string-db.org/network/{id}"
}
]
},
"tpmi-phewas-skill": {
"source_name": "Taiwan Precision Medicine Initiative PheWeb",
"homepage_url": "https://pheweb.ibms.sinica.edu.tw/",
"record_url_templates": [
{
"identifier_type": "variant",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"variant_name",
"canonical",
"variant_identifier",
"rsid"
],
"template": "https://pheweb.ibms.sinica.edu.tw/variant/{id}"
},
{
"identifier_type": "phenotype",
"identifier_fields": [
"phenotype_id",
"phenotypeId",
"phenotype",
"phenocode",
"pheno"
],
"template": "https://pheweb.ibms.sinica.edu.tw/pheno/{id}"
}
]
},
"ukb-topmed-phewas-skill": {
"source_name": "UKB-TOPMed PheWeb",
"homepage_url": "https://pheweb.org/UKB-TOPMed/",
"record_url_templates": [
{
"identifier_type": "variant",
"identifier_fields": [
"variant_id",
"variantId",
"variant",
"variant_name",
"canonical",
"variant_identifier",
"rsid"
],
"template": "https://pheweb.org/UKB-TOPMed/variant/{id}"
},
{
"identifier_type": "phenotype",
"identifier_fields": [
"phenotype_id",
"phenotypeId",
"phenotype",
"phenocode",
"pheno"
],
"template": "https://pheweb.org/UKB-TOPMed/pheno/{id}"
}
]
},
"uniprot-skill": {
"source_name": "UniProt",
"homepage_url": "https://www.uniprot.org/",
"request_url_prefixes": [
"https://rest.uniprot.org/"
],
"record_url_templates": [
{
"identifier_type": "UniProtKB accession",
"identifier_fields": [
"primaryAccession",
"uniprot_accession",
"uniprotAccession",
"accession"
],
"template": "https://www.uniprot.org/uniprotkb/{id}/entry"
},
{
"identifier_type": "UniRef cluster",
"identifier_fields": [
"cluster_id",
"uniref_id",
"uniref",
"id"
],
"template": "https://www.uniprot.org/uniref/{id}"
},
{
"identifier_type": "UniParc accession",
"identifier_fields": [
"upi",
"uniparc_id",
"uniparc_accession",
"accession"
],
"template": "https://www.uniprot.org/uniparc/{id}/entry"
}
]
}
}
}
SHA-256: 224d098120813c6af42307b79eb7a430ab12c489f7fc5aecfce5ccb83ba0a028