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config.json
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config.json
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{
"input_directory": "input_data",
"download_directory": "babel_downloads",
"intermediate_directory": "babel_outputs/intermediate",
"output_directory": "babel_outputs",
"biolink_version": "4.2.2",
"umls_version": "2024AA",
"rxnorm_version": "08052024",
"drugbank_version": "5-1-12",
"ncbi_files": ["gene2ensembl.gz", "gene_info.gz", "gene_orthologs.gz", "gene_refseq_uniprotkb_collab.gz", "mim2gene_medgen"],
"ubergraph_ontologies": ["UBERON", "CL", "GO", "NCIT", "ECO", "ECTO", "ENVO", "HP", "UPHENO","BFO","BSPO","CARO","CHEBI","CP","GOREL","IAO","MAXO","MONDO","PATO","PR","RO","UBPROP"],
"mods": ["WormBase","FB","MGI","ZFIN","RGD","SGD"],
"anatomy_prefixes": ["UBERON","GO","CL","UMLS","MESH","NCIT","SNOMEDCT"],
"anatomy_ids": ["UBERON","GO","CL","UMLS","MESH","NCIT"],
"anatomy_concords": ["UBERON","GO","CL","UMLS", "WIKIDATA"],
"anatomy_outputs": ["AnatomicalEntity.txt", "Cell.txt", "CellularComponent.txt","GrossAnatomicalStructure.txt"],
"gene_labels": ["HGNC","NCBIGene","UMLS"],
"gene_ids": ["ENSEMBL","HGNC","NCBIGene","UMLS","OMIM","ZFIN","WormBase","FB","MGI","RGD","SGD"],
"gene_concords": ["NCBIGene","NCBIGeneENSEMBL","medgen","UMLS"],
"gene_outputs": ["Gene.txt"],
"protein_labels": ["UniProtKB","PR","UMLS"],
"protein_synonyms": ["PR", "UMLS"],
"protein_ids": ["ENSEMBL","UniProtKB","PR","UMLS"],
"protein_concords": ["UniProtKB","PR","NCIT_UniProtKB","NCIT_UMLS"],
"protein_outputs": ["Protein.txt"],
"disease_labelsandsynonyms": ["MONDO","DOID","Orphanet","HP","MESH","NCIT","UMLS","SNOMEDCT","EFO"],
"disease_ids": ["MONDO","DOID","Orphanet","HP","MESH","NCIT","UMLS","OMIM","EFO"],
"disease_concords": ["HP","MONDO","UMLS","DOID","EFO", "Manual"],
"disease_outputs": ["Disease.txt", "PhenotypicFeature.txt"],
"process_labels": ["GO","REACT","RHEA","EC","SMPDB","PANTHER.PATHWAY"],
"process_ids": ["GO","REACT","RHEA","EC","SMPDB","PANTHER.PATHWAY"],
"process_concords": ["GO","RHEA"],
"process_outputs": ["Pathway.txt", "BiologicalProcess.txt", "MolecularActivity.txt"],
"unichem_datasources": ["CHEMBL.COMPOUND","DRUGBANK","GTOPDB","KEGG.COMPOUND","CHEBI","UNII","HMDB","PUBCHEM.COMPOUND","DrugCentral"],
"chemical_labels": ["CHEMBL.COMPOUND","GTOPDB","KEGG.COMPOUND","CHEBI","UNII","HMDB","PUBCHEM.COMPOUND","DrugCentral","UMLS", "DRUGBANK"],
"chemical_synonyms": ["GTOPDB","CHEBI","UNII","HMDB","PUBCHEM.COMPOUND","UMLS", "DRUGBANK"],
"chemical_concords": ["wikipedia_mesh_chebi","PUBCHEM_MESH","mesh_cas","mesh_unii","PUBCHEM_CAS","GTOPDB","CHEBI","UMLS","DrugCentral","RXNORM"],
"chemical_ids": ["CHEMBL.COMPOUND","GTOPDB","KEGG.COMPOUND","CHEBI","UNII","HMDB","PUBCHEM.COMPOUND","DrugCentral","DRUGBANK","MESH","UMLS","RXNORM"],
"chemical_outputs": ["MolecularMixture.txt", "SmallMolecule.txt", "Polypeptide.txt", "ComplexMolecularMixture.txt", "ChemicalEntity.txt", "ChemicalMixture.txt", "Drug.txt"],
"drugchemicalconflated_synonym_outputs": ["DrugChemicalConflated.txt"],
"taxon_labels": ["NCBITaxon","MESH","UMLS"],
"taxon_synonyms": ["NCBITaxon","UMLS"],
"taxon_ids": ["NCBITaxon","MESH","UMLS"],
"taxon_concords": ["NCBI_MESH", "UMLS"],
"taxon_outputs": ["OrganismTaxon.txt"],
"genefamily_labels": ["PANTHER.FAMILY","HGNC.FAMILY"],
"genefamily_ids": ["PANTHER.FAMILY","HGNC.FAMILY"],
"genefamily_outputs": ["GeneFamily.txt"],
"umls_outputs": ["umls.txt"],
"macromolecularcomplex_outputs": ["MacromolecularComplex.txt"],
"ubergraph_iri_stem_to_prefix_map": {
"https://identifiers.org/ncbigene/": "NCBIGene",
"http://www.ncbi.nlm.nih.gov/gene/": "NCBIGene",
"http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=": "HGNC",
"http://www.informatics.jax.org/marker/MGI:": "MGI",
"http://www.pombase.org/spombe/result/": "PomBase",
"http://www.wormbase.org/species/c_elegans/gene/": "WormBase",
"http://flybase.org/reports/": "FB",
"http://www.ecogene.org/gene/": "ecogene",
"http://zfin.org/action/marker/view/": "ZFIN",
"http://birdgenenames.org/cgnc/GeneReport?id=": "cgnc",
"http://www.ensemblgenomes.org/id/": "ENSEMBL",
"http://www.ensembl.org/id/": "ENSEMBL",
"http://purl.obolibrary.org/obo/AISM_": "AISM",
"http://purl.obolibrary.org/obo/BCO_": "BCO",
"http://purl.obolibrary.org/obo/CDNO_": "CDNO",
"http://purl.obolibrary.org/obo/CLAO_": "CLAO",
"http://purl.obolibrary.org/obo/GNO_": "GNO",
"http://purl.obolibrary.org/obo/HAO_": "HAO",
"http://purl.obolibrary.org/obo/LEPAO_": "LEPAO",
"http://purl.obolibrary.org/obo/MMO_": "MMO",
"http://purl.obolibrary.org/obo/MRO_": "MRO",
"http://purl.obolibrary.org/obo/MmusDv_": "MmusDv",
"http://purl.obolibrary.org/obo/OARCS_": "OARCS",
"http://purl.obolibrary.org/obo/OBA_": "OBA",
"http://purl.obolibrary.org/obo/PCL_": "PCL",
"http://purl.obolibrary.org/obo/PECO_": "PECO",
"http://purl.obolibrary.org/obo/PPO_": "PPO",
"http://purl.obolibrary.org/obo/TS_": "TS",
"http://purl.obolibrary.org/obo/UO_": "UO",
"http://purl.obolibrary.org/obo/PCO_": "PCO",
"http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=": "RGD"
},
"publication_outputs": ["Publication.txt"],
"geneprotein_outputs": ["GeneProtein.txt"],
"drugchemical_outputs": ["DrugChemical.txt"],
"preferred_name_boost_prefixes": {
"biolink:ChemicalEntity": [
"DRUGBANK",
"GTOPDB",
"DrugCentral",
"CHEMBL.COMPOUND",
"RXCUI",
"CHEBI",
"HMDB",
"PUBCHEM.COMPOUND"
]
},
"ensembl_datasets_to_skip": [
"elucius_gene_ensembl",
"hgfemale_gene_ensembl",
"charengus_gene_ensembl",
"otshawytscha_gene_ensembl",
"aocellaris_gene_ensembl"
]
}