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: '2025-11-22T14:56:11.181079'
    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: '2025-11-22T14:57:43.761937'
    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: '2025-11-22T14:57:43.808080'
    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: 6208
        count_distinct_curies: 12257
        predicates:
          xref: 6208
        prefix_counts:
          xref(CHEBI, MESH): 6208
    created_at: '2025-11-21T19:46:25.076528'
    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: 15638
        count_distinct_curies: 30417
        predicates:
          xref: 15638
        prefix_counts:
          xref(CHEBI, KEGG.COMPOUND): 15638
    created_at: '2025-11-22T14:56:40.785789'
    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: 11177
        count_distinct_curies: 22127
        predicates:
          xref: 11177
        prefix_counts:
          xref(GTOPDB, INCHIKEY): 11177
    created_at: '2025-11-22T02:56:59.491686'
    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: 4220873
        count_distinct_curies: 8110624
        predicates:
          xref: 4220873
        prefix_counts:
          xref(CAS, PUBCHEM.COMPOUND): 4220873
    created_at: '2025-11-22T14:57:44.773901'
    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: 77747
        count_distinct_curies: 155494
        predicates:
          xref: 77747
        prefix_counts:
          xref(MESH, PUBCHEM.COMPOUND): 77747
    created_at: '2025-11-22T14:56:14.140457'
    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: 273432
        count_distinct_curies: 536032
        predicates:
          eq: 273432
        prefix_counts:
          eq(DRUGBANK, UMLS): 8003
          eq(MESH, UMLS): 148791
          eq(RXCUI, UMLS): 116638
    created_at: '2025-11-22T14:57:10.054956'
    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: 5212
        count_distinct_curies: 10285
        predicates:
          eq: 5212
        prefix_counts:
          eq(DRUGBANK, RXCUI): 5212
    created_at: '2025-11-22T14:56:16.536539'
    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: '2025-11-25T12:45:57.700351'
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: ''
