id: monarch-kg
version: '2026-10-07'
generated_at: '2026-10-07T03:22:02Z'
packages:
  biolink: 4.4.2
  koza: 2.6.2
  monarch-ingest: 0.8.0
artifacts:
- path: monarch-kg.tar.gz
  sha256: 71b506f5d0f125f591846b952141251dccde7a012fc23b857b3e3f8d675b93ef
- path: merged_graph_stats.yaml
  sha256: 697925b2b4059cdcfeb387755b495b5165570f5407ae6af65b1db9d82f30ad33
- path: qc_report.yaml
  sha256: 8c32cf860c2448c23449ade311d89f4c30a7c7935db2d63c9bf9ba3585ba9a3d
- path: connectivity_summary.yaml
  sha256: f6e4fee5449291b78b1f7a0c2f2903c6e92fac7a46cfbbab59550e3d3bbcfea4
- path: monarch-kg_schema_report.yaml
  sha256: a62367438a1711c645724324e68f33df231d7cd6ecfadb5c77f3c69fd5de64ca
sources:
- id: alliance-ingest
  version: 9.1.0
  transform_version: b0d7654e
  biolink_version: 4.3.6
  build_version: alliance-ingest_9.1.0_b0d7654e_4.3.6
  generated_at: '2026-10-01T04:44:13Z'
  sources:
  - id: infores:agr
    name: Alliance of Genome Resources
    urls:
    - https://fms.alliancegenome.org/download/DISEASE-ALLIANCE_COMBINED.tsv.gz
    - https://fms.alliancegenome.org/download/PHENOTYPE_RGD.json.gz
    - https://fms.alliancegenome.org/download/PHENOTYPE_MGI.json.gz
    - https://fms.alliancegenome.org/download/PHENOTYPE_WB.json.gz
    - https://fms.alliancegenome.org/download/BGI_MGI.json.gz
    - https://fms.alliancegenome.org/download/BGI_RGD.json.gz
    - https://fms.alliancegenome.org/download/BGI_WB.json.gz
    - https://fms.alliancegenome.org/download/BGI_FB.json.gz
    - https://fms.alliancegenome.org/download/BGI_ZFIN.json.gz
    - https://fms.alliancegenome.org/download/BGI_SGD.json.gz
    - https://fms.alliancegenome.org/download/BGI_XBXL.json.gz
    - https://fms.alliancegenome.org/download/BGI_XBXT.json.gz
    - https://fms.alliancegenome.org/download/VARIANT-ALLELE_NCBITaxon6239.tsv.gz
    - https://fms.alliancegenome.org/download/VARIANT-ALLELE_NCBITaxon7955.tsv.gz
    - https://fms.alliancegenome.org/download/VARIANT-ALLELE_NCBITaxon10090.tsv.gz
    - https://fms.alliancegenome.org/download/VARIANT-ALLELE_NCBITaxon10116.tsv.gz
    - https://fms.alliancegenome.org/download/AGM_MGI.json.gz
    - https://fms.alliancegenome.org/download/AGM_ZFIN.json.gz
    - https://fms.alliancegenome.org/download/AGM_RGD.json.gz
    - https://fms.alliancegenome.org/download/EXPRESSION_RGD.json.gz
    - https://fms.alliancegenome.org/download/EXPRESSION_MGI.json.gz
    - https://fms.alliancegenome.org/download/EXPRESSION_ZFIN.json.gz
    - https://fms.alliancegenome.org/download/EXPRESSION_FB.json.gz
    - https://fms.alliancegenome.org/download/EXPRESSION_WB.json.gz
    - https://fms.alliancegenome.org/download/EXPRESSION_SGD.json.gz
    version: 9.1.0
    version_method: alliance_fms_api
    retrieved_at: '2026-10-01T04:44:11Z'
    sources:
    - id: infores:flybase
      name: FlyBase
      urls:
      - https://fms.alliancegenome.org/download/BGI_FB.json.gz
      - https://fms.alliancegenome.org/download/EXPRESSION_FB.json.gz
      version: '2026-03-05'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
    - id: infores:mgi
      name: Mouse Genome Informatics
      urls:
      - https://fms.alliancegenome.org/download/AGM_MGI.json.gz
      - https://fms.alliancegenome.org/download/BGI_MGI.json.gz
      - https://fms.alliancegenome.org/download/EXPRESSION_MGI.json.gz
      - https://fms.alliancegenome.org/download/PHENOTYPE_MGI.json.gz
      version: '2026-04-24'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
    - id: infores:rgd
      name: Rat Genome Database
      urls:
      - https://fms.alliancegenome.org/download/AGM_RGD.json.gz
      - https://fms.alliancegenome.org/download/BGI_RGD.json.gz
      - https://fms.alliancegenome.org/download/EXPRESSION_RGD.json.gz
      - https://fms.alliancegenome.org/download/PHENOTYPE_RGD.json.gz
      version: '2026-03-06'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
    - id: infores:sgd
      name: Saccharomyces Genome Database
      urls:
      - https://fms.alliancegenome.org/download/BGI_SGD.json.gz
      - https://fms.alliancegenome.org/download/EXPRESSION_SGD.json.gz
      version: '2026-03-18'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
    - id: infores:wormbase
      name: WormBase
      urls:
      - https://fms.alliancegenome.org/download/BGI_WB.json.gz
      - https://fms.alliancegenome.org/download/EXPRESSION_WB.json.gz
      - https://fms.alliancegenome.org/download/PHENOTYPE_WB.json.gz
      version: '2025-11-13'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
    - id: infores:xenbase
      name: Xenbase
      urls:
      - https://fms.alliancegenome.org/download/BGI_XBXL.json.gz
      - https://fms.alliancegenome.org/download/BGI_XBXT.json.gz
      version: '2026-03-25'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
    - id: infores:zfin
      name: ZFIN
      urls:
      - https://fms.alliancegenome.org/download/AGM_ZFIN.json.gz
      - https://fms.alliancegenome.org/download/BGI_ZFIN.json.gz
      - https://fms.alliancegenome.org/download/EXPRESSION_ZFIN.json.gz
      version: '2026-03-17'
      version_method: alliance_fms_submission
      retrieved_at: '2026-10-01T04:44:11Z'
  artifacts:
  - path: alliance_allele_edges.tsv
    sha256: 7f7b7283332f27c0e83bb8dce8f1448938b27b792fe63ccfb15f152a0f13433c
  - path: alliance_allele_nodes.tsv
    sha256: 449a1168e5105d3af7dbdc5a1b03eed66889d2759cf8b4fcfdb235d4f96320c4
  - path: alliance_disease_edges.tsv
    sha256: 46f46d474564ab31064d3340948d0610aabe79518ee7a6669e40e82f19910ed6
  - path: alliance_gene_nodes.tsv
    sha256: d834b87b214289fe0c19031f2b7f5e45f840ff995195b156ca75c7faf4a481e2
  - path: alliance_gene_to_expression_edges.tsv
    sha256: f0d309d83a89162c919c45b3fd075fabfe1a7f3a021dc67776973946346759b4
  - path: alliance_genotype_edges.tsv
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  - path: alliance_genotype_nodes.tsv
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  - path: alliance_phenotype_edges.tsv
    sha256: e378b143846985bbb2218e136b9cbed2965aa9f9507291c36944308273eaa891
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: bgee-ingest
  version: '15.2'
  transform_version: b1611c8f
  biolink_version: 4.4.5
  build_version: bgee-ingest_15.2_b1611c8f_4.4.5
  generated_at: '2026-10-01T05:25:46Z'
  sources:
  - id: infores:bgee
    name: "BGee \u2014 Gene Expression"
    urls:
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Homo_sapiens_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Bos_taurus_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Canis_lupus_familiaris_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Gallus_gallus_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Sus_scrofa_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Rattus_norvegicus_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Mus_musculus_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Danio_rerio_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Xenopus_laevis_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Drosophila_melanogaster_expr_simple.tsv.gz
    - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Caenorhabditis_elegans_expr_simple.tsv.gz
    version: '15.2'
    version_method: ftp_index_probe
    retrieved_at: '2026-10-01T05:25:45Z'
  artifacts:
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    sha256: bd4084584cce7707a37ac589252d69a583ab55e5aac4709651a9cf824c58f966
  tools:
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    kghub_downloader: 0.5.0
- id: biogrid-ingest
  version: 4.4.226
  transform_version: 181c6cf7
  biolink_version: 4.3.6
  build_version: biogrid-ingest_4.4.226_181c6cf7_4.3.6
  generated_at: '2026-10-01T05:01:44Z'
  sources:
  - id: infores:biogrid
    name: "BioGRID \u2014 Gene/Protein Interactions"
    urls:
    - https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-4.4.226/BIOGRID-ALL-4.4.226.mitab.zip
    version: 4.4.226
    version_method: url_path
    retrieved_at: '2026-10-01T05:01:43Z'
  artifacts:
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    sha256: 51a9fc92c3e2b7a37489238f48098cea205d72891c7dd2149c8f75059cd191a2
  tools:
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    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: clingen-ingest
  version: '2026-08-31'
  transform_version: 5af4af58
  biolink_version: 4.3.6
  build_version: clingen-ingest_2026-08-31_5af4af58_4.3.6
  generated_at: '2026-09-01T03:29:32Z'
  sources:
  - id: infores:clingen
    name: "ClinGen \u2014 Clinical Genome Resource"
    urls:
    - http://erepo.clinicalgenome.org/redmine/projects/evrepo/pcer/api/classifications/all?format=tabbed
    version: '2026-08-31'
    version_method: max_published_date
    retrieved_at: '2026-09-01T03:29:31Z'
  - id: infores:hgnc
    name: HUGO Gene Nomenclature Committee
    urls:
    - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
    version: '2026-08-28'
    version_method: http_last_modified
    retrieved_at: '2026-09-01T03:29:31Z'
  artifacts:
  - path: clingen_gene_disease_edges.tsv
    sha256: f03a332f62a919ed63510baa8c5a9411ad46ebef906b7e8e214b0f6e34964ad3
  - path: clingen_variant_edges.tsv
    sha256: d7dc64d9199ec227df6ab5a045ddae6b5b90f28823adb331f5d63bb13066feb3
  - path: clingen_variant_nodes.tsv
    sha256: 2fcd225024bfc914e75d761e36d0a58e8977210f84b33bf4760e35e69dc72de1
  tools:
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    kghub_downloader: 0.4.4
- id: clinvar-ingest
  version: '2026-09-29'
  transform_version: bf8e652e
  biolink_version: 4.3.6
  build_version: clinvar-ingest_2026-09-29_bf8e652e_4.3.6
  generated_at: '2026-10-01T02:52:28Z'
  sources:
  - id: infores:clinvar
    name: ClinVar
    urls:
    - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
    - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
    - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz
    - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz
    version: '2026-09-29'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T02:52:27Z'
  - id: infores:medgen
    name: MedGen
    urls:
    - https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz
    version: '2026-09-30'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T02:52:27Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-09-09'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T02:52:27Z'
  artifacts:
  - path: clinvar_variant_edges.tsv
    sha256: e6ad45de40a836922efc2333290b0d61dc05c64383efa83ce73259abcf4b5935
  - path: clinvar_variant_nodes.tsv
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  tools:
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- id: cureid-ingest
  version: '2026-05-28'
  transform_version: 7ce72810
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  build_version: cureid-ingest_2026-05-28_7ce72810_4.4.5
  generated_at: '2026-10-01T03:43:33Z'
  sources:
  - id: infores:cureid
    name: "CureID \u2014 Drug Repurposing Database"
    urls:
    - https://opendata.ncats.nih.gov/public/cureid/cureid_data.tsv
    version: '2026-05-28'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T03:43:33Z'
  artifacts:
  - path: cureid_edges.tsv
    sha256: f5d98832b4698d7f7746adfd724f3f21c18bb1afefd1d89220b44b6c03eb1c07
  - path: cureid_nodes.tsv
    sha256: f008f6f85d8023921ecc8d61989e82a4d0c9c61eacb2cb91095c0810f731db4c
  tools:
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    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
- id: dictybase-ingest
  version: unknown
  transform_version: d01bb330
  biolink_version: 4.4.4
  build_version: dictybase-ingest_unknown_d01bb330_4.4.4
  generated_at: '2026-09-02T03:20:17Z'
  sources:
  - id: infores:dictybase
    name: dictyBase
    urls:
    - http://dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=general&ID=gene_information.txt
    - http://dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=mutant_phenotypes&ID=all-mutants-ddb_g.txt
    version: unknown
    version_method: unavailable
    retrieved_at: '2026-09-02T03:20:17Z'
  artifacts:
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    sha256: 068c66340828b45e9643f65196fecdd0ff61bcd685ebd78c098c057ad07a24d1
  - path: dictybase_gene_to_phenotype_edges.tsv
    sha256: def17621d9f2fb94c5fe696cd5c8152d9159d03eac49af78153a08646370e380
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- id: go-ingest
  version: '2026-07-28'
  transform_version: a7cd768d
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  build_version: go-ingest_2026-07-28_a7cd768d_4.3.6
  generated_at: '2026-10-01T05:24:57Z'
  sources:
  - id: infores:goa
    name: GO Annotations (GOA)
    urls:
    - http://current.geneontology.org/annotations/gaf/HUMAN-uniprot.gaf.gz
    - http://current.geneontology.org/annotations/gaf/MOUSE-mod.gaf.gz
    - http://current.geneontology.org/annotations/gaf/RAT-mod.gaf.gz
    - http://current.geneontology.org/annotations/gaf/CANLF-uniprot.gaf.gz
    - http://current.geneontology.org/annotations/gaf/BOVIN-uniprot.gaf.gz
    - http://current.geneontology.org/annotations/gaf/PIG-uniprot.gaf.gz
    - http://current.geneontology.org/annotations/gaf/CHICK-uniprot.gaf.gz
    - http://current.geneontology.org/annotations/gaf/DANRE-mod.gaf.gz
    - http://current.geneontology.org/annotations/gaf/DROME-mod.gaf.gz
    - http://current.geneontology.org/annotations/gaf/CAEEL-mod.gaf.gz
    - http://current.geneontology.org/annotations/gaf/DICDI-mod.gaf.gz
    - http://current.geneontology.org/annotations/gaf/YEAST-mod.gaf.gz
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    version: '2026-07-28'
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    retrieved_at: '2026-10-01T05:24:55Z'
    sources:
    - id: infores:dictybase
      name: dictyBase
      urls:
      - http://current.geneontology.org/annotations/gaf/DICDI-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:flybase
      name: FlyBase
      urls:
      - http://current.geneontology.org/annotations/gaf/DROME-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:goa-chicken
      name: GOA Chicken (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/CHICK-uniprot.gaf.gz
      version: '2026-07-28'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:goa-cow
      name: GOA Cow (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/BOVIN-uniprot.gaf.gz
      version: '2026-07-28'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:goa-dog
      name: GOA Dog (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/CANLF-uniprot.gaf.gz
      version: '2026-07-28'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:goa-human
      name: GOA Human (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/HUMAN-uniprot.gaf.gz
      version: '2026-07-28'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:goa-pig
      name: GOA Pig (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/PIG-uniprot.gaf.gz
      version: '2026-07-28'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:mgi
      name: Mouse Genome Informatics
      urls:
      - http://current.geneontology.org/annotations/gaf/MOUSE-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:pombase
      name: PomBase
      urls:
      - http://current.geneontology.org/annotations/gaf/SCHPO-mod.gaf.gz
      version: '2026-07-28'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:rgd
      name: Rat Genome Database
      urls:
      - http://current.geneontology.org/annotations/gaf/RAT-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:sgd
      name: Saccharomyces Genome Database
      urls:
      - http://current.geneontology.org/annotations/gaf/YEAST-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:wormbase
      name: WormBase
      urls:
      - http://current.geneontology.org/annotations/gaf/CAEEL-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
    - id: infores:zfin
      name: ZFIN
      urls:
      - http://current.geneontology.org/annotations/gaf/DANRE-mod.gaf.gz
      version: '2026-08-04'
      version_method: file_header
      retrieved_at: '2026-10-01T05:24:55Z'
  - id: infores:eco
    name: Evidence & Conclusion Ontology (gaf-eco-mapping)
    urls:
    - https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/gaf-eco-mapping.txt
    version: 6bbc0730
    version_method: github_branch_head
    retrieved_at: '2026-10-01T05:24:55Z'
  artifacts:
  - path: go_annotation_edges.tsv
    sha256: 144533668f986ae011c9b889c06ff47cc18194b34c98610ba21efa4e12c4b51d
  tools:
    koza: 2.6.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: hgnc-ingest
  version: '2026-08-28'
  transform_version: 425c6c6d
  biolink_version: 4.4.4
  build_version: hgnc-ingest_2026-08-28_425c6c6d_4.4.4
  generated_at: '2026-09-01T02:23:33Z'
  sources:
  - id: infores:hgnc
    name: HUGO Gene Nomenclature Committee
    urls:
    - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
    version: '2026-08-28'
    version_method: rest_info_api
    retrieved_at: '2026-09-01T02:23:33Z'
  - id: infores:agr
    name: Alliance of Genome Resources
    urls:
    - https://fms.alliancegenome.org/download/BGI_HUMAN.json.gz
    version: 9.1.0
    version_method: alliance_fms_api
    retrieved_at: '2026-09-01T02:23:33Z'
  artifacts:
  - path: hgnc_gene.nt.gz
    sha256: ba855fe23fec6bd333a7729d9ed905d4d03503bef68b5ff6d2d3d38fa58f4d36
  - path: hgnc_gene_nodes.tsv
    sha256: d0c4661cabfd60d8fb1ae1e9969d81e8ab404603b72f3edcdc97c8137b6b7d45
  tools:
    koza: 2.6.2
    biolink_model: 4.4.4
    kghub_downloader: 0.5.0
- id: kg-phenio
  version: v2026-10-07
  transform_version: eaa738d3
  biolink_version: 4.2.5
  build_version: kg-phenio_v2026-10-07_eaa738d3_4.2.5
  generated_at: '2026-10-07T01:19:20Z'
  sources:
  - id: phenio
    name: PHENIO
    urls:
    - https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.json
    version: v2026-10-07
    version_method: github_release_api
    retrieved_at: '2026-10-07T01:19:19Z'
    sources:
    - id: infores:bfo
      name: BFO
      urls:
      - http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl
      version: '2019-08-26'
      version_method: owl_version_iri
    - id: infores:bspo
      name: BSPO
      urls:
      - http://purl.obolibrary.org/obo/bspo/releases/2023-05-27/bspo-base.owl
      version: '2023-05-27'
      version_method: owl_version_iri
    - id: infores:chebi
      name: CHEBI
      urls:
      - http://purl.obolibrary.org/obo/chebi/obophenotype/releases/2026-08-28/chebi_slim.owl
      version: '2026-08-28'
      version_method: owl_version_iri
    - id: infores:eco
      name: ECO
      urls:
      - http://purl.obolibrary.org/obo/eco/releases/2026-07-10/eco.owl
      version: '2026-07-10'
      version_method: owl_version_iri
    - id: infores:fbdv
      name: FBDV
      urls:
      - http://purl.obolibrary.org/obo/fbdv/releases/2026-09-30/fbdv-base.owl
      version: '2026-09-30'
      version_method: owl_version_iri
    - id: infores:foodon
      name: FOODON
      urls:
      - http://purl.obolibrary.org/obo/foodon/releases/2026-09-20/foodon.owl
      version: '2026-02-02'
      version_method: owl_version_iri
    - id: infores:hgnc
      name: HGNC
      urls: []
      version: unknown
      version_method: owl_version_iri
    - id: infores:monochrom
      name: MONOCHROM
      urls:
      - http://purl.obolibrary.org/obo/chr/releases/2025-10-15/chr-base.owl
      version: '2025-10-15'
      version_method: owl_version_iri
    - id: infores:mpath
      name: MPATH
      urls:
      - http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl
      version: '2020-05-19'
      version_method: owl_version_iri
    - id: infores:nbo
      name: NBO
      urls:
      - http://purl.obolibrary.org/obo/nbo/releases/2023-07-04/nbo.owl
      version: '2023-07-04'
      version_method: owl_version_iri
    - id: infores:ncbigene
      name: NCBIGENE
      urls: []
      version: unknown
      version_method: owl_version_iri
    - id: infores:ncbitaxon-taxslim
      name: NCBITAXON-TAXSLIM
      urls:
      - http://purl.obolibrary.org/obo/ncbitaxon/releases/2026-07-12/subsets/taxslim.owl
      version: '2026-07-12'
      version_method: owl_version_iri
    - id: infores:pato
      name: PATO
      urls:
      - http://purl.obolibrary.org/obo/pato/releases/2026-10-01/pato-base.owl
      version: '2026-10-01'
      version_method: owl_version_iri
    - id: infores:pr
      name: PR
      urls:
      - http://purl.obolibrary.org/obo/pr/obophenotype/releases/2026-09-15/pr_slim.owl
      version: '2026-09-15'
      version_method: owl_version_iri
    - id: infores:ro
      name: RO
      urls:
      - http://purl.obolibrary.org/obo/ro/releases/2026-09-04/ro-base.owl
      version: '2026-09-04'
      version_method: owl_version_iri
    - id: infores:so
      name: SO
      urls:
      - http://purl.obolibrary.org/obo/so/2026-08-07/so.owl
      version: '2026-08-07'
      version_method: owl_version_iri
    - id: infores:upheno-alignments
      name: UPHENO-ALIGNMENTS
      urls:
      - http://purl.obolibrary.org/obo/upheno/releases/2025-10-12/components/upheno-alignments.owl
      version: '2025-10-12'
      version_method: owl_version_iri
    - id: infores:upheno-bridge
      name: UPHENO-BRIDGE
      urls:
      - http://purl.obolibrary.org/obo/upheno/releases/2025-10-08/components/upheno-bridge.owl
      version: '2025-10-08'
      version_method: owl_version_iri
    - id: infores:wbls
      name: WBLS
      urls:
      - http://purl.obolibrary.org/obo/wbls/releases/2026-04-16/wbls-base.owl
      version: '2026-04-16'
      version_method: owl_version_iri
    - id: infores:zfs
      name: ZFS
      urls:
      - http://purl.obolibrary.org/obo/zfa/releases/2026-07-16/zfa.owl
      version: '2026-07-16'
      version_method: owl_version_iri
    - id: infores:cl
      name: CL
      urls:
      - http://purl.obolibrary.org/obo/cl/releases/2026-06-08/cl-base.owl
      version: '2026-06-08'
      version_method: owl_version_iri
    - id: infores:ddanat
      name: DDANAT
      urls: []
      version: '2026-10-06'
      version_method: owl_version_iri
    - id: infores:ddpheno
      name: DDPHENO
      urls:
      - http://purl.obolibrary.org/obo/ddpheno/releases/2023-08-26/ddpheno-base.owl
      version: '2023-08-26'
      version_method: owl_version_iri
    - id: infores:dpo
      name: DPO
      urls:
      - http://purl.obolibrary.org/obo/dpo/releases/2026-10-01/dpo-base.owl
      version: '2026-10-01'
      version_method: owl_version_iri
    - id: infores:emapa
      name: EMAPA
      urls:
      - http://purl.obolibrary.org/obo/emapa/releases/2026-10-02/emapa.owl
      version: '2026-10-06'
      version_method: owl_version_iri
    - id: infores:fbbt
      name: FBBT
      urls:
      - http://purl.obolibrary.org/obo/fbbt/releases/2026-10-01/fbbt.owl
      version: '2026-10-01'
      version_method: owl_version_iri
    - id: infores:fypo
      name: FYPO
      urls:
      - http://purl.obolibrary.org/obo/fypo/releases/2026-09-08/fypo-base.owl
      version: '2026-09-08'
      version_method: owl_version_iri
    - id: infores:go
      name: GO
      urls:
      - http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-base.owl
      version: '2026-07-26'
      version_method: owl_version_iri
    - id: infores:hp
      name: HP
      urls:
      - http://purl.obolibrary.org/obo/hp/releases/2026-09-01/hp-base.owl
      version: '2026-09-01'
      version_method: owl_version_iri
    - id: infores:hsapdv
      name: HSAPDV
      urls:
      - http://purl.obolibrary.org/obo/life-stages/releases/2025-01-23/components/hsapdv.owl
      version: '2025-01-23'
      version_method: owl_version_iri
    - id: infores:mondo
      name: MONDO
      urls:
      - http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mondo-base.owl
      version: '2026-10-06'
      version_method: owl_version_iri
    - id: infores:mp
      name: MP
      urls:
      - http://purl.obolibrary.org/obo/mp/releases/2026-09-23/mp-base.owl
      version: '2026-09-23'
      version_method: owl_version_iri
    - id: infores:oba
      name: OBA
      urls:
      - http://purl.obolibrary.org/obo/oba/releases/2026-07-14/oba-base.owl
      version: '2026-07-14'
      version_method: owl_version_iri
    - id: infores:uberon
      name: UBERON
      urls:
      - http://purl.obolibrary.org/obo/uberon/releases/2026-10-01/uberon-base.owl
      version: '2026-10-01'
      version_method: owl_version_iri
    - id: infores:upheno
      name: UPHENO
      urls:
      - http://purl.obolibrary.org/obo/upheno/releases/2025-10-12/upheno-base.owl
      version: '2025-10-12'
      version_method: owl_version_iri
    - id: infores:wbbt
      name: WBBT
      urls:
      - http://purl.obolibrary.org/obo/wbbt/releases/2025-08-19/wbbt.owl
      version: '2026-10-06'
      version_method: owl_version_iri
    - id: infores:wbphenotype
      name: WBPHENOTYPE
      urls:
      - http://purl.obolibrary.org/obo/wbphenotype/releases/2026-04-15/wbphenotype-base.owl
      version: '2026-04-15'
      version_method: owl_version_iri
    - id: infores:xao
      name: XAO
      urls:
      - http://purl.obolibrary.org/obo/xao/releases/2024-09-03/xao.owl
      version: '2026-10-06'
      version_method: owl_version_iri
    - id: infores:xpo
      name: XPO
      urls:
      - http://purl.obolibrary.org/obo/xpo/releases/2025-07-25/xpo-base.owl
      version: '2025-07-25'
      version_method: owl_version_iri
    - id: infores:zfa
      name: ZFA
      urls:
      - http://purl.obolibrary.org/obo/zfa/releases/2026-07-16/zfa.owl
      version: '2026-07-16'
      version_method: owl_version_iri
    - id: infores:zp
      name: ZP
      urls:
      - http://purl.obolibrary.org/obo/zp/releases/2024-04-18/zp-base.owl
      version: '2024-04-18'
      version_method: owl_version_iri
    - id: infores:doid
      name: DOID
      urls:
      - http://purl.obolibrary.org/obo/doid/releases/2026-08-31/doid.owl
      version: '2026-08-31'
      version_method: owl_version_iri
    - id: infores:icd10cm
      name: ICD10CM
      urls:
      - https://data.bioontology.org/ontologies/ICD10CM/submissions/27/icd10cm.owl
      version: 2024ab
      version_method: owl_version_iri
    - id: infores:icd11foundation
      name: ICD11FOUNDATION
      urls: []
      version: '2025-01-26'
      version_method: owl_version_iri
    - id: infores:ncit
      name: NCIT
      urls:
      - http://purl.obolibrary.org/obo/ncit/releases/2026-03-19/ncit.owl
      version: 26.02d
      version_method: owl_version_iri
    - id: infores:omim
      name: OMIM
      urls:
      - http://purl.obolibrary.org/obo/mondo/releases/2026-09-16/omim.owl
      version: '2026-09-16'
      version_method: owl_version_iri
    - id: infores:omo
      name: OMO
      urls:
      - http://purl.obolibrary.org/obo/omo/releases/2026-03-16/omo.owl
      version: '2026-03-16'
      version_method: owl_version_iri
    - id: infores:ordo
      name: ORDO
      urls:
      - https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.7.owl
      version: '4.7'
      version_method: owl_version_iri
  - id: infores:upheno-cross-species
    name: UPheno cross-species mappings
    urls:
    - https://data.monarchinitiative.org/mappings/latest/upheno-cross-species.sssom.tsv
    version: '2026-10-04'
    version_method: http_last_modified
    retrieved_at: '2026-10-07T01:19:19Z'
  - id: infores:upheno-species-independent
    name: UPheno species-independent mappings
    urls:
    - https://data.monarchinitiative.org/mappings/latest/upheno-species-independent.sssom.tsv
    version: '2026-10-04'
    version_method: http_last_modified
    retrieved_at: '2026-10-07T01:19:19Z'
  artifacts:
  - path: merged-kg.tar.gz
  tools:
    koza: 1.0.0
    biolink_model: 4.2.5
    kghub_downloader: 0.4.5
- id: loinc-ingest
  version: '2.80'
  transform_version: 56d78bb1
  biolink_version: 4.4.5
  build_version: loinc-ingest_2.80_56d78bb1_4.4.5
  generated_at: '2026-10-01T03:32:34Z'
  sources:
  - id: infores:loinc
    name: LOINC release table (via Tuva terminology 0.16.0)
    urls:
    - https://tuva-public-resources.s3.amazonaws.com/versioned_terminology/0.16.0/loinc.csv_0_0_0.csv.gz
    version: '2.80'
    version_method: loinc_table_max_version_last_changed
    retrieved_at: '2026-10-01T03:32:34Z'
  - id: infores:omop2obo
    name: OMOP2OBO Measurement Mappings
    urls:
    - https://doi.org/10.5281/zenodo.6949858
    version: V1.1
    version_method: static
    retrieved_at: '2026-10-01T03:32:34Z'
  - id: infores:comploinc
    name: CompLOINC (is_a hierarchy)
    urls:
    - https://github.com/loinc/comp-loinc/releases/tag/v2022-12-05
    version: v2022-12-05
    version_method: github_release
    retrieved_at: '2026-10-01T03:32:34Z'
    notes: is_a hierarchy from CompLOINC v2022-12-05 (built on LOINC ~2.73); node
      table is LOINC 2.80. ~10% of leaf nodes get a parent in this release.
  artifacts:
  - path: loinc_composition_edges.tsv
    sha256: c99cb936592f0ff3b105fec084fbf11595285f578f9c0c2d3302a51cea373f2f
  - path: loinc_hierarchy_edges.tsv
    sha256: a2629ae8a68addef31d241ef1f0b09d3344d156cf2f657a9b4416c9fea24cd05
  - path: loinc_nodes_nodes.tsv
    sha256: 246623447b1e63d9cbb5f53a3a9bdf1462630884c8613d1f0698abd6c79e4cf3
  - path: loinc_parts_nodes.tsv
    sha256: 51d4624c34967ac5db59a295a7d93d6d2c9e37e1bdad0d0fee0618ae7581e733
  - path: loinc_phenotype_edges.tsv
    sha256: ae2a8b5d420f129120dbbe2c2be621613bd16b738f4a4ea9569ab58c32694326
  tools:
    koza: 2.6.2
    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
- id: mmrrc-ingest
  version: '2026-09-27'
  transform_version: 56303fc8
  biolink_version: 4.2.5
  build_version: mmrrc-ingest_2026-09-27_56303fc8_4.2.5
  generated_at: '2026-10-01T04:30:09Z'
  sources:
  - id: infores:mmrrc
    name: Mutant Mouse Resource & Research Centers (MMRRC)
    urls:
    - https://www.mmrrc.org/about/mmrrc_catalog_data.csv
    version: '2026-09-27'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T04:30:08Z'
  artifacts:
  - path: mmrrc_allele_to_genotype_edges.tsv
    sha256: c5b05c868e12d56374e1a49e17588506a39ec174dce2ccbc167976064d3dfba1
  - path: mmrrc_genotype_nodes.tsv
    sha256: 1831ac54c95770f8c517b3884a5683bbb89a61e4db62eb1f644be3f0f16263aa
  - path: mmrrc_genotype_to_gene_edges.tsv
    sha256: 99cf23c39e438348f3cd928e284d6f055965a8173da0074d7589ef330830af4d
  - path: mmrrc_genotype_to_phenotype_edges.tsv
    sha256: cd563b9281a5f7a51e226811ffe666962cd7e89e0b087819e56c955214658377
  tools:
    koza: 2.0.0
    biolink_model: 4.2.5
    kghub_downloader: 0.4.2
- id: monarch-phenotype-profile-ingest
  version: '2026-09-02'
  transform_version: eeb42f6b
  biolink_version: 4.3.6
  build_version: monarch-phenotype-profile-ingest_2026-09-02_eeb42f6b_4.3.6
  generated_at: '2026-10-03T03:01:12Z'
  sources:
  - id: infores:hpoa
    name: HPO Annotations (HPOA)
    urls:
    - http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt
    - http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt
    - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
    version: '2026-09-02'
    version_method: file_header
    retrieved_at: '2026-10-03T03:01:11Z'
    sources:
    - id: infores:omim
      name: OMIM
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2026-08-27'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-10-03T03:01:11Z'
    - id: infores:orphanet
      name: Orphanet
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2026-09-02'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-10-03T03:01:11Z'
    - id: infores:decipher
      name: DECIPHER
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2013-05-29'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-10-03T03:01:11Z'
  - id: infores:hp
    name: Human Phenotype Ontology (HP)
    urls:
    - http://purl.obolibrary.org/obo/hp.obo
    version: '2026-09-02'
    version_method: http_last_modified
    retrieved_at: '2026-10-03T03:01:11Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-09-09'
    version_method: http_last_modified
    retrieved_at: '2026-10-03T03:01:11Z'
  artifacts:
  - path: hpoa_disease_mode_of_inheritance_edges.tsv
    sha256: d0107f1d62a1c14ec7316bb49e8bb3aa84d6a92661debc36e1dad867942f4037
  - path: hpoa_disease_to_phenotype_edges.tsv
    sha256: ea89c38c162ab7d3b5c8cedf5f4978781df9028fd2bd2fb9c51f16f12e94a104
  - path: hpoa_gene_to_disease_edges.tsv
    sha256: 20931de25212df95ac289d8c4c1fb8ff17cfa41a8fdda1715e612e5fc68946ff
  - path: hpoa_gene_to_phenotype_edges.tsv
    sha256: f81cca70b4de73334a7e68d02d91a774a9efbf58bae968bd075252de67de780a
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: ncbi-gene
  version: '2026-10-02'
  transform_version: 9fc4ca75
  biolink_version: 4.3.6
  build_version: ncbi-gene_2026-10-02_9fc4ca75_4.3.6
  generated_at: '2026-10-03T03:55:42Z'
  sources:
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
    version: '2026-10-02'
    version_method: http_last_modified
    retrieved_at: '2026-10-03T03:55:41Z'
  artifacts:
  - path: ncbi_gene.nt.gz
    sha256: df9b3e91c3fa19ce1067158cf46f04b13057638ea81a5a81c7895fa553c79ebb
  - path: ncbi_gene_nodes.tsv
    sha256: 5f56ae919dd1401b9e415c5fcc07559b2a1fbb822fd3fa72772454e43c99d236
  tools:
    koza: 2.2.0
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: omim-ingest
  version: '2026-09-30'
  transform_version: b617a53b
  biolink_version: 4.3.6
  build_version: omim-ingest_2026-09-30_b617a53b_4.3.6
  generated_at: '2026-10-01T05:06:52Z'
  sources:
  - id: infores:omim
    name: OMIM (Online Mendelian Inheritance in Man)
    urls:
    - https://data.omim.org/downloads/{MONARCH_OMIM_DOWNLOAD_KEY}/morbidmap.txt
    version: '2026-09-30'
    version_method: file_header
    retrieved_at: '2026-10-01T05:06:52Z'
  artifacts:
  - path: omim_gene_to_disease_edges.tsv
    sha256: 2efcb7d231cfa74e085b1965d34a977164198ff780919828849978fb48bf7828
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: pantherdb-orthologs-ingest
  version: '2024-04-02'
  transform_version: ca67e22d
  biolink_version: 4.3.6
  build_version: pantherdb-orthologs-ingest_2024-04-02_ca67e22d_4.3.6
  generated_at: '2026-10-01T02:56:47Z'
  sources:
  - id: infores:panther
    name: PantherDB Orthologs
    urls:
    - http://data.pantherdb.org/ftp/ortholog/current_release/AllOrthologs.tar.gz
    version: '2024-04-02'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T02:56:45Z'
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
    version: '2026-09-30'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T02:56:45Z'
  artifacts:
  - path: panther_genome_orthologs_edges.tsv
    sha256: 63735a3c3895b9381d52df1fb23bebe6cd61a8b81c3dd97231b70c430ef47cfd
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: phenopacket-ingest
  version: 0.1.26
  transform_version: 33a8b263
  biolink_version: 4.3.6
  build_version: phenopacket-ingest_0.1.26_33a8b263_4.3.6
  generated_at: '2026-05-13T23:01:15Z'
  sources:
  - id: infores:phenopacket-store
    name: Phenopacket Store
    urls:
    - https://github.com/monarch-initiative/phenopacket-store/releases/latest/download/all_phenopackets.zip
    version: 0.1.26
    version_method: github_release_api
    retrieved_at: '2026-05-13T23:01:14Z'
  artifacts:
  - path: phenopacket_ingest_edges.tsv
    sha256: e4c0388b0facc867696baa7416fd97c3855f61e26dcf42023f76e8ed26982cfc
  - path: phenopacket_ingest_nodes.tsv
    sha256: b14b0badec30409da5b0a1ad01f9dd6ece20de40c24ae9094d5f1408eb459104
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: pombase-ingest
  version: '2026-10-01'
  transform_version: be65ca88
  biolink_version: 4.4.5
  build_version: pombase-ingest_2026-10-01_be65ca88_4.4.5
  generated_at: '2026-10-01T02:56:59Z'
  sources:
  - id: infores:pombase
    name: PomBase
    urls:
    - https://www.pombase.org/data/names_and_identifiers/gene_IDs_names_products.tsv
    - https://www.pombase.org/data/annotations/Phenotype_annotations/phenotype_annotations.pombase.phaf.gz
    version: '2026-10-01'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T02:56:59Z'
  artifacts:
  - path: pombase_gene_nodes.tsv
    sha256: 1ba8c9a9cdbc9fe73f4a828a4266dcda7ad80f091cc218dcded34fbdfb6f15d5
  - path: pombase_gene_to_phenotype_edges.tsv
    sha256: b69633537110eeba88a951e4d5a133d99132b472fd58726e1d58ea5c862d64b9
  tools:
    koza: 2.6.2
    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
- id: reactome-ingest
  version: '97'
  transform_version: b244eb83
  biolink_version: 4.4.5
  build_version: reactome-ingest_97_b244eb83_4.4.5
  generated_at: '2026-10-01T05:28:41Z'
  sources:
  - id: infores:reactome
    name: Reactome
    urls:
    - https://reactome.org/download/current/ReactomePathways.txt
    - https://reactome.org/download/current/NCBI2Reactome.txt
    - https://reactome.org/download/current/ChEBI2Reactome.txt
    version: '97'
    version_method: reactome_content_service
    retrieved_at: '2026-10-01T05:28:41Z'
  artifacts:
  - path: reactome_chemical_to_pathway_edges.tsv
    sha256: 14650bc3325c6cf5755a10bfef95aca2f2940730aef100456dc2b2ce4f20f831
  - path: reactome_gene_to_pathway_edges.tsv
    sha256: 5af3fb58f335f83f9d4b61f39c19b08f03fde621908ff4c54dff25d7735e74db
  - path: reactome_pathway_nodes.tsv
    sha256: 7882c3ae1fd3ef21ee941481cc6c903b46ef6b9e49f683a59f28bd76cf791ac7
  tools:
    koza: 2.6.2
    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
- id: string-ingest
  version: '12.0'
  transform_version: f96320f0
  biolink_version: 4.4.4
  build_version: string-ingest_12.0_f96320f0_4.4.4
  generated_at: '2026-09-01T02:18:17Z'
  sources:
  - id: infores:string
    name: "STRING \u2014 Functional Protein Interaction Networks"
    urls:
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9606.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/10116.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/10090.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9615.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9913.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9031.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/8364.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/7955.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/7227.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/6239.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/44689.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/227321.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/284812.protein.links.detailed.v12.0.txt.gz
    - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/4932.protein.links.detailed.v12.0.txt.gz
    - https://string-db.org/mapping_files/entrez/all_organisms.entrez_2_string.tsv
    version: '12.0'
    version_method: url_path
    retrieved_at: '2026-09-01T02:18:17Z'
  artifacts:
  - path: string_protein_links_edges.tsv
    sha256: 0fba6fbf3bfd7cd2cd1e92e34ea9024fb6c83e5feacdc818dc3f5f7f9ae92d21
  tools:
    koza: 2.6.2
    biolink_model: 4.4.4
    kghub_downloader: 0.5.0
- id: upheno-cross-species-ingest
  version: 531e30c7
  transform_version: 71415b00
  biolink_version: 4.4.5
  build_version: upheno-cross-species-ingest_531e30c7_71415b00_4.4.5
  generated_at: '2026-10-01T04:40:13Z'
  sources:
  - id: infores:upheno
    name: uPheno Cross-Species Phenotype Mappings
    urls:
    - https://github.com/obophenotype/upheno-dev/raw/refs/heads/master/src/mappings/upheno-cross-species.sssom.tsv
    version: 531e30c7
    version_method: github_branch_head
    retrieved_at: '2026-10-01T04:40:13Z'
  artifacts:
  - path: upheno_phenotype_to_phenotype_edges.tsv
    sha256: e9563d1a1b4bf75219c43fa7e727c6e943d45352c1505af5e1cf77251acc33b6
  - path: upheno_phenotype_to_phenotype_nodes.tsv
    sha256: 6d64b989b8dd52cf74ae157634931cada329d9e57c7c89132ca866b322a27c81
  tools:
    koza: 2.6.2
    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
- id: xenbase-ingest
  version: '2026-09-30'
  transform_version: 8c8d0fe6
  biolink_version: 4.4.5
  build_version: xenbase-ingest_2026-09-30_8c8d0fe6_4.4.5
  generated_at: '2026-10-01T05:33:45Z'
  sources:
  - id: infores:xenbase
    name: Xenbase
    urls:
    - https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneHumanOrthologMapping.txt
    - https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneMouseOrthologMapping.txt
    - https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneZebrafishOrthologMapping.txt
    - https://download.xenbase.org/xenbase/GenePageReports/XenbaseGenepageToGeneIdMapping.txt
    - https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneNonEntrezOrthologMapping.txt
    version: '2026-09-30'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T05:33:44Z'
  - id: infores:monarchinitiative-xpo-spo
    name: Xenopus XPO/SPO mapping (Monarch-curated)
    urls:
    - https://storage.googleapis.com/monarch-ingest/manually-uploaded-data/xb_xpo_spo_v_v1.tab
    version: '2022-09-27'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T05:33:44Z'
  artifacts:
  - path: xenbase_gene_to_phenotype_edges.tsv
    sha256: 742a65e85bf20ecf54bc3c4c2c3f0cdc136f159ad2ba0ee12dec993cd0f84749
  - path: xenbase_gene_to_phenotype_nodes.tsv
    sha256: 2bed91c8b666008748233133166d7ca895f164261eacd107b4e3c5ae288509c5
  - path: xenbase_non_entrez_orthologs_edges.tsv
    sha256: ef095664a744b7d4dd311c1a3f061a87fefe0c36d371d470f8480bd554af67ca
  - path: xenbase_orthologs_edges.tsv
    sha256: f4bcb69245091720a60ae17ef5bdb0ddc40f20c4d560bed03c7dee6699ad2497
  tools:
    koza: 2.6.2
    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
- id: zfin-ingest
  version: '2026-09-30'
  transform_version: 15c3cda5
  biolink_version: 4.4.5
  build_version: zfin-ingest_2026-09-30_15c3cda5_4.4.5
  generated_at: '2026-10-01T03:13:47Z'
  sources:
  - id: infores:zfin
    name: Zebrafish Information Network (ZFIN)
    urls:
    - https://zfin.org/downloads/phenoGeneCleanData_fish.txt
    - https://zfin.org/downloads/phenotype_fish.txt
    - https://zfin.org/downloads/pheno_environment_fish.txt
    - https://zfin.org/downloads/pub_to_pubmed_id_translation.txt
    - https://zfin.org/downloads/fly_orthos.txt
    - https://zfin.org/downloads/human_orthos.txt
    - https://zfin.org/downloads/mouse_orthos.txt
    version: '2026-09-30'
    version_method: http_last_modified
    retrieved_at: '2026-10-01T03:13:46Z'
  - id: infores:zp
    name: Zebrafish Phenotype Ontology id_map
    urls:
    - https://raw.githubusercontent.com/obophenotype/zebrafish-phenotype-ontology/master/src/curation/id_map_zfin.tsv
    version: e2e9c286
    version_method: github_branch_head
    retrieved_at: '2026-10-01T03:13:46Z'
  artifacts:
  - path: zfin_gene_to_phenotype_edges.tsv
    sha256: c15d48db02425eefaaea3d7b7b297c47909ab17753e1f51e37a46a6201b03c28
  - path: zfin_genotype_to_phenotype_edges.tsv
    sha256: 4f026fdfa736c846f337c8aa4e8b65404c88b7c877232d5ebc6d804a5e4c3859
  - path: zfin_orthology_edges.tsv
    sha256: fcd2345623063959b8c3625cd988438f080138158e3671cb037bb80f5a17632c
  tools:
    koza: 2.6.2
    biolink_model: 4.4.5
    kghub_downloader: 0.5.0
disagreements: []
version_drift:
- id: infores:ncbi-gene
  versions_observed:
  - '2026-09-30'
  - '2026-10-02'
  by_ingest:
    ncbi-gene: '2026-10-02'
    pantherdb-orthologs-ingest: '2026-09-30'