biomedical-id-autocomplete
Version:
autocomplete biomedical ids
250 lines (249 loc) • 8.51 kB
JavaScript
exports.ID_RESOLVING_APIS = {
"Gene": {
"id_ranks": [
"NCBIGene",
"ENSEMBL",
"HGNC",
"UMLS",
"UNIPROTKB",
"SYMBOL",
"OMIM",
"MGI",
],
"semantic": "Gene",
"api_name": "mygene.info",
"url": "https://mygene.info/v3",
"mapping": {
"NCBIGene": ["entrezgene"],
"name": ["name"],
"SYMBOL": ["symbol"],
"UMLS": ["umls.cui", "umls.protein_cui"],
"HGNC": ["HGNC"],
"UNIPROTKB": ["uniprot.Swiss-Prot"],
"ENSEMBL": ["ensembl.gene"],
"OMIM": ["OMIM"],
"MGI": ["MGI"],
},
},
"SequenceVariant": {
"id_ranks": ["DBSNP", "MYVARIANT_HG19", "HGVS", "ClinVar"],
"api_name": "myvariant.info",
"semantic": "SequenceVariant",
"url": "https://myvariant.info/v1",
"mapping": {
"DBSNP": ["dbsnp.rsid", "clinvar.rsid", "dbnsfp.rsid"],
"HGVS": [
"clinvar.hgvs.genomic",
"clinvar.hgvs.protein",
"clinvar.hgvs.coding",
],
"ClinVar": ["clinvar.rcv.accession"],
"name": ["dbsnp.rsid", "clinvar.rsid", "dbnsfp.rsid"],
},
},
"ChemicalSubstance": {
"id_ranks": [
"CHEBI",
"CHEMBL.COMPOUND",
"DRUGBANK",
"PUBCHEM",
"MESH",
"UNII",
"UMLS",
"CAS",
"IUPAC",
"formula",
],
"semantic": "ChemicalSubstance",
"api_name": "mychem.info",
"url": "https://mychem.info/v1",
"mapping": {
"CHEMBL.COMPOUND": [
"chembl.molecule_chembl_id",
"drugbank.xrefs.chembl",
"drugcentral.xrefs.chembl_id",
],
"DRUGBANK": [
"drugcentral.xrefs.drugbank_id",
"pharmgkb.xrefs.drugbank",
"chebi.xrefs.drugbank",
"drugbank.id",
],
"PUBCHEM": [
"pubchem.cid",
"drugbank.xrefs.pubchem.cid",
"drugcentral.xrefs.pubchem_cid",
"pharmgkb.xrefs.pubchem.cid",
],
"CHEBI": [
"chebi.id",
"chembl.chebi_par_id",
"drugbank.xrefs.chebi",
"drugcentral.xrefs.chebi",
],
"UMLS": ["drugcentral.xrefs.umlscui", "pharmgkb.xrefs.umls", "umls.cui"],
"MESH": [
"umls.mesh",
"drugcentral.xrefs.mesh_descriptor_ui",
"ginas.xrefs.MESH",
"pharmgkb.xrefs.mesh",
],
"UNII": [
"drugcentral.xrefs.unii",
"unii.unii",
"aeolus.unii",
"ginas.unii",
],
"INCHIKEY": [
"drugbank.inchi_key",
"ginas.inchikey",
"unii.inchikey",
"chebi.inchikey",
],
"INCHI": ["drugbank.inchi", "chebi.inchi", "chembl.inchi"],
"KEGG": ["drugbank.xrefs.kegg.cid"],
"name": [
"chembl.pref_name",
"drugbank.name",
"umls.name",
"ginas.preferred_name",
"pharmgkb.name",
"chebi.name",
"drugbank.international_brands.name",
"chembl.molecule_synonyms.synonyms",
"drugbank.synonyms",
"drugcentral.synonyms",
"chebi.synonyms",
],
"CAS": ["ginas.cas_primary", "pharmgkb.xrefs.cas", "chebi.xrefs.cas"],
"IUPAC": ["pubchem.iupac.traditional", "drugbank.iupac"],
"formula": [
"chebi.formulae",
"drugbank.formula",
"pubchem.molecular_formula",
],
},
},
"Disease": {
"id_ranks": ["MONDO", "DOID", "OMIM", "ORPHANET", "UMLS", "MESH"],
"semantic": "Disease",
"api_name": "mydisease.info",
"url": "https://mydisease.info/v1",
"mapping": {
"MONDO": ["mondo.mondo"],
"DOID": ["mondo.xrefs.doid"],
"UMLS": ["mondo.xrefs.umls", "disgenet.xrefs.umls"],
"name": ["mondo.label", "disgenet.xrefs.disease_name", "mondo.synonyms"],
"MESH": ["mondo.xrefs.mesh", "disease_ontology.xrefs.mesh", "ctd.mesh"],
"OMIM": ["mondo.xrefs.omim", "hpo.omim"],
"ORPHANET": ["hpo.orphanet", "mondo.xrefs.orphanet"],
},
},
"PhenotypicFeature": {
"id_ranks": [
"UMLS",
"SNOMEDCT",
"HP",
"MEDDRA",
"EFO",
"NCIT",
"MESH",
"MP",
],
"semantic": "PhenotypicFeature",
"api_name": "HPO API",
"url": "https://biothings.ncats.io/hpo",
"mapping": {
"UMLS": ["xrefs.umls"],
"SNOMEDCT": ["xrefs.snomed_ct"],
"HP": ["hp"],
"MEDDRA": ["xrefs.meddra"],
"EFO": ["xrefs.efo"],
"NCIT": ["xrefs.ncit"],
"MESH": ["xrefs.mesh"],
"MP": ["xrefs.mp"],
"name": ["name", "synonym.exact", "synonym.related", "synonym.broad"],
},
},
"MolecularActivity": {
"id_ranks": ["GO", "MetaCyc", "RHEA", "KEGG", "REACT"],
"semantic": "MolecularActivity",
"api_name": "Gene Ontology Molecular Function API",
"url": "https://biothings.ncats.io/go_mf",
"mapping": {
"GO": ["go"],
"MetaCyc": ["xrefs.metacyc"],
"RHEA": ["xrefs.rhea"],
"KEGG": ["xrefs.kegg_reaction"],
"REACT": ["xrefs.reactome"],
"name": ["name", "synonym.exact", "synonym.related", "synonym.broad"],
},
},
"BiologicalProcess": {
"id_ranks": ["GO", "MetaCyc", "REACT", "KEGG"],
"semantic": "BiologicalProcess",
"api_name": "Gene Ontology Biological Process API",
"url": "https://biothings.ncats.io/go_bp",
"mapping": {
"GO": ["go"],
"MetaCyc": ["xrefs.metacyc"],
"KEGG": ["xrefs.kegg_pathway"],
"REACT": ["xrefs.reactome"],
"name": ["name", "synonym.exact", "synonym.related", "synonym.broad"],
},
},
"CellularComponent": {
"id_ranks": ["GO", "MetaCyc", "RHEA", "name"],
"semantic": "CellularComponent",
"api_name": "Gene Ontology Cellular Component API",
"url": "https://biothings.ncats.io/go_cc",
"mapping": {
"GO": ["go"],
"MetaCyc": ["xrefs.metacyc"],
"RHEA": ["xrefs.rhea"],
"name": ["name", "synonym.exact", "synonym.related", "synonym.broad"],
},
},
"Pathway": {
"id_ranks": ["REACT", "KEGG", "PHARMGKB", "WIKIPATHWAYS", "name"],
"semantic": "Pathway",
"api_name": "geneset API",
"url": "https://biothings.ncats.io/geneset",
"mapping": {
"REACT": ["reactome"],
"WIKIPATHWAYS": ["wikipathways"],
"KEGG": ["kegg"],
"PHARMGKB": ["pharmgkb"],
"name": ["name"],
},
},
"AnatomicalEntity": {
"id_ranks": ["UBERON", "UMLS", "MESH", "NCIT", "name"],
"semantic": "AnatomicalEntity",
"api_name": "UBERON API",
"url": "https://biothings.ncats.io/uberon",
"mapping": {
"UBERON": ["uberon"],
"UMLS": ["xrefs.umls"],
"MESH": ["xrefs.mesh"],
"NCIT": ["xrefs.ncit"],
"name": ["name", "synonym.exact", "synonym.related", "synonym.broad"],
},
},
"Cell": {
"id_ranks": ["CL", "NCIT", "MESH", "EFO", "name"],
"semantic": "Cell",
"api_name": "Cell Ontology API",
"url": "https://biothings.ncats.io/cell_ontology",
"mapping": {
"CL": ["cl"],
"NCIT": ["xrefs.ncit"],
"MESH": ["xrefs.mesh"],
"EFO": ["xrefs.efo"],
"name": ["name", "synonym.exact", "synonym.related", "synonym.broad"],
},
},
}
exports.CURIE = {
ALWAYS_PREFIXED: ['RHEA', 'GO', 'CHEBI', 'HP', 'MONDO', 'DOID', 'EFO', 'UBERON', 'MP', 'CL', 'MGI'],
}