diff --git a/src/config.ts b/src/config.ts index e76d376..b4c9873 100644 --- a/src/config.ts +++ b/src/config.ts @@ -32,6 +32,20 @@ export const APIMETA: MetaDataItemsObject = { type_of_gene: ['type_of_gene'], }, }, + Transcript: { + id_ranks: ['ENSEMBL', 'SYMBOL', 'name'], + semantic: 'Transcript', + api_name: 'mygene.info', + url: 'https://mygene.info/v3/query', + mapping: { + ENSEMBL: ['ensembl.transcript'], + SYMBOL: ['symbol'], + name: ['name'], + }, + additional_attributes_mapping: { + interpro: ['interpro.desc'], + }, + }, Protein: { id_ranks: ['UniProtKB', 'ENSEMBL', 'SYMBOL', 'UMLS', 'name'], semantic: 'Protein', @@ -56,8 +70,8 @@ export const APIMETA: MetaDataItemsObject = { mapping: { MYVARIANT_HG19: ['_id'], DBSNP: ['dbsnp.rsid', 'clinvar.rsid', 'dbnsfp.rsid'], - HGVS: ['clinvar.hgvs.genomic', 'clinvar.hgvs.protein', 'clinvar.hgvs.coding'], - ClINVAR: ['clinvar.rcv.accession'], + HGVS: ['clinvar.hgvs.genomic', 'clinvar.hgvs.protein', 'clinvar.hgvs.coding', 'dbnsfp.clinvar.hgvs'], + ClINVAR: ['clinvar.variant_id', 'dbnsfp.clinvar.clinvar_id'], }, additional_attributes_mapping: { cadd_consequence: ['cadd.consequence'], @@ -67,42 +81,24 @@ export const APIMETA: MetaDataItemsObject = { sift_category: ['cadd.sift.cat'], }, }, - ChemicalSubstance: { - id_ranks: [ - 'CHEBI', - 'CHEMBL.COMPOUND', - 'DRUGBANK', - 'PUBCHEM.COMPOUND', - 'MESH', - 'INCHI', - 'INCHIKEY', - 'UNII', - 'KEGG', - 'UMLS', - 'RHEA', - 'name', - ], - semantic: 'ChemicalSubstance', + SmallMolecule: { + id_ranks: ['CHEBI', 'CHEMBL.COMPOUND', 'DRUGBANK', 'PUBCHEM.COMPOUND', 'MESH', 'INCHI', 'INCHIKEY', 'UNII', 'UMLS', 'CAS', 'HMDB', 'LINCS', 'name'], + semantic: 'SmallMolecule', api_name: 'mychem.info', url: 'https://mychem.info/v1/query', 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.COMPOUND': [ - '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'], + 'CHEMBL.COMPOUND': ['chembl.molecule_chembl_id', 'drugbank.xrefs.chembl', 'drugcentral.xrefs.chembl_id', 'unichem.chembl'], + DRUGBANK: ['drugcentral.xrefs.drugbank_id', 'pharmgkb.xrefs.drugbank', 'chebi.xrefs.drugbank', 'drugbank.id', 'unichem.drugbank'], + 'PUBCHEM.COMPOUND': ['pubchem.cid', 'drugbank.xrefs.pubchem.cid', 'drugcentral.xrefs.pubchem_cid', 'pharmgkb.xrefs.pubchem.cid', 'chebi.xrefs.pubchem.cid', 'unichem.pubchem'], + CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi', 'pharmgkb.xrefs.chebi', 'unichem.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'], - LINCS: ['unichem.lincs'], - RHEA: ['chebi.xrefs.rhea'], + INCHIKEY: ['drugbank.inchi_key', 'ginas.inchikey', 'unii.inchikey', 'chebi.inchikey', 'chembl.inchi_key', 'pubchem.inchi_key'], + INCHI: ['drugbank.inchi', 'chebi.inchi', 'chembl.inchi', 'pharmgkb.inchi', 'pubchem.inchi'], + LINCS: ['unichem.lincs', 'chebi.xrefs.lincs'], + CAS: ['chebi.xrefs.cas', 'ginas.cas_primary', 'pharmgkb.xrefs.cas'], + HMDB: ['chebi.xrefs.hmdb', 'pharmgkb.xrefs.hmdb'], name: ['chembl.pref_name', 'drugbank.name', 'umls.name', 'ginas.preferred_name', 'pharmgkb.name', 'chebi.name'], }, additional_attributes_mapping: { @@ -120,22 +116,8 @@ export const APIMETA: MetaDataItemsObject = { }, }, Drug: { - id_ranks: [ - 'CHEBI', - 'CHEMBL.COMPOUND', - 'DRUGBANK', - 'PUBCHEM.COMPOUND', - 'MESH', - 'INCHI', - 'INCHIKEY', - 'UNII', - 'KEGG', - 'UMLS', - 'LINCS', - 'RHEA', - 'name', - ], - semantic: 'ChemicalSubstance', + id_ranks: ['CHEBI', 'CHEMBL.COMPOUND', 'DRUGBANK', 'PUBCHEM.COMPOUND', 'MESH', 'INCHI', 'INCHIKEY', 'UNII', 'UMLS', 'CAS', 'HMDB', 'LINCS', 'RXCUI', 'NDC', 'name'], + semantic: 'Drug', api_name: 'mychem.info', url: 'https://mychem.info/v1/query', mapping: { @@ -147,14 +129,20 @@ export const APIMETA: MetaDataItemsObject = { 'drugcentral.xrefs.pubchem_cid', 'pharmgkb.xrefs.pubchem.cid', ], - CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi'], + 'CHEMBL.COMPOUND': ['chembl.molecule_chembl_id', 'drugbank.xrefs.chembl', 'drugcentral.xrefs.chembl_id', 'unichem.chembl'], + DRUGBANK: ['drugcentral.xrefs.drugbank_id', 'pharmgkb.xrefs.drugbank', 'chebi.xrefs.drugbank', 'drugbank.id', 'unichem.drugbank'], + 'PUBCHEM.COMPOUND': ['pubchem.cid', 'drugbank.xrefs.pubchem.cid', 'drugcentral.xrefs.pubchem_cid', 'pharmgkb.xrefs.pubchem.cid', 'chebi.xrefs.pubchem.cid', 'unichem.pubchem'], + CHEBI: ['chebi.id', 'chembl.chebi_par_id', 'drugbank.xrefs.chebi', 'drugcentral.xrefs.chebi', 'pharmgkb.xrefs.chebi', 'unichem.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'], - RHEA: ['chebi.xrefs.rhea'], + INCHIKEY: ['drugbank.inchi_key', 'ginas.inchikey', 'unii.inchikey', 'chebi.inchikey', 'chembl.inchi_key', 'pubchem.inchi_key'], + INCHI: ['drugbank.inchi', 'chebi.inchi', 'chembl.inchi', 'pharmgkb.inchi', 'pubchem.inchi'], + LINCS: ['unichem.lincs', 'chebi.xrefs.lincs'], + CAS: ['chebi.xrefs.cas', 'ginas.cas_primary', 'pharmgkb.xrefs.cas'], + HMDB: ['chebi.xrefs.hmdb', 'pharmgkb.xrefs.hmdb'], + RXCUI: ['ginas.xrefs.RXCUI', 'unii.rxcui', 'aeolus.rxcui'], + NDC: ['pharmgkb.xrefs.ndc'], name: ['chembl.pref_name', 'drugbank.name', 'umls.name', 'ginas.preferred_name', 'pharmgkb.name', 'chebi.name'], }, additional_attributes_mapping: { @@ -178,7 +166,7 @@ export const APIMETA: MetaDataItemsObject = { url: 'https://biothings.ncats.io/hpo/query', mapping: { UMLS: ['xrefs.umls'], - SNOMEDCT: ['xrefs.snomed_ct'], + SNOMEDCT: ['xrefs.snomed_ct', 'xrefs.snomedct_us'], HP: ['_id'], MEDDRA: ['xrefs.meddra'], EFO: ['xrefs.efo'], @@ -189,31 +177,39 @@ export const APIMETA: MetaDataItemsObject = { }, }, Disease: { - id_ranks: ['MONDO', 'DOID', 'OMIM', 'ORPHANET', 'EFO', 'UMLS', 'MESH', 'HP', 'GARD', 'name'], + id_ranks: ['MONDO', 'DOID', 'OMIM', 'ORPHANET', 'EFO', 'UMLS', 'MESH', 'HP', 'GARD', 'SNOMEDCT', 'NCIT', 'name'], semantic: 'Disease', api_name: 'mydisease.info', url: 'https://mydisease.info/v1/query', mapping: { - MONDO: ['mondo.mondo'], - DOID: ['mondo.xrefs.doid'], - UMLS: [ - 'mondo.xrefs.umls', - 'mondo.xrefs.umls_cui', - 'disgenet.xrefs.umls', - 'umls.umls', - 'disease_ontology.xrefs.umls_cui', - ], - name: ['mondo.label', 'disgenet.xrefs.disease_name'], + MONDO: ['mondo.mondo', 'disgenet.xrefs.mondo'], + DOID: ['mondo.xrefs.doid', 'disease_ontology.doid', 'disgenet.xrefs.doid'], + UMLS: ['mondo.xrefs.umls', 'mondo.xrefs.umls_cui', 'disgenet.xrefs.umls', 'umls.umls', 'disease_ontology.xrefs.umls_cui'], + name: ['mondo.label', 'disgenet.xrefs.disease_name', 'disease_ontology.name'], MESH: ['mondo.xrefs.mesh', 'disease_ontology.xrefs.mesh', 'ctd.mesh'], - OMIM: ['mondo.xrefs.omim', 'hpo.omim', 'disgenet.xrefs.omim'], - EFO: ['mondo.xrefs.efo'], + OMIM: ['mondo.xrefs.omim', 'hpo.omim', 'disgenet.xrefs.omim', 'disease_ontology.xrefs.omim'], + EFO: ['mondo.xrefs.efo', 'disgenet.xrefs.efo', 'disease_ontology.xrefs.efo'], ORPHANET: ['hpo.orphanet', 'mondo.xrefs.orphanet'], GARD: ['mondo.xrefs.gard', 'disease_ontology.xrefs.gard'], - HP: ['mondo.xrefs.hp'], + HP: ['mondo.xrefs.hp', 'disgenet.xrefs.hp'], + SNOMEDCT: ['mondo.xrefs.sctid', 'umls.snomed.preferred', 'umls.snomed.non-preferred'], + NCIT: ['mondo.xrefs.ncit', 'disease_ontology.xrefs.ncit'] + }, + }, + ClinicalFinding: { + id_ranks: ['LOINC', 'NCIT', 'EFO', 'name'], + semantic: 'Disease', + api_name: 'mydisease.info', + url: 'https://mydisease.info/v1/query', + mapping: { + LOINC: ['mondo.xrefs.loinc'], + NCIT: ['mondo.xrefs.ncit', 'disease_ontology.xrefs.ncit'] + EFO: ['mondo.xrefs.efo', 'disgenet.xrefs.efo', 'disease_ontology.xrefs.efo'], + name: ['mondo.label', 'disgenet.xrefs.disease_name', 'disease_ontology.name'], }, }, MolecularActivity: { - id_ranks: ['GO', 'MetaCyc', 'RHEA', 'KEGG', 'REACT', 'name'], + id_ranks: ['GO', 'MetaCyc', 'RHEA', 'KEGG.REACTION', 'REACT', 'name'], semantic: 'MolecularActivity', api_name: 'Gene Ontology Molecular Function API', url: 'https://biothings.ncats.io/go_mf/query', @@ -221,47 +217,46 @@ export const APIMETA: MetaDataItemsObject = { GO: ['_id'], MetaCyc: ['xrefs.metacyc'], RHEA: ['xrefs.rhea'], - KEGG: ['xrefs.kegg_reaction'], + "KEGG.REACTION": ['xrefs.kegg_reaction'], REACT: ['xrefs.reactome'], name: ['name'], }, }, BiologicalProcess: { - id_ranks: ['GO', 'MetaCyc', 'REACT', 'KEGG', 'name'], + id_ranks: ['GO', 'MetaCyc', 'REACT', 'name'], semantic: 'BiologicalProcess', api_name: 'Gene Ontology Biological Process API', url: 'https://biothings.ncats.io/go_bp/query', mapping: { GO: ['_id'], MetaCyc: ['xrefs.metacyc'], - KEGG: ['xrefs.kegg_pathway'], REACT: ['xrefs.reactome'], name: ['name'], }, }, CellularComponent: { - id_ranks: ['GO', 'MetaCyc', 'RHEA', 'name'], + id_ranks: ['GO', 'name'], semantic: 'CellularComponent', api_name: 'Gene Ontology Cellular Component API', url: 'https://biothings.ncats.io/go_cc/query', mapping: { GO: ['_id'], - MetaCyc: ['xrefs.metacyc'], - RHEA: ['xrefs.rhea'], name: ['name'], }, }, Pathway: { - id_ranks: ['REACT', 'KEGG', 'PHARMGKB', 'WIKIPATHWAYS', 'BIOCARTA', 'name'], + id_ranks: ['REACT', 'KEGG', 'PHARMGKB.PATHWAYS', 'WIKIPATHWAYS', 'BIOCARTA', 'GO', 'SMPDB', 'name'], semantic: 'Pathway', - api_name: 'geneset API', + api_name: 'Geneset API', url: 'https://biothings.ncats.io/geneset/query', mapping: { REACT: ['reactome'], WIKIPATHWAYS: ['wikipathways'], KEGG: ['kegg'], BIOCARTA: ['biocarta'], - PHARMGKB: ['pharmgkb'], + "PHARMGKB.PATHWAYS": ['pharmgkb'], + GO: ['go'], + SMPDB: ['smpdb'], name: ['name'], }, additional_attributes_mapping: { @@ -269,7 +264,7 @@ export const APIMETA: MetaDataItemsObject = { }, }, AnatomicalEntity: { - id_ranks: ['UBERON', 'UMLS', 'MESH', 'NCIT', 'name'], + id_ranks: ['UBERON', 'UMLS', 'MESH', 'name'], semantic: 'AnatomicalEntity', api_name: 'UBERON API', url: 'https://biothings.ncats.io/uberon/query', @@ -277,20 +272,18 @@ export const APIMETA: MetaDataItemsObject = { UBERON: ['_id'], UMLS: ['xrefs.umls'], MESH: ['xrefs.mesh'], - NCIT: ['xrefs.ncit'], name: ['name'], }, }, Cell: { - id_ranks: ['CL', 'NCIT', 'MESH', 'EFO', 'name'], + id_ranks: ['CL', 'NCIT', 'MESH', 'name'], semantic: 'Cell', - api_name: 'Cell Onotlogy API', + api_name: 'Cell Ontology API', url: 'https://biothings.ncats.io/cell_ontology/query', mapping: { CL: ['_id'], NCIT: ['xrefs.ncit'], MESH: ['xrefs.mesh'], - EFO: ['xrefs.efo'], name: ['name'], }, },