@biothings-explorer/annotator
Version:
A nodejs package providing batch annotating features for biomedical entities
184 lines (182 loc) • 6.56 kB
JavaScript
exports.APIMETA = {
"Gene": {
"semantic": "Gene",
"api_name": "mygene.info",
"url": "https://mygene.info/v3/query",
"id": {
"rank": ["NCBIGene", "ENSEMBL", "HGNC", "SYMBOL", "OMIM", "UniProtKB", "UMLS", "MGI", "name"],
"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"]
}
},
"mapping": {
"alias": {
"fields": ["alias"],
"nested": false
},
"ec": {
"fields": ["ec"],
"nested": false
},
"generif": {
"fields": ["generif"],
"nested": true
},
"genomic_position": {
"fields": ["genomic_pos"],
"nested": true
},
"biological_process": {
"fields": ["go.BP"],
"nested": true
},
"cellular_component": {
"fields": ["go.CC"],
"nested": true
},
"molecular_function": {
"fields": ["go.MF"],
"nested": true
},
"interpro": {
"fields": ["interpro"],
"nested": true
},
"ipi": {
"fields": ["ipi"],
"nested": false
},
"biocarta": {
"fields": ["pathway.biocarta"],
"nested": true
},
"kegg": {
"fields": ["pathway.kegg"],
"nested": true
},
"reactome": {
"fields": ["pathway.reactome"],
"nested": true
},
"wikipathways": {
"fields": ["pathway.wikipathways"],
"nested": true
},
"pfam": {
"fields": ["pfam"],
"nested": false
},
"summary": {
"fields": ["summary"],
"nested": false
},
"type": {
"fields": ["type_of_gene"],
"nested": false
}
}
},
"ChemicalSubstance": {
"semantic": "ChemicalSubstance",
"api_name": "mychem.info",
"url": "https://mychem.info/v1/query",
"id": {
"rank": ["CHEBI", "CHEMBL.COMPOUND", "DRUGBANK", "PUBCHEM", "MESH", "INCHI", "INCHIKEY", "UNII", "KEGG", "UMLS", "name"],
"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"]
}
},
"mapping": {
"max_phase": {
"fields": ["chembl.max_phase"],
"nested": false
},
"molecular_weight": {
"fields": ["chembl.molecule_properties.full_mwt", "drugbank.weight.average"],
"nested": false
},
"AlogP": {
"fields": ["chembl.molecule_properties.alogp"],
"nested": false
},
"ATC_classification": {
"fields": ["chembl.atc_classifications", "drugbank.xrefs.atc_codes"],
"nested": false
},
"molecule_type": {
"fields": ["chembl.molecule_type"],
"nested": false
},
"targets": {
"fields": ["drugbank.targets"],
"nested": true
},
"enzymes": {
"fields": ["drugbank.enzymes"],
"nested": true
},
"transporters": {
"fields": ["drugbank.transporters"],
"nested": true
},
"formula": {
"fields": ["drugbank.formula"],
"nested": false
},
"absorption": {
"fields": ["drugbank.pharmacology.absorption"],
"nested": false
},
"indication": {
"fields": ["drugbank.pharmacology.indication"],
"nested": false
},
"metabolism": {
"fields": ["drugbank.pharmacology.metabolism"],
"nested": false
},
"pharmacodynamics": {
"fields": ["drugbank.pharmacology.pharmacodynamics"],
"nested": false
},
"protein_binding": {
"fields": ["drugbank.pharmacology.protein_binding"],
"nested": false
},
"salts": {
"fields": ["drugbank.salts"],
"nested": true
},
"synonyms": {
"fields": ["drugbank.synonyms"],
"nested": false
},
"drug-class": {
"fields": ["drugbank.taxonomy.class"],
"nested": false
}
}
}
}
exports.MAX_CONCURRENT_QUERIES = 4;
exports.CURIE = {
ALWAYS_PREFIXED: ["GO", "CHEBI", "HP", "MONDO", "DOID", "EFO", "UBERON", "MP", "CL", "MGI"]
}