combined_from:
  chemicals.build_untyped_compendia():
    combined_from:
      build_drugcentral_relations():
        combined_from: []
        counts:
          concords:
            count_concords: 35361
            count_distinct_curies: 39172
            predicates:
              xref: 35361
            prefix_counts:
              xref(CHEBI, DrugCentral): 4302
              xref(CHEMBL.COMPOUND, DrugCentral): 7129
              xref(DRUGBANK, DrugCentral): 4368
              xref(DrugCentral, GTOPDB): 2106
              xref(DrugCentral, MESH): 2014
              xref(DrugCentral, PUBCHEM.COMPOUND): 5013
              xref(DrugCentral, UMLS): 5244
              xref(DrugCentral, UNII): 5185
        created_at: '2025-08-03T05:57:38.067846'
        description: 'Build xrefs from DrugCentral (babel_downloads/DrugCentral/xrefs)
          to DrugCentral using the prefix map {''CHEBI'': ''CHEBI'', ''ChEMBL_ID'':
          ''CHEMBL.COMPOUND'', ''DRUGBANK_ID'': ''DRUGBANK'', ''IUPHAR_LIGAND_ID'':
          ''GTOPDB'', ''MESH_DESCRIPTOR_UI'': ''MESH'', ''PUBCHEM_CID'': ''PUBCHEM.COMPOUND'',
          ''UMLSCUI'': ''UMLS'', ''UNII'': ''UNII''}.'
        name: build_drugcentral_relations()
        sources: []
        type: concord
        url: ''
      get_mesh_relationships():
      - combined_from: []
        counts:
          concords:
            count_concords: 48440
            count_distinct_curies: 96874
            predicates:
              xref: 48440
            prefix_counts:
              xref(CAS, MESH): 48440
        created_at: '2025-08-03T05:44:27.618726'
        description: get_mesh_relationships() iterates through the MeSH registry,
          filters it to the MeSH IDs in babel_outputs/intermediate/chemicals/ids/MESH,
          then writes out CAS mappings to babel_outputs/intermediate/chemicals/concords/mesh_cas
        name: get_mesh_relationships()
        sources:
        - name: MeSH Registry
          type: MeSH Registry
        type: concord
        url: ''
      - combined_from: []
        counts:
          concords:
            count_concords: 18077
            count_distinct_curies: 35894
            predicates:
              xref: 18077
            prefix_counts:
              xref(MESH, UNII): 18077
        created_at: '2025-08-03T05:44:27.691372'
        description: get_mesh_relationships() iterates through the MeSH registry,
          filters it to the MeSH IDs in babel_outputs/intermediate/chemicals/ids/MESH,
          then writes out non-CAS mappings (i.e. UNII mappings) to babel_outputs/intermediate/chemicals/concords/mesh_unii
        name: get_mesh_relationships()
        sources:
        - name: MeSH Registry
          type: MeSH Registry
        type: concord
        url: ''
      get_wikipedia_relationships():
        combined_from: []
        counts:
          concords:
            count_concords: 6122
            count_distinct_curies: 12087
            predicates:
              xref: 6122
            prefix_counts:
              xref(CHEBI, MESH): 6122
        created_at: '2025-08-03T05:57:20.654412'
        description: Wikidata SPARQL query to find Wikidata entities with both CHEBI
          and MESH IDs, and build a concordance between them.
        name: get_wikipedia_relationships()
        sources:
        - name: Wikidata SPARQL query
          type: Wikidata
        type: concord
        url: ''
      make_chebi_relations():
        combined_from: []
        counts:
          concords:
            count_concords: 190910
            count_distinct_curies: 369489
            predicates:
              xref: 190910
            prefix_counts:
              xref(CHEBI, KEGG.COMPOUND): 11088
              xref(CHEBI, PUBCHEM.COMPOUND): 179822
        created_at: '2025-08-28T08:23:11.269599'
        description: make_chebi_relations() creates xrefs from the ChEBI database
          (babel_downloads/CHEBI/ChEBI_complete.sdf) to PUBCHEM.COMPOUND and KEGG.COMPOUND.
        name: make_chebi_relations()
        sources: []
        type: concord
        url: ''
      make_gtopdb_relations():
        combined_from: []
        counts:
          concords:
            count_concords: 10970
            count_distinct_curies: 21713
            predicates:
              xref: 10970
            prefix_counts:
              xref(GTOPDB, INCHIKEY): 10970
        created_at: '2025-08-03T05:19:25.001389'
        description: Transform Ligand ID/InChIKey mappings from babel_downloads/GTOPDB/ligands.tsv
          into a concord.
        name: make_gtopdb_relations()
        sources: []
        type: concord
        url: ''
      make_pubchem_cas_concord():
        combined_from: []
        counts:
          concords:
            count_concords: 4209172
            count_distinct_curies: 8086905
            predicates:
              xref: 4209172
            prefix_counts:
              xref(CAS, PUBCHEM.COMPOUND): 4209172
        created_at: '2025-08-03T05:51:10.749010'
        description: make_pubchem_cas_concord() creates xrefs from PUBCHEM identifiers
          in the PubChem synonyms file (babel_downloads/PUBCHEM.COMPOUND/synonyms)
          to Chemical Abstracts Service (CAS) identifiers.
        name: make_pubchem_cas_concord()
        sources: []
        type: concord
        url: ''
      make_pubchem_mesh_concord():
        combined_from: []
        counts:
          concords:
            count_concords: 77860
            count_distinct_curies: 155715
            predicates:
              xref: 77860
            prefix_counts:
              xref(MESH, PUBCHEM.COMPOUND): 77860
        created_at: '2025-08-06T16:11:51.346556'
        description: make_pubchem_mesh_concord() loads MeSH labels from babel_downloads/MESH/labels,
          then creates xrefs from PubChem identifiers in the PubChem input file (babel_downloads/PUBCHEM.COMPOUND/CID-MeSH)
          to those MeSH identifiers using the labels as keys.
        name: make_pubchem_mesh_concord()
        sources: []
        type: concord
        url: ''
      umls.build_sets():
      - combined_from: []
        counts:
          concords:
            count_concords: 272123
            count_distinct_curies: 533871
            predicates:
              eq: 272123
            prefix_counts:
              eq(DRUGBANK, UMLS): 7832
              eq(MESH, UMLS): 148735
              eq(RXCUI, UMLS): 115556
        created_at: '2025-08-03T05:42:00.067826'
        description: 'umls.build_sets() using UMLS MRCONSO with prefixes: {''MSH'':
          ''MESH'', ''DRUGBANK'': ''DRUGBANK'', ''RXNORM'': ''RXCUI''} with cui_prefix
          set to UMLS'
        name: umls.build_sets()
        sources:
        - name: MRCONSO
          type: UMLS
        type: concord
        url: ''
      - combined_from: []
        counts:
          concords:
            count_concords: 5182
            count_distinct_curies: 10227
            predicates:
              eq: 5182
            prefix_counts:
              eq(DRUGBANK, RXCUI): 5182
        created_at: '2025-08-03T05:26:05.199619'
        description: 'umls.build_sets() using UMLS MRCONSO with prefixes: {''MSH'':
          ''MESH'', ''DRUGBANK'': ''DRUGBANK''} with cui_prefix set to RXCUI'
        name: umls.build_sets()
        sources:
        - name: MRCONSO
          type: UMLS
        type: concord
        url: ''
    counts: []
    created_at: '2025-08-30T23:57:27.286886'
    description: Generate an untyped compendium from concordances babel_outputs/intermediate/chemicals/concords/wikipedia_mesh_chebi
      babel_outputs/intermediate/chemicals/concords/PUBCHEM_MESH babel_outputs/intermediate/chemicals/concords/mesh_cas
      babel_outputs/intermediate/chemicals/concords/mesh_unii babel_outputs/intermediate/chemicals/concords/PUBCHEM_CAS
      babel_outputs/intermediate/chemicals/concords/GTOPDB babel_outputs/intermediate/chemicals/concords/CHEBI
      babel_outputs/intermediate/chemicals/concords/UMLS babel_outputs/intermediate/chemicals/concords/DrugCentral
      babel_outputs/intermediate/chemicals/concords/RXNORM, identifiers babel_outputs/intermediate/chemicals/ids/CHEMBL.COMPOUND
      babel_outputs/intermediate/chemicals/ids/GTOPDB babel_outputs/intermediate/chemicals/ids/KEGG.COMPOUND
      babel_outputs/intermediate/chemicals/ids/CHEBI babel_outputs/intermediate/chemicals/ids/UNII
      babel_outputs/intermediate/chemicals/ids/HMDB babel_outputs/intermediate/chemicals/ids/PUBCHEM.COMPOUND
      babel_outputs/intermediate/chemicals/ids/DrugCentral babel_outputs/intermediate/chemicals/ids/DRUGBANK
      babel_outputs/intermediate/chemicals/ids/MESH babel_outputs/intermediate/chemicals/ids/UMLS
      babel_outputs/intermediate/chemicals/ids/RXNORM, " +unichem_partial babel_outputs/intermediate/chemicals/partials/UNICHEM,
      untyped_concord babel_outputs/intermediate/chemicals/partials/untyped_compendium,
      and type file babel_outputs/intermediate/chemicals/partials/types.
    name: chemicals.build_untyped_compendia()
    sources: []
    type: untyped_compendium
    url: ''
counts:
  cliques: 504
  eq_ids: 528
  property_sources: !!python/object/apply:collections.defaultdict
    args:
    - !!python/name:builtins.int ''
    dictitems:
      Listed as a CHEBI secondary ID in the ChEBI SDF file (babel_downloads/CHEBI/ChEBI_complete.sdf): 2
  synonyms: 1957
created_at: '2025-09-01T09:50:23.924986'
description: ''
name: ChemicalMixture.txt
sources: []
type: compendium
url: ''
