id: monarch-kg
version: '2026-07-11'
generated_at: '2026-07-11T04:04:50Z'
packages:
  biolink: 4.4.2
  koza: 2.6.1
  monarch-ingest: 0.8.0
artifacts:
- path: monarch-kg.tar.gz
  sha256: c4fff8119dcd69d935a751c0ae167950daa36e7407946fe80cd84de1ab4f712d
- path: merged_graph_stats.yaml
  sha256: 73e5586a61fe5c311bcc9171ab0d9fb2b171e9f4521feae4b7c4e5d9a5fcacf5
- path: qc_report.yaml
  sha256: fa8876de909722f2a5fa20376b2fac1ddae08d350608bcd29cd0831d2b051740
- path: connectivity_summary.yaml
  sha256: f79f0fbca427e93e6fd9ef27672e9817f1c9a0e500a401739b4ed0a3ae68153a
- path: monarch-kg_schema_report.yaml
  sha256: 609059f3d2423eeb37436e71b61b023360a32a9360cd3db28126f6c3290db09b
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: '2026-07-01T04:07:50Z'
  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: '2026-07-01T04:07:49Z'
    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: '2026-07-01T04:07:49Z'
    - 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: '2026-07-01T04:07:49Z'
    - 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: '2026-07-01T04:07:49Z'
    - 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: '2026-07-01T04:07:49Z'
    - 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: '2026-07-01T04:07:49Z'
    - 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: '2026-07-01T04:07:49Z'
    - 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: '2026-07-01T04:07:49Z'
  artifacts:
  - path: alliance_allele_edges.tsv
    sha256: 8d69007125b09911ed1032b5bce42b9280140aed81c0e839015d6d80cc4e3f89
  - path: alliance_allele_nodes.tsv
    sha256: 449a1168e5105d3af7dbdc5a1b03eed66889d2759cf8b4fcfdb235d4f96320c4
  - path: alliance_disease_edges.tsv
    sha256: b230aa2c2d58ae097205293375b538a6fad63a25e2db3c38a7ec3243c923a933
  - path: alliance_gene_nodes.tsv
    sha256: 49609c23e20834299546b9aa700e9a274edefe5bc103e26e41e2ac1ffddb9204
  - path: alliance_gene_to_expression_edges.tsv
    sha256: 6a96c4357d5e582eb00f23147eafe8ccc7bedc0a1b9ae6dd597525fb0dda26e7
  - path: alliance_genotype_edges.tsv
    sha256: 5dfcf2097c50fd33043f13238e2be992998f8467b3e5225554c4d66d35352f55
  - path: alliance_genotype_nodes.tsv
    sha256: 18e1e4f86f493b1e0ae76989b7e9fb82220ab3111fe992d7fb90b885fb09d64f
  - path: alliance_phenotype_edges.tsv
    sha256: 9c9e59ebbe60b6518e511e6612cfd31c3eb736c3f3727e4b29f5b1b746828b8a
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: bgee-ingest
  version: '15.2'
  transform_version: 040fbaf8
  biolink_version: 4.4.2
  build_version: bgee-ingest_15.2_040fbaf8_4.4.2
  generated_at: '2026-06-01T02:35:53Z'
  sources:
  - id: infores:bgee
    name: "BGee \u2014 Gene Expression"
    urls:
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Homo_sapiens_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Bos_taurus_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Canis_lupus_familiaris_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Gallus_gallus_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Sus_scrofa_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Rattus_norvegicus_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Mus_musculus_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Danio_rerio_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Xenopus_laevis_expr_simple.tsv.gz
    - https://bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Drosophila_melanogaster_expr_simple.tsv.gz
    - https://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: '2026-06-01T02:35:52Z'
  artifacts:
  - path: bgee_gene_to_expression_edges.tsv
    sha256: cad65ca66807b5db41531094a666912fb071b0a7c1fe14f1b3bb9e332bc642c9
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- 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: '2026-07-01T04:16:43Z'
  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: '2026-07-01T04:16:42Z'
  artifacts:
  - path: biogrid_gene_to_gene_edges.tsv
    sha256: 1c4a988695dd08d20ba363f29d1bead09322425ced8b61d3040c82ba2aba8f2e
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: clingen-ingest
  version: '2026-06-30'
  transform_version: 5af4af58
  biolink_version: 4.3.6
  build_version: clingen-ingest_2026-06-30_5af4af58_4.3.6
  generated_at: '2026-07-01T03:35:35Z'
  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: '2026-06-30'
    version_method: max_published_date
    retrieved_at: '2026-07-01T03:35:34Z'
  - id: infores:hgnc
    name: HUGO Gene Nomenclature Committee
    urls:
    - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
    version: '2026-06-30'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T03:35:34Z'
  artifacts:
  - path: clingen_gene_disease_edges.tsv
    sha256: 9dae9b229ee314c7ffe49b3b3f73aa9ccdf07c2c63e210e3f3e9add6384507a8
  - path: clingen_variant_edges.tsv
    sha256: a8d26260e0fb8d78cae115e312b76f2abe68886cec53447292ee1fdbac1995e7
  - path: clingen_variant_nodes.tsv
    sha256: c4570c159480cb612af9f7e01c91d36c6031194c095aba9629f55a9320932bab
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: clinvar-ingest
  version: '2026-06-28'
  transform_version: 53c243d5
  biolink_version: 4.3.6
  build_version: clinvar-ingest_2026-06-28_53c243d5_4.3.6
  generated_at: '2026-07-01T02:12:56Z'
  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
    version: '2026-06-28'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:12:55Z'
  - id: infores:medgen
    name: MedGen
    urls:
    - https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz
    version: '2026-06-30'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:12:55Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-06-28'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:12:55Z'
  artifacts:
  - path: clinvar_variant_edges.tsv
    sha256: 91bac39b679d07bc6203f8784d39b0350ff759d279e5697d303f908bbe4d2ad1
  - path: clinvar_variant_nodes.tsv
    sha256: 8c852885e1550fc91d2bfb7b9d6ca43ad6188a0c9c7e76c138ad3c6a00e0589b
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.5
- id: ctd-ingest
  version: '2026-05-28'
  transform_version: 9855dc58
  biolink_version: 4.4.3
  build_version: ctd-ingest_2026-05-28_9855dc58_4.4.3
  generated_at: '2026-07-01T02:10:03Z'
  sources:
  - id: infores:ctd
    name: Comparative Toxicogenomics Database (CTD)
    urls:
    - http://ctdbase.org/reports/CTD_chemicals_diseases.tsv.gz
    version: '2026-05-28'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:10:03Z'
  artifacts:
  - path: ctd_chemical_to_disease_edges.tsv
    sha256: 7973687e112734d0de633fcb36a80f3e692d8b567b15705658c102c082946af0
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: cureid-ingest
  version: '2026-05-28'
  transform_version: 7ce72810
  biolink_version: 4.4.3
  build_version: cureid-ingest_2026-05-28_7ce72810_4.4.3
  generated_at: '2026-07-01T02:57:23Z'
  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: '2026-07-01T02:57:23Z'
  artifacts:
  - path: cureid_edges.tsv
    sha256: 4edb391ce79598572434f334bc62a53d67bfb16492a9dc2dd747764198c01cbe
  - path: cureid_nodes.tsv
    sha256: f008f6f85d8023921ecc8d61989e82a4d0c9c61eacb2cb91095c0810f731db4c
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: dictybase-ingest
  version: unknown
  transform_version: d01bb330
  biolink_version: 4.4.3
  build_version: dictybase-ingest_unknown_d01bb330_4.4.3
  generated_at: '2026-07-01T03:37:52Z'
  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: '2026-07-01T03:37:52Z'
  - id: infores:ddpheno
    name: Dicty Phenotype Ontology (BBOP SQLite)
    urls:
    - https://s3.amazonaws.com/bbop-sqlite/ddpheno.db
    version: '2026-05-11'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T03:37:52Z'
  artifacts:
  - path: dictybase_gene_nodes.tsv
    sha256: 068c66340828b45e9643f65196fecdd0ff61bcd685ebd78c098c057ad07a24d1
  - path: dictybase_gene_to_phenotype_edges.tsv
    sha256: 756bdd0ae7ef415073a83e53e05294df98f1355370cd5240545743c2c9d69fa5
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: go-ingest
  version: '2026-06-18'
  transform_version: a7cd768d
  biolink_version: 4.3.6
  build_version: go-ingest_2026-06-18_a7cd768d_4.3.6
  generated_at: '2026-07-11T01:03:58Z'
  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
    - http://current.geneontology.org/annotations/gaf/SCHPO-mod.gaf.gz
    version: '2026-06-18'
    version_method: file_header
    retrieved_at: '2026-07-11T01:03:56Z'
    sources:
    - id: infores:dictybase
      name: dictyBase
      urls:
      - http://current.geneontology.org/annotations/gaf/DICDI-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:flybase
      name: FlyBase
      urls:
      - http://current.geneontology.org/annotations/gaf/DROME-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:goa-chicken
      name: GOA Chicken (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/CHICK-uniprot.gaf.gz
      version: '2026-06-18'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:goa-cow
      name: GOA Cow (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/BOVIN-uniprot.gaf.gz
      version: '2026-06-18'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:goa-dog
      name: GOA Dog (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/CANLF-uniprot.gaf.gz
      version: '2026-06-18'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:goa-human
      name: GOA Human (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/HUMAN-uniprot.gaf.gz
      version: '2026-06-18'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:goa-pig
      name: GOA Pig (UniProt)
      urls:
      - http://current.geneontology.org/annotations/gaf/PIG-uniprot.gaf.gz
      version: '2026-06-18'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:mgi
      name: Mouse Genome Informatics
      urls:
      - http://current.geneontology.org/annotations/gaf/MOUSE-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:pombase
      name: PomBase
      urls:
      - http://current.geneontology.org/annotations/gaf/SCHPO-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:rgd
      name: Rat Genome Database
      urls:
      - http://current.geneontology.org/annotations/gaf/RAT-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:sgd
      name: Saccharomyces Genome Database
      urls:
      - http://current.geneontology.org/annotations/gaf/YEAST-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:wormbase
      name: WormBase
      urls:
      - http://current.geneontology.org/annotations/gaf/CAEEL-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
    - id: infores:zfin
      name: ZFIN
      urls:
      - http://current.geneontology.org/annotations/gaf/DANRE-mod.gaf.gz
      version: '2026-06-17'
      version_method: file_header
      retrieved_at: '2026-07-11T01:03:56Z'
  - 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: '2026-07-11T01:03:56Z'
  artifacts:
  - path: go_annotation_edges.tsv
    sha256: f540603c1408f1db009dfee350554061c4b59714a4a269e82affc683fcc8fc99
  tools:
    koza: 2.6.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: hgnc-ingest
  version: '2026-06-23'
  transform_version: 425c6c6d
  biolink_version: 4.4.3
  build_version: hgnc-ingest_2026-06-23_425c6c6d_4.4.3
  generated_at: '2026-07-01T02:11:38Z'
  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: '2026-06-23'
    version_method: rest_info_api
    retrieved_at: '2026-07-01T02:11:38Z'
  - 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: '2026-07-01T02:11:38Z'
  artifacts:
  - path: hgnc_gene.nt.gz
    sha256: 17c1acd03a96034cecb1595bbf67b654cf86cf5d7d62d7a90783cbb36b91158e
  - path: hgnc_gene_nodes.tsv
    sha256: fd6fb612aa6dfe8208ce969b90ec159dcba3d78b989e97a902c1c4dd35d2967f
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: kg-phenio
  version: v2026-07-07
  transform_version: 5603207a
  biolink_version: 4.2.5
  build_version: kg-phenio_v2026-07-07_5603207a_4.2.5
  generated_at: '2026-07-08T09:30:11Z'
  sources:
  - id: phenio
    name: PHENIO
    urls:
    - https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.json
    version: v2026-07-07
    version_method: github_release_api
    retrieved_at: '2026-07-08T09:30:10Z'
    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/2026-06-10/chebi_slim.owl
      version: '2026-06-10'
      version_method: owl_version_iri
    - id: infores:eco
      name: ECO
      urls:
      - http://purl.obolibrary.org/obo/eco/releases/2026-05-15/eco.owl
      version: '2026-05-15'
      version_method: owl_version_iri
    - id: infores:fbdv
      name: FBDV
      urls:
      - http://purl.obolibrary.org/obo/fbdv/releases/2026-04-02/fbdv-base.owl
      version: '2026-04-02'
      version_method: owl_version_iri
    - id: infores:foodon
      name: FOODON
      urls:
      - http://purl.obolibrary.org/obo/foodon/releases/2025-12-30/foodon.owl
      version: '2025-12-30'
      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/2026-05-13/subsets/taxslim.owl
      version: '2026-05-13'
      version_method: owl_version_iri
    - id: infores:pato
      name: PATO
      urls:
      - http://purl.obolibrary.org/obo/pato/releases/2025-05-14/pato-base.owl
      version: '2025-05-14'
      version_method: owl_version_iri
    - id: infores:pr
      name: PR
      urls:
      - http://purl.obolibrary.org/obo/pr/obophenotype/releases/2026-06-18/pr_slim.owl
      version: '2026-06-18'
      version_method: owl_version_iri
    - id: infores:ro
      name: RO
      urls:
      - http://purl.obolibrary.org/obo/ro/releases/2025-12-17/ro-base.owl
      version: '2025-12-17'
      version_method: owl_version_iri
    - id: infores:so
      name: SO
      urls:
      - http://purl.obolibrary.org/obo/so/2024-11-18/so.owl
      version: '2024-11-18'
      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/2026-06-02/zfa.owl
      version: '2026-06-02'
      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: '2026-07-07'
      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/2026-04-03/dpo-base.owl
      version: '2026-04-03'
      version_method: owl_version_iri
    - id: infores:emapa
      name: EMAPA
      urls:
      - http://purl.obolibrary.org/obo/emapa/releases/2026-06-26/emapa.owl
      version: '2026-07-07'
      version_method: owl_version_iri
    - id: infores:fbbt
      name: FBBT
      urls:
      - http://purl.obolibrary.org/obo/fbbt/releases/2026-06-11/fbbt.owl
      version: '2026-06-11'
      version_method: owl_version_iri
    - id: infores:fypo
      name: FYPO
      urls:
      - http://purl.obolibrary.org/obo/fypo/releases/2026-07-02/fypo-base.owl
      version: '2026-07-02'
      version_method: owl_version_iri
    - id: infores:go
      name: GO
      urls:
      - http://purl.obolibrary.org/obo/go/releases/2026-06-15/go-base.owl
      version: '2026-06-15'
      version_method: owl_version_iri
    - id: infores:hp
      name: HP
      urls:
      - http://purl.obolibrary.org/obo/hp/releases/2026-06-23/hp-base.owl
      version: '2026-06-23'
      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:maxo
      name: MAXO
      urls:
      - http://purl.obolibrary.org/obo/maxo/releases/2026-01-15/maxo-base.owl
      version: '2026-01-15'
      version_method: owl_version_iri
    - id: infores:mondo
      name: MONDO
      urls:
      - http://purl.obolibrary.org/obo/mondo/releases/2026-07-06/mondo-base.owl
      version: '2026-07-07'
      version_method: owl_version_iri
    - id: infores:mp
      name: MP
      urls:
      - http://purl.obolibrary.org/obo/mp/releases/2026-06-17/mp-base.owl
      version: '2026-06-17'
      version_method: owl_version_iri
    - id: infores:oba
      name: OBA
      urls:
      - http://purl.obolibrary.org/obo/oba/releases/2026-05-15/oba-base.owl
      version: '2026-05-15'
      version_method: owl_version_iri
    - id: infores:uberon
      name: UBERON
      urls:
      - http://purl.obolibrary.org/obo/uberon/releases/2026-06-19/uberon-base.owl
      version: '2026-06-19'
      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: '2026-07-07'
      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: '2026-07-07'
      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/2026-06-02/zfa.owl
      version: '2026-06-02'
      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/2026-05-30/doid.owl
      version: '2026-05-30'
      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:icd10who
      name: ICD10WHO
      urls: []
      version: unknown
      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/2026-06-03/omim.owl
      version: '2026-06-03'
      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: '2026-07-05'
    version_method: http_last_modified
    retrieved_at: '2026-07-08T09:30:10Z'
  - id: infores:upheno-species-independent
    name: UPheno species-independent mappings
    urls:
    - https://data.monarchinitiative.org/mappings/latest/upheno-species-independent.sssom.tsv
    version: '2026-07-05'
    version_method: http_last_modified
    retrieved_at: '2026-07-08T09:30:10Z'
  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: 3b7b40fb
  biolink_version: 4.4.3
  build_version: loinc-ingest_2.80_3b7b40fb_4.4.3
  generated_at: '2026-07-01T02:50:36Z'
  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: '2026-07-01T02:50:36Z'
  - id: infores:omop2obo
    name: OMOP2OBO Measurement Mappings
    urls:
    - https://doi.org/10.5281/zenodo.6949858
    version: V1.1
    version_method: static
    retrieved_at: '2026-07-01T02:50:36Z'
  - 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: '2026-07-01T02:50:36Z'
    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: 56864651ba318e3759190899d8e1e9fd854f2a6fd1fa55c6a1306bb073f70847
  - path: loinc_hierarchy_edges.tsv
    sha256: ce1b6c0e085a828903d06a1196c5f0cb189f66540d0f73aa8b90a355f7175860
  - path: loinc_nodes_nodes.tsv
    sha256: 246623447b1e63d9cbb5f53a3a9bdf1462630884c8613d1f0698abd6c79e4cf3
  - path: loinc_parts_nodes.tsv
    sha256: 51d4624c34967ac5db59a295a7d93d6d2c9e37e1bdad0d0fee0618ae7581e733
  - path: loinc_phenotype_edges.tsv
    sha256: 525ce716d368c54ef838d8d38d4b9477e44c8e16121b67bca135f46110362c5a
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: medic-ingest
  version: 1.3.0
  transform_version: 838bf9c5
  biolink_version: 4.4.3
  build_version: medic-ingest_1.3.0_838bf9c5_4.4.3
  generated_at: '2026-07-01T03:11:07Z'
  sources:
  - id: infores:medic
    name: "MeDIC \u2014 Medicines, Diseases, Indications and Contraindications"
    urls:
    - https://ndownloader.figshare.com/files/59187533
    version: 1.3.0
    version_method: local_name_regex
    retrieved_at: '2026-07-01T03:11:07Z'
  - id: infores:mondo
    name: "MONDO disease ontology \u2014 SSSOM exact-match mappings (disease id normalization)"
    urls:
    - http://purl.obolibrary.org/obo/mondo/mappings/mondo.sssom.tsv
    version: v2026-06-02
    version_method: github_release_api
    retrieved_at: '2026-07-01T03:11:07Z'
  - id: infores:sri-node-normalizer
    name: SRI Node Normalizer (drug id normalization)
    urls:
    - https://nodenormalization-sri.renci.org/status
    version: 2025sep1
    version_method: status_endpoint
    service_version: 2.4.1
    biolink_model_version: v4.2.6-rc5
    retrieved_at: '2026-07-01T03:11:07Z'
  artifacts:
  - path: medic_indication_edges.jsonl
    sha256: 79692f7a19a055dc5311a088c0ed274104774872433d6189ff9e80ef3edc2a1d
  - path: medic_indication_nodes.jsonl
    sha256: 605fc676d8c402289a692c8f9c7cd18817c555077f34da71a125c574e2ce2925
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: mmrrc-ingest
  version: '2026-07-05'
  transform_version: 56303fc8
  biolink_version: 4.2.5
  build_version: mmrrc-ingest_2026-07-05_56303fc8_4.2.5
  generated_at: '2026-07-11T00:14:12Z'
  sources:
  - id: infores:mmrrc
    name: Mutant Mouse Resource & Research Centers (MMRRC)
    urls:
    - https://www.mmrrc.org/about/mmrrc_catalog_data.csv
    version: '2026-07-05'
    version_method: http_last_modified
    retrieved_at: '2026-07-11T00:14:12Z'
  artifacts:
  - path: mmrrc_allele_to_genotype_edges.tsv
    sha256: 360dd767b4cf1d09b5c9d1e0a91f8740b14f05fabb2abe2f68c14189e8415374
  - path: mmrrc_genotype_nodes.tsv
    sha256: d8956c647ffc821af4347288f71aa857496c1ef718c7ed1c8f3a37ebba1eb62e
  - path: mmrrc_genotype_to_gene_edges.tsv
    sha256: 66543af493ce7a7c3c7273b513fd01b26d22010bcc90b27f823cdd943c362cf0
  - path: mmrrc_genotype_to_phenotype_edges.tsv
    sha256: 21ccd3932b688b49cfd9fbf16616dc7046f522fd367dc89a2d5294afb2f2b0c1
  tools:
    koza: 2.0.0
    biolink_model: 4.2.5
    kghub_downloader: 0.4.2
- id: monarch-phenotype-profile-ingest
  version: '2026-06-23'
  transform_version: eeb42f6b
  biolink_version: 4.3.6
  build_version: monarch-phenotype-profile-ingest_2026-06-23_eeb42f6b_4.3.6
  generated_at: '2026-07-03T02:04:24Z'
  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: '2026-06-23'
    version_method: file_header
    retrieved_at: '2026-07-03T02:04:23Z'
    sources:
    - id: infores:omim
      name: OMIM
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2026-06-23'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-07-03T02:04:23Z'
    - id: infores:orphanet
      name: Orphanet
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2026-06-23'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-07-03T02:04:23Z'
    - 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: '2026-07-03T02:04:23Z'
  - id: infores:hp
    name: Human Phenotype Ontology (HP)
    urls:
    - http://purl.obolibrary.org/obo/hp.obo
    version: '2026-06-23'
    version_method: http_last_modified
    retrieved_at: '2026-07-03T02:04:23Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-06-28'
    version_method: http_last_modified
    retrieved_at: '2026-07-03T02:04:23Z'
  artifacts:
  - path: hpoa_disease_mode_of_inheritance_edges.tsv
    sha256: ad78307b762e571165feb2f5605865e23859fa2191d605ee72c4bbb170637a77
  - path: hpoa_disease_to_phenotype_edges.tsv
    sha256: bda25d8199673b91d4a211d8b6f21823bb742dfd2a482a0e44ae05468a83d8f4
  - path: hpoa_gene_to_disease_edges.tsv
    sha256: 959f078da271cdca0f25734e94fccd4c59fcf441edf4b8a1481e7427556c6f4b
  - path: hpoa_gene_to_phenotype_edges.tsv
    sha256: dc8e24cf929100a978f5ead804f6d72db2ef03371cb425130bec628d3f650694
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: ncbi-gene
  version: '2026-07-02'
  transform_version: 9fc4ca75
  biolink_version: 4.3.6
  build_version: ncbi-gene_2026-07-02_9fc4ca75_4.3.6
  generated_at: '2026-07-03T02:58:04Z'
  sources:
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
    version: '2026-07-02'
    version_method: http_last_modified
    retrieved_at: '2026-07-03T02:58:03Z'
  artifacts:
  - path: ncbi_gene.nt.gz
    sha256: b8e1a0fe35fc917ad9ac3e64c3b0972484327b0e50ecd76d3c765194d5ef8579
  - path: ncbi_gene_nodes.tsv
    sha256: 45d6a93551867264840454408ad348befc75497758ba75a45677b35617411273
  tools:
    koza: 2.2.0
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: omim-ingest
  version: '2026-06-30'
  transform_version: b617a53b
  biolink_version: 4.3.6
  build_version: omim-ingest_2026-06-30_b617a53b_4.3.6
  generated_at: '2026-07-01T04:19:09Z'
  sources:
  - id: infores:omim
    name: OMIM (Online Mendelian Inheritance in Man)
    urls:
    - https://data.omim.org/downloads/{MONARCH_OMIM_DOWNLOAD_KEY}/morbidmap.txt
    version: '2026-06-30'
    version_method: file_header
    retrieved_at: '2026-07-01T04:19:09Z'
  artifacts:
  - path: omim_gene_to_disease_edges.tsv
    sha256: 992d1b8a6df8bd72fb9bc77eed1e7c4e6787fc3637fe4466383d916e4a3b0526
  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: '2026-07-01T02:18:13Z'
  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: '2026-07-01T02:18:11Z'
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
    version: '2026-06-30'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:18:11Z'
  artifacts:
  - path: panther_genome_orthologs_edges.tsv
    sha256: 23c4db11a3e1d24ff7a11e81c91a9fb10e13f10b34c8284da0408ace206aac4f
  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: '2026-07-01'
  transform_version: be65ca88
  biolink_version: 4.4.3
  build_version: pombase-ingest_2026-07-01_be65ca88_4.4.3
  generated_at: '2026-07-01T02:15:15Z'
  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: '2026-07-01'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:15:15Z'
  artifacts:
  - path: pombase_gene_nodes.tsv
    sha256: 5b8517a8974e078da2458be89b339ca984d95a5232b623b0dfd2c180624208a9
  - path: pombase_gene_to_phenotype_edges.tsv
    sha256: 6bc9773dec2d2b78421cd664ec73d86681cea5565103d0d5ef4717c4e16d8e3e
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: reactome-ingest
  version: '97'
  transform_version: b244eb83
  biolink_version: 4.4.3
  build_version: reactome-ingest_97_b244eb83_4.4.3
  generated_at: '2026-07-01T04:43:30Z'
  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: '2026-07-01T04:43:30Z'
  artifacts:
  - path: reactome_chemical_to_pathway_edges.tsv
    sha256: 06499fd301047d643a4cb2377df022233adabf308d5714c9f8144a837ea22ce0
  - path: reactome_gene_to_pathway_edges.tsv
    sha256: b9ce9799467f0b7341ba3538a958aaf84d0eee0b0018e18cd2b25de471c8ee46
  - path: reactome_pathway_nodes.tsv
    sha256: 7882c3ae1fd3ef21ee941481cc6c903b46ef6b9e49f683a59f28bd76cf791ac7
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: string-ingest
  version: '12.0'
  transform_version: f96320f0
  biolink_version: 4.4.3
  build_version: string-ingest_12.0_f96320f0_4.4.3
  generated_at: '2026-07-01T02:15:31Z'
  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: '2026-07-01T02:15:31Z'
  artifacts:
  - path: string_protein_links_edges.tsv
    sha256: 3574b135ad26938a47ba5e68ce984d18142e0b1132b6a7c8215074b9405f3678
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: upheno-cross-species-ingest
  version: 531e30c7
  transform_version: 71415b00
  biolink_version: 4.4.3.post1.dev0+39fe46d15
  build_version: upheno-cross-species-ingest_531e30c7_71415b00_4.4.3.post1.dev0+39fe46d15
  generated_at: '2026-07-01T04:03:34Z'
  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: '2026-07-01T04:03:34Z'
  artifacts:
  - path: upheno_phenotype_to_phenotype_edges.tsv
    sha256: 23d7de9acf736351cb413ddacc447150e7065b90d1a251b10ae53aa5ead09ef2
  - path: upheno_phenotype_to_phenotype_nodes.tsv
    sha256: 6d64b989b8dd52cf74ae157634931cada329d9e57c7c89132ca866b322a27c81
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3.post1.dev0+39fe46d15
    kghub_downloader: 0.4.5
- id: xenbase-ingest
  version: '2026-06-24'
  transform_version: 8c8d0fe6
  biolink_version: 4.4.3
  build_version: xenbase-ingest_2026-06-24_8c8d0fe6_4.4.3
  generated_at: '2026-07-01T04:45:51Z'
  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: '2026-06-24'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T04:45:50Z'
  - 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: '2026-07-01T04:45:50Z'
  artifacts:
  - path: xenbase_gene_to_phenotype_edges.tsv
    sha256: 92d5ba62672b50cc9c58f65aea8bcebd6b210a71be0deec88faf29a00b077a7d
  - path: xenbase_gene_to_phenotype_nodes.tsv
    sha256: 2bed91c8b666008748233133166d7ca895f164261eacd107b4e3c5ae288509c5
  - path: xenbase_non_entrez_orthologs_edges.tsv
    sha256: 56893c98700883aeaea80954aa0762bf2b9216ce917b5b1b46187ef6cedffa91
  - path: xenbase_orthologs_edges.tsv
    sha256: 03b19e4ff5ba9aadc1a150b366ca376a0c0ff899d94ab357f5f2b2865fe2b490
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
- id: zfin-ingest
  version: '2026-06-30'
  transform_version: 15c3cda5
  biolink_version: 4.4.3
  build_version: zfin-ingest_2026-06-30_15c3cda5_4.4.3
  generated_at: '2026-07-01T02:39:38Z'
  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: '2026-06-30'
    version_method: http_last_modified
    retrieved_at: '2026-07-01T02:39:37Z'
  - 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: b72b0cdf
    version_method: github_branch_head
    retrieved_at: '2026-07-01T02:39:37Z'
  artifacts:
  - path: zfin_gene_to_phenotype_edges.tsv
    sha256: 3b2b2f8da02a1b1636f6300b3342043437dadba504266f8866950155ce306fc1
  - path: zfin_genotype_to_phenotype_edges.tsv
    sha256: a89dace45cc979966d791ca84803d6b28d10fffc02fd0d51f421f44477c1aecd
  - path: zfin_orthology_edges.tsv
    sha256: d31fe5ad19801f09b7eb8cb03e1a5d47be7d059321eb917e25de1c9866677045
  tools:
    koza: 2.6.0
    biolink_model: 4.4.3
    kghub_downloader: 0.4.5
disagreements:
- id: infores:hgnc
  versions_observed:
  - '2026-06-23'
  - '2026-06-30'
  by_ingest:
    clingen-ingest: '2026-06-30'
    hgnc-ingest: '2026-06-23'
- id: infores:mondo
  versions_observed:
  - '2026-06-28'
  - v2026-06-02
  by_ingest:
    clinvar-ingest: '2026-06-28'
    medic-ingest: v2026-06-02
    monarch-phenotype-profile-ingest: '2026-06-28'
version_drift:
- id: infores:ncbi-gene
  versions_observed:
  - '2026-06-30'
  - '2026-07-02'
  by_ingest:
    ncbi-gene: '2026-07-02'
    pantherdb-orthologs-ingest: '2026-06-30'