combined_from:
  build_gene_medgen_relationships():
    combined_from: []
    counts:
      concords:
        count_concords: 17495
        count_distinct_curies: 34977
        predicates:
          eq: 17495
        prefix_counts:
          eq(NCBIGene, OMIM): 17495
    created_at: '2025-08-03T05:19:08.737193'
    description: Extracts gene-OMIM relationships from the mim2gene_medgen file (babel_downloads/NCBIGene/mim2gene_medgen)
    name: build_gene_medgen_relationships()
    sources:
    - filename: babel_downloads/NCBIGene/mim2gene_medgen
      name: MIM2Gene MEDGEN
    type: concord
    url: ''
  build_gene_ncbi_ensembl_relationships():
    combined_from: []
    counts:
      concords:
        count_concords: 13269588
        count_distinct_curies: 26489939
        predicates:
          eq: 13269588
        prefix_counts:
          eq(ENSEMBL, NCBIGene): 13269588
    created_at: '2025-08-03T05:29:32.560564'
    description: Extracts gene-ensembl relationships from the NCBIGene gene2ensembl.gz
      file (babel_downloads/NCBIGene/gene2ensembl.gz), filtering to NCBIGene IDs in
      babel_outputs/intermediate/gene/ids/NCBIGene
    name: build_gene_ncbi_ensembl_relationships()
    sources:
    - filename: babel_downloads/NCBIGene/gene2ensembl.gz
      name: NCBIGene gene2ensembl.gz
      type: NCBIGENE
    type: concord
    url: ''
  build_gene_ncbigene_xrefs():
    combined_from: []
    counts:
      concords:
        count_concords: 517330
        count_distinct_curies: 1034660
        predicates:
          xref: 517330
        prefix_counts:
          xref(FB, NCBIGene): 17872
          xref(HGNC, NCBIGene): 43581
          xref(MGI, NCBIGene): 58199
          xref(NCBIGene, RGD): 303125
          xref(NCBIGene, SGD): 6471
          xref(NCBIGene, WormBase): 46890
          xref(NCBIGene, ZFIN): 27300
          xref(NCBIGene, dictyBase): 13892
    created_at: '2025-08-03T05:31:30.912407'
    description: Extracts gene-xref relationships from the NCBIGene gene_info.gz file
      (babel_downloads/NCBIGene/gene_info.gz), filtering to NCBIGene IDs in babel_outputs/intermediate/gene/ids/NCBIGene
      and extracting mappings for prefixes dict_values(['WormBase', 'FB', 'ZFIN',
      'HGNC', 'MGI', 'RGD', 'dictyBase', 'SGD'])
    name: build_gene_ncbigene_xrefs()
    sources:
    - filename: babel_downloads/NCBIGene/gene_info.gz
      name: NCBIGene gene_info.gz
      type: NCBIGENE
    type: concord
    url: ''
  get_umls_gene_protein_mappings:
    combined_from: []
    counts:
      concords:
        count_concords: 23036
        count_distinct_curies: 27608
        predicates:
          oio:closeMatch: 23036
        prefix_counts:
          oio:closeMatch(NCBIGene, UMLS): 23036
    created_at: '2025-08-03T05:57:11.876833'
    description: Download UMLS-UniProtKB gene mappings from https://raw.githubusercontent.com/cbizon/UMLS_UniProtKB/refs/heads/main/outputs/UMLS_UniProtKB.tsv
    name: get_umls_gene_protein_mappings
    sources:
    - name: UMLS-UniProtKB mappings
      type: download
      url: https://raw.githubusercontent.com/cbizon/UMLS_UniProtKB/refs/heads/main/outputs/UMLS_UniProtKB.tsv
    type: concord
    url: ''
  umls.build_sets():
    combined_from: []
    counts:
      concords:
        count_concords: 43840
        count_distinct_curies: 87665
        predicates:
          eq: 43840
        prefix_counts:
          eq(HGNC, UMLS): 43840
    created_at: '2025-08-03T05:39:32.682192'
    description: 'umls.build_sets() using UMLS MRCONSO with prefixes: {''HGNC'': ''HGNC''}
      with cui_prefix set to UMLS'
    name: umls.build_sets()
    sources:
    - name: MRCONSO
      type: UMLS
    type: concord
    url: ''
counts:
  cliques: 65628491
  eq_ids: 79427652
  property_sources: !!python/object/apply:collections.defaultdict
  - !!python/name:builtins.int ''
  synonyms: 126284024
created_at: '2025-08-14T22:58:00.404064'
description: ''
name: Gene.txt
sources: []
type: compendium
url: ''
