combined_from:
  Experimental Factor Ontology (EFO) cross-references:
    combined_from: []
    counts:
      concords:
        count_concords: 28559
        count_distinct_curies: 30699
        predicates:
          oboInOwl:hasDbXref: 11826
          skos:exactMatch: 16733
        prefix_counts:
          oboInOwl:hasDbXref( MedDRA, EFO): 1
          oboInOwl:hasDbXref(ADO, EFO): 1
          oboInOwl:hasDbXref(BTO, EFO): 1
          oboInOwl:hasDbXref(CAS, EFO): 20
          oboInOwl:hasDbXref(CHEBI, EFO): 1
          oboInOwl:hasDbXref(CLO, EFO): 1
          oboInOwl:hasDbXref(CMO, EFO): 18
          oboInOwl:hasDbXref(DI, EFO): 1
          oboInOwl:hasDbXref(DOID, EFO): 157
          oboInOwl:hasDbXref(EFO, EFO): 9
          oboInOwl:hasDbXref(EFO, ENM): 2
          oboInOwl:hasDbXref(EFO, GO): 1
          oboInOwl:hasDbXref(EFO, HMDB): 90
          oboInOwl:hasDbXref(EFO, HP): 27
          oboInOwl:hasDbXref(EFO, ICD10): 166
          oboInOwl:hasDbXref(EFO, ICD10CM): 2
          oboInOwl:hasDbXref(EFO, ICD11): 1
          oboInOwl:hasDbXref(EFO, ICD9): 40
          oboInOwl:hasDbXref(EFO, ICD9CM): 1
          oboInOwl:hasDbXref(EFO, ISBN-10): 1
          oboInOwl:hasDbXref(EFO, ISBN-13): 1
          oboInOwl:hasDbXref(EFO, KEGG COMPOUND): 99
          oboInOwl:hasDbXref(EFO, MEDDRA): 504
          oboInOwl:hasDbXref(EFO, MEDGEN): 5
          oboInOwl:hasDbXref(EFO, MESH): 406
          oboInOwl:hasDbXref(EFO, MO): 7
          oboInOwl:hasDbXref(EFO, MONDO): 38
          oboInOwl:hasDbXref(EFO, MP): 23
          oboInOwl:hasDbXref(EFO, MPATH): 2
          oboInOwl:hasDbXref(EFO, MedGen): 13
          oboInOwl:hasDbXref(EFO, Medgen): 13
          oboInOwl:hasDbXref(EFO, NCIT): 556
          oboInOwl:hasDbXref(EFO, NCIm): 1
          oboInOwl:hasDbXref(EFO, NIFSTD): 5
          oboInOwl:hasDbXref(EFO, NPO): 1
          oboInOwl:hasDbXref(EFO, OAE): 1
          oboInOwl:hasDbXref(EFO, OBI): 2
          oboInOwl:hasDbXref(EFO, OMIM): 172
          oboInOwl:hasDbXref(EFO, OMIMPS): 2
          oboInOwl:hasDbXref(EFO, OMIT): 4
          oboInOwl:hasDbXref(EFO, ORCID): 6
          oboInOwl:hasDbXref(EFO, ORDO): 4
          oboInOwl:hasDbXref(EFO, PERSON): 2
          oboInOwl:hasDbXref(EFO, PMID): 6204
          oboInOwl:hasDbXref(EFO, PR): 1
          oboInOwl:hasDbXref(EFO, PubChem): 24
          oboInOwl:hasDbXref(EFO, RRID): 4
          oboInOwl:hasDbXref(EFO, SCDO): 1
          oboInOwl:hasDbXref(EFO, SCTID): 9
          oboInOwl:hasDbXref(EFO, SNOMEDCT): 315
          oboInOwl:hasDbXref(EFO, SYMP): 2
          oboInOwl:hasDbXref(EFO, T3DB): 9
          oboInOwl:hasDbXref(EFO, UMLS): 161
          oboInOwl:hasDbXref(EFO, Wikipedia): 68
          oboInOwl:hasDbXref(EFO, doi): 1
          oboInOwl:hasDbXref(EFO, http): 8
          oboInOwl:hasDbXref(EFO, https): 29
          oboInOwl:hasDbXref(EFO, modelled on http): 1
          oboInOwl:hasDbXref(EFO, uniprot): 2581
          skos:exactMatch(DOID, EFO): 1893
          skos:exactMatch(EFO, EFO): 2386
          skos:exactMatch(EFO, ICD10CM): 665
          skos:exactMatch(EFO, MEDDRA): 103
          skos:exactMatch(EFO, MEDGEN): 2513
          skos:exactMatch(EFO, MESH): 1655
          skos:exactMatch(EFO, NCIT): 1890
          skos:exactMatch(EFO, OMIM): 232
          skos:exactMatch(EFO, OMIM.PS): 41
          skos:exactMatch(EFO, SNOMEDCT): 1799
          skos:exactMatch(EFO, UMLS): 2637
          skos:exactMatch(EFO, http): 792
          skos:exactMatch(EFO, https): 127
    created_at: '2025-11-22T23:41:05.011670'
    description: Cross-references from the Experimental Factor Ontology (EFO) for
      the EFO IDs in babel_outputs/intermediate/disease/ids/EFO
    name: Experimental Factor Ontology (EFO) cross-references
    sources:
    - name: Experimental Factor Ontology
      url: http://www.ebi.ac.uk/efo/efo.owl
    type: concord
    url: ''
  Manual Disease/Phenotype Concords:
    combined_from: []
    counts:
      concords:
        count_concords: 88
        count_distinct_curies: 105
        predicates:
          oio:closeMatch: 81
          oio:exactMatch: 1
          xref: 6
        prefix_counts:
          oio:closeMatch(DOID, MONDO): 3
          oio:closeMatch(EFO, MONDO): 1
          oio:closeMatch(EFO, UMLS): 6
          oio:closeMatch(HP, NCIT): 1
          oio:closeMatch(HP, UMLS): 1
          oio:closeMatch(MONDO, UMLS): 61
          oio:closeMatch(UMLS, UMLS): 8
          oio:exactMatch(MONDO, UMLS): 1
          xref(EFO, UMLS): 1
          xref(HP, MONDO): 2
          xref(MESH, MONDO): 1
          xref(MONDO, UMLS): 2
    created_at: '2025-12-10T19:20:48.144579'
    description: Manually curated Disease/Phenotype cross-references from the Babel
      repository
    name: Manual Disease/Phenotype Concords
    sources:
    - name: Babel repository
      url: https://github.com/TranslatorSRI/Babel
    type: concord
    url: https://github.com/TranslatorSRI/Babel/blob/master/input_data/manual_concords/disease.txt
  build_disease_doid_relationships():
    combined_from: []
    counts:
      concords:
        count_concords: 38566
        count_distinct_curies: 47850
        predicates:
          xref: 38566
        prefix_counts:
          xref(DOID, EFO): 111
          xref(DOID, GARD): 2173
          xref(DOID, ICD0): 492
          xref(DOID, ICD10): 3663
          xref(DOID, ICD11): 4
          xref(DOID, ICD9): 2251
          xref(DOID, KEGG.DISEASE): 42
          xref(DOID, MEDDRA): 42
          xref(DOID, MESH): 4054
          xref(DOID, MIM): 6300
          xref(DOID, NCIT): 4903
          xref(DOID, ORDO): 2268
          xref(DOID, SNOMEDCT): 1
          xref(DOID, SNOMEDCT_US_2021_07_31): 1
          xref(DOID, SNOMEDCT_US_2021_09_01): 28
          xref(DOID, SNOMEDCT_US_2022_07_31): 1
          xref(DOID, SNOMEDCT_US_2023_03_01): 5156
          xref(DOID, SNOMEDCT_US_2023_09_01): 2
          xref(DOID, SNOMEDCT_US_2023_10_01): 1
          xref(DOID, SNOMEDCT_US_2023_11_01): 1
          xref(DOID, SNOMEDCT_US_2024_03_01): 1
          xref(DOID, SNOMEDCT_US_2025_03_01): 3
          xref(DOID, SNOMEDCT_US_2025_04_25): 2
          xref(DOID, SNOMEDCT_US_2025_05_01): 23
          xref(DOID, SNOMEDCT_US_2025_09_01): 3
          xref(DOID, UMLS): 7040
    created_at: '2025-11-22T02:57:02.130450'
    description: 'build_disease_doid_relationships() using the DOID ID file babel_downloads/DOID/doid.json
      and other_prefixes {''ICD10CM'': ''ICD10'', ''ICD9CM'': ''ICD9'', ''ICDO'':
      ''ICD0'', ''NCI'': ''NCIT'', ''SNOMEDCT_US_2018_03_01'': ''SNOMEDCT'', ''SNOMEDCT_US_2019_09_01'':
      ''SNOMEDCT'', ''SNOMEDCT_US_2020_03_01'': ''SNOMEDCT'', ''SNOMEDCT_US_2020_09_01'':
      ''SNOMEDCT'', ''UMLS_CUI'': ''UMLS'', ''KEGG'': ''KEGG.DISEASE''}'
    name: build_disease_doid_relationships()
    sources:
    - name: doid.build_xrefs
      type: DOID
    type: concord
    url: ''
  build_disease_obo_relationships():
  - combined_from: []
    counts:
      concords:
        count_concords: 17962
        count_distinct_curies: 28870
        predicates:
          xref: 17962
        prefix_counts:
          xref(COHD, HP): 1
          xref(DOID, HP): 2
          xref(EFO, HP): 1
          xref(EPCC, HP): 13
          xref(Fyler, HP): 222
          xref(HP, ICD0): 3
          xref(HP, ICD10): 39
          xref(HP, ICD9): 4
          xref(HP, MEDDRA): 92
          xref(HP, MONDO): 1
          xref(HP, MP): 10
          xref(HP, MPATH): 4
          xref(HP, NCIT): 221
          xref(HP, PMID): 2
          xref(HP, SNOMEDCT): 4578
          xref(HP, UMLS): 12769
    created_at: '2025-11-21T19:47:08.193665'
    description: 'ubergraph.build_sets() of HP:0000118 with other_prefixes {''MSH'':
      ''MESH'', ''SNOMEDCT_US'': ''SNOMEDCT'', ''SNOMED_CT'': ''SNOMEDCT'', ''ORPHANET'':
      ''orphanet'', ''ICD-9'': ''ICD9'', ''ICD-10'': ''ICD10'', ''ICD-0'': ''ICD0'',
      ''ICD-O'': ''ICD0''}'
    name: build_disease_obo_relationships()
    sources:
    - name: HP
      type: UberGraph
    type: concord
    url: ''
  - combined_from: []
    counts:
      concords:
        count_concords: 107021
        count_distinct_curies: 128219
        predicates:
          oio:exactMatch: 107021
        prefix_counts:
          oio:exactMatch(DOID, MONDO): 11703
          oio:exactMatch(EFO, MONDO): 2380
          oio:exactMatch(ICD10CM, MONDO): 2021
          oio:exactMatch(MEDDRA, MONDO): 2
          oio:exactMatch(MEDGEN, MONDO): 21641
          oio:exactMatch(MESH, MONDO): 8122
          oio:exactMatch(MONDO, NCIT): 7341
          oio:exactMatch(MONDO, OMIM): 9836
          oio:exactMatch(MONDO, OMIM.PS): 604
          oio:exactMatch(MONDO, SNOMEDCT): 9008
          oio:exactMatch(MONDO, UMLS): 21641
          oio:exactMatch(MONDO, http): 4142
          oio:exactMatch(MONDO, https): 206
          oio:exactMatch(MONDO, orphanet): 8374
    created_at: '2025-11-21T19:47:14.127079'
    description: ubergraph.build_sets() (exact) of MONDO:0000001 and MONDO:0042489,
      including ORPHANET prefixes
    name: build_disease_obo_relationships()
    sources:
    - name: MONDO
      type: UberGraph
    type: concord
    url: ''
  umls.build_sets():
    combined_from: []
    counts:
      concords:
        count_concords: 92443
        count_distinct_curies: 168008
        predicates:
          eq: 92443
        prefix_counts:
          eq(HP, UMLS): 20664
          eq(MESH, UMLS): 12082
          eq(NCIT, UMLS): 48081
          eq(OMIM, UMLS): 11616
    created_at: '2025-11-22T14:57:02.332801'
    description: 'umls.build_sets() using UMLS MRCONSO with prefixes: {''SNOMEDCT_US'':
      ''SNOMEDCT'', ''MSH'': ''MESH'', ''NCI'': ''NCIT'', ''HPO'': ''HP'', ''MDR'':
      ''MEDDRA'', ''OMIM'': ''OMIM''} with cui_prefix set to UMLS'
    name: umls.build_sets()
    sources:
    - name: MRCONSO
      type: UMLS
    type: concord
    url: ''
counts:
  cliques: 113542
  eq_ids: 271592
  property_sources: !!python/object/apply:collections.defaultdict
  - !!python/name:builtins.int ''
  synonyms: 479037
created_at: '2025-12-10T19:24:20.539880'
description: ''
name: Disease.txt
sources: []
type: compendium
url: ''
