id: monarch-kg
version: '2026-06-05'
generated_at: '2026-06-05T18:27:15Z'
packages:
  biolink: 4.4.2
  koza: 2.5.0
  monarch-ingest: 0.8.0
artifacts:
- path: monarch-kg.tar.gz
  sha256: 02cef41cfb45a219e6ad3b520539999326b41731005662fa4744b101327fcff2
- path: merged_graph_stats.yaml
  sha256: 9399f1280799446d87ce2cfca8ea4a7196afc0059065ebff25d6dc6b938acc24
- path: qc_report.yaml
  sha256: c7bcf5f6b0557bc18f92bc3609a5cbbca2344eab0ab0a6908dbb4af23384bead
- path: connectivity_summary.yaml
  sha256: ba07ebf30934c374c267ec61815712bc743243d4717f4dbf5fe3adc34b2a8b04
- path: monarch-kg_schema_report.yaml
  sha256: 662f4f1b1f6ca004216a281d13d200726bf1769f71ad88ae7a0ef12549a4e442
sources:
- id: alliance-ingest
  version: 9.0.0
  transform_version: b0d7654e
  biolink_version: 4.3.6
  build_version: alliance-ingest_9.0.0_b0d7654e_4.3.6
  generated_at: '2026-06-01T04:19:38Z'
  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: 9.0.0
    version_method: alliance_fms_api
    retrieved_at: '2026-06-01T04:19:36Z'
    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: '2026-06-01T04:19:36Z'
    - 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: '2026-06-01T04:19:36Z'
    - 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: '2026-06-01T04:19:36Z'
    - 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: '2026-06-01T04:19:36Z'
    - 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: '2026-06-01T04:19:36Z'
    - 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: '2026-06-01T04:19:36Z'
    - 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: '2026-06-01T04:19:36Z'
  artifacts:
  - path: alliance_allele_edges.tsv
    sha256: dfce84433b9721c2ad8eb6dbc1ccc45db5bd290c82e1cd21206d572c0217ea5f
  - path: alliance_allele_nodes.tsv
    sha256: 449a1168e5105d3af7dbdc5a1b03eed66889d2759cf8b4fcfdb235d4f96320c4
  - path: alliance_disease_edges.tsv
    sha256: cb7ed626493d17b381acb1ea245b85754c49881841cb56faef9f73284df252d6
  - path: alliance_gene_nodes.tsv
    sha256: 49609c23e20834299546b9aa700e9a274edefe5bc103e26e41e2ac1ffddb9204
  - path: alliance_gene_to_expression_edges.tsv
    sha256: 07f131e5eb5fcfb454d42fe028c1782b7b10c0b5afd6755794837eb34621c6b5
  - path: alliance_genotype_edges.tsv
    sha256: ac5151537f8f3b603a31b6b5088d8ef89b5002b72b2bf1661189bc5c8fce6300
  - path: alliance_genotype_nodes.tsv
    sha256: 18e1e4f86f493b1e0ae76989b7e9fb82220ab3111fe992d7fb90b885fb09d64f
  - path: alliance_phenotype_edges.tsv
    sha256: ab3a9ffb2cd0188cf009e8c99e3ec5fa3a1822d2f54473b9a565a2789b1cf3e1
  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: '2026-06-01T04:29:34Z'
  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: '2026-06-01T04:29:33Z'
  artifacts:
  - path: biogrid_gene_to_gene_edges.tsv
    sha256: 726b5cc691fe50c4da00bee993425c0541e2b41a9624ba62b692862e8857ccb0
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: clingen-ingest
  version: '2026-05-30'
  transform_version: 5af4af58
  biolink_version: 4.3.6
  build_version: clingen-ingest_2026-05-30_5af4af58_4.3.6
  generated_at: '2026-06-01T03:46:30Z'
  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: '2026-05-30'
    version_method: max_published_date
    retrieved_at: '2026-06-01T03:46:29Z'
  - id: infores:hgnc
    name: HUGO Gene Nomenclature Committee
    urls:
    - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
    version: '2026-05-29'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T03:46:29Z'
  artifacts:
  - path: clingen_gene_disease_edges.tsv
    sha256: 5a3dfaa257e25c10b7f402c3b3cef2cba686df3805f8be115ca748a661aadeac
  - path: clingen_variant_edges.tsv
    sha256: 0f5e75ffa6e0d26d07a0dd676f6e89cfcd3b95d6e5dd230c90f575563f01bd4c
  - path: clingen_variant_nodes.tsv
    sha256: b940922e75eb3d782ac141c05bf3a5ecdd91065cf98b3d570991b76beab64b68
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: clinvar-ingest
  version: '2026-05-25'
  transform_version: 53c243d5
  biolink_version: 4.3.6
  build_version: clinvar-ingest_2026-05-25_53c243d5_4.3.6
  generated_at: '2026-06-01T02:19:11Z'
  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: '2026-05-25'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:19:10Z'
  - id: infores:medgen
    name: MedGen
    urls:
    - https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz
    version: '2026-05-31'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:19:10Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-05-26'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:19:10Z'
  artifacts:
  - path: clinvar_variant_edges.tsv
    sha256: 8cb243ff965567367b7765c858b31b1fa81e04d503486dd6eedb1b02d9391978
  - path: clinvar_variant_nodes.tsv
    sha256: 0a562b28336770b2e7e92648e6d82d0143e341d1448684c7a7b23856370abc9f
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.5
- id: ctd-ingest
  version: '2026-04-30'
  transform_version: 9855dc58
  biolink_version: 4.4.2
  build_version: ctd-ingest_2026-04-30_9855dc58_4.4.2
  generated_at: '2026-06-01T02:30:31Z'
  sources:
  - id: infores:ctd
    name: Comparative Toxicogenomics Database (CTD)
    urls:
    - http://ctdbase.org/reports/CTD_chemicals_diseases.tsv.gz
    version: '2026-04-30'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:30:31Z'
  artifacts:
  - path: ctd_chemical_to_disease_edges.tsv
    sha256: 8772039e2c022fabb236073d25a325cb2a949ab8ba5beddd6bbd3f7e068529bf
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: cureid-ingest
  version: '2026-05-28'
  transform_version: 7ce72810
  biolink_version: 4.4.2
  build_version: cureid-ingest_2026-05-28_7ce72810_4.4.2
  generated_at: '2026-06-01T03:32:56Z'
  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: '2026-06-01T03:32:56Z'
  artifacts:
  - path: cureid_edges.tsv
    sha256: c570d42f3cdf197dd9e2db3c54fc77f05f7883e3b120b9f5643195e01b76ad8f
  - path: cureid_nodes.tsv
    sha256: f008f6f85d8023921ecc8d61989e82a4d0c9c61eacb2cb91095c0810f731db4c
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: dictybase-ingest
  version: unknown
  transform_version: d01bb330
  biolink_version: 4.4.2
  build_version: dictybase-ingest_unknown_d01bb330_4.4.2
  generated_at: '2026-06-01T03:52:50Z'
  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: '2026-06-01T03:52:50Z'
  - 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: '2026-06-01T03:52:50Z'
  artifacts:
  - path: dictybase_gene_nodes.tsv
    sha256: 068c66340828b45e9643f65196fecdd0ff61bcd685ebd78c098c057ad07a24d1
  - path: dictybase_gene_to_phenotype_edges.tsv
    sha256: d9a2231ae9e22fd23fdb9e470e8ff97db75a913603275a804b6a7d0b29050281
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: go-ingest
  version: '2026-05-21'
  transform_version: eaa8100d
  biolink_version: 4.3.6
  build_version: go-ingest_2026-05-21_eaa8100d_4.3.6
  generated_at: '2026-06-01T05:00:40Z'
  sources:
  - id: infores:goa
    name: GO Annotations (GOA)
    urls:
    - http://current.geneontology.org/annotations/goa_human.gaf.gz
    - http://current.geneontology.org/annotations/mgi.gaf.gz
    - http://current.geneontology.org/annotations/rgd.gaf.gz
    - http://current.geneontology.org/annotations/goa_dog.gaf.gz
    - http://current.geneontology.org/annotations/goa_cow.gaf.gz
    - http://current.geneontology.org/annotations/goa_pig.gaf.gz
    - http://current.geneontology.org/annotations/goa_chicken.gaf.gz
    - http://current.geneontology.org/annotations/zfin.gaf.gz
    - http://current.geneontology.org/annotations/fb.gaf.gz
    - http://current.geneontology.org/annotations/wb.gaf.gz
    - http://current.geneontology.org/annotations/dictybase.gaf.gz
    - http://current.geneontology.org/annotations/sgd.gaf.gz
    - http://current.geneontology.org/annotations/pombase.gaf.gz
    version: '2026-05-21'
    version_method: file_header
    retrieved_at: '2026-06-01T05:00:38Z'
    sources:
    - id: infores:dictybase
      name: dictyBase
      urls:
      - http://current.geneontology.org/annotations/dictybase.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:flybase
      name: FlyBase
      urls:
      - http://current.geneontology.org/annotations/fb.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:goa-chicken
      name: GOA Chicken (UniProt)
      urls:
      - http://current.geneontology.org/annotations/goa_chicken.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:goa-cow
      name: GOA Cow (UniProt)
      urls:
      - http://current.geneontology.org/annotations/goa_cow.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:goa-dog
      name: GOA Dog (UniProt)
      urls:
      - http://current.geneontology.org/annotations/goa_dog.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:goa-human
      name: GOA Human (UniProt)
      urls:
      - http://current.geneontology.org/annotations/goa_human.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:goa-pig
      name: GOA Pig (UniProt)
      urls:
      - http://current.geneontology.org/annotations/goa_pig.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:mgi
      name: Mouse Genome Informatics
      urls:
      - http://current.geneontology.org/annotations/mgi.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:pombase
      name: PomBase
      urls:
      - http://current.geneontology.org/annotations/pombase.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:rgd
      name: Rat Genome Database
      urls:
      - http://current.geneontology.org/annotations/rgd.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:sgd
      name: Saccharomyces Genome Database
      urls:
      - http://current.geneontology.org/annotations/sgd.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:wormbase
      name: WormBase
      urls:
      - http://current.geneontology.org/annotations/wb.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
    - id: infores:zfin
      name: ZFIN
      urls:
      - http://current.geneontology.org/annotations/zfin.gaf.gz
      version: '2026-05-21'
      version_method: file_header
      retrieved_at: '2026-06-01T05:00:38Z'
  - id: infores:eco
    name: Evidence & Conclusion Ontology (gaf-eco-mapping)
    urls:
    - https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/gaf-eco-mapping.txt
    version: 7a1f3a3e
    version_method: github_branch_head
    retrieved_at: '2026-06-01T05:00:38Z'
  artifacts:
  - path: go_annotation_edges.tsv
    sha256: dac098c867e34284919844cf64440cd66292187a1b5bcdd68ce8779b3ec48103
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: hgnc-ingest
  version: '2026-05-29'
  transform_version: 425c6c6d
  biolink_version: 4.4.2
  build_version: hgnc-ingest_2026-05-29_425c6c6d_4.4.2
  generated_at: '2026-06-01T02:31:58Z'
  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: '2026-05-29'
    version_method: rest_info_api
    retrieved_at: '2026-06-01T02:31:58Z'
  - id: infores:agr
    name: Alliance of Genome Resources
    urls:
    - https://fms.alliancegenome.org/download/BGI_HUMAN.json.gz
    version: 9.0.0
    version_method: alliance_fms_api
    retrieved_at: '2026-06-01T02:31:58Z'
  artifacts:
  - path: hgnc_gene.nt.gz
    sha256: 47840252d39eaf5429c9637339912c8b792dbf4a2e5a54796fcbc166e0dc2bd0
  - path: hgnc_gene_nodes.tsv
    sha256: 490341989c3c9ed961e30a84feddf24b5b3e48b73c01771ae7193e59eae001be
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: kg-phenio
  version: v2026-06-03
  transform_version: 5603207a
  biolink_version: 4.2.5
  build_version: kg-phenio_v2026-06-03_5603207a_4.2.5
  generated_at: '2026-06-05T16:12:42Z'
  sources:
  - id: phenio
    name: PHENIO
    urls:
    - https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.json
    version: v2026-06-03
    version_method: github_release_api
    retrieved_at: '2026-06-05T16:12:41Z'
    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/2026-05-26/chebi_slim.owl
      version: '2026-05-26'
      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/2026-05-26/pr_slim.owl
      version: '2026-05-26'
      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/2026-03-26/cl-base.owl
      version: '2026-03-26'
      version_method: owl_version_iri
    - id: infores:ddanat
      name: DDANAT
      urls: []
      version: '2026-06-03'
      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/2026-05-29/emapa.owl
      version: '2026-06-03'
      version_method: owl_version_iri
    - id: infores:fbbt
      name: FBBT
      urls:
      - http://purl.obolibrary.org/obo/fbbt/releases/2026-04-03/fbbt.owl
      version: '2026-04-03'
      version_method: owl_version_iri
    - id: infores:fypo
      name: FYPO
      urls:
      - http://purl.obolibrary.org/obo/fypo/releases/2026-05-21/fypo-base.owl
      version: '2026-05-21'
      version_method: owl_version_iri
    - id: infores:go
      name: GO
      urls:
      - http://purl.obolibrary.org/obo/go/releases/2026-05-19/go-base.owl
      version: '2026-05-19'
      version_method: owl_version_iri
    - id: infores:hp
      name: HP
      urls:
      - http://purl.obolibrary.org/obo/hp/releases/2026-02-16/hp-base.owl
      version: '2026-02-16'
      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/2026-06-02/mondo-base.owl
      version: '2026-06-03'
      version_method: owl_version_iri
    - id: infores:mp
      name: MP
      urls:
      - http://purl.obolibrary.org/obo/mp/releases/2026-05-19/mp-base.owl
      version: '2026-05-19'
      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/2026-04-01/uberon-base.owl
      version: '2026-04-01'
      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: '2026-06-03'
      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: '2026-06-03'
      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/2026-04-30/doid.owl
      version: '2026-04-30'
      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/2026-05-13/omim.owl
      version: '2026-05-13'
      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: '2026-05-26'
    version_method: http_last_modified
    retrieved_at: '2026-06-05T16:12:41Z'
  - id: infores:upheno-species-independent
    name: UPheno species-independent mappings
    urls:
    - https://data.monarchinitiative.org/mappings/latest/upheno-species-independent.sssom.tsv
    version: '2026-05-26'
    version_method: http_last_modified
    retrieved_at: '2026-06-05T16:12:41Z'
  artifacts:
  - path: merged-kg.tar.gz
  tools:
    koza: 1.0.0
    biolink_model: 4.2.5
    kghub_downloader: 0.4.5
- id: medic-ingest
  version: 1.3.0
  transform_version: 92b44a82
  biolink_version: 4.4.2
  build_version: medic-ingest_1.3.0_92b44a82_4.4.2
  generated_at: '2026-06-01T02:35:38Z'
  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: '2026-06-01T02:35:38Z'
  artifacts:
  - path: medic_indication_edges.tsv
    sha256: 370da1708db2827b7d5f777fbcacb4cf9578b9560becc18bccd18df5d3baf1d0
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: mmrrc-ingest
  version: '2026-05-31'
  transform_version: bcfb4af4
  biolink_version: 4.2.5
  build_version: mmrrc-ingest_2026-05-31_bcfb4af4_4.2.5
  generated_at: '2026-06-01T04:07:34Z'
  sources:
  - id: infores:mmrrc
    name: Mutant Mouse Resource & Research Centers (MMRRC)
    urls:
    - https://www.mmrrc.org/about/mmrrc_catalog_data.csv
    version: '2026-05-31'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T04:07:34Z'
  artifacts:
  - path: mmrrc_allele_to_genotype_edges.tsv
    sha256: b7db584ee62c606562294a3298b1ed335e442c72c7b70272b8aa450d74328ced
  - path: mmrrc_genotype_nodes.tsv
    sha256: 5ebb82472b61d38624560ce9498b7445e0153f5316533918f19837b67275ef20
  - path: mmrrc_genotype_to_phenotype_edges.tsv
    sha256: 6a7d8937041aca773474ed0d4488cee416e93f8e57fb0488467fc06b30b67a4f
  tools:
    koza: 2.0.0
    biolink_model: 4.2.5
    kghub_downloader: 0.4.2
- id: monarch-phenotype-profile-ingest
  version: '2026-02-16'
  transform_version: eeb42f6b
  biolink_version: 4.3.6
  build_version: monarch-phenotype-profile-ingest_2026-02-16_eeb42f6b_4.3.6
  generated_at: '2026-06-03T02:53:23Z'
  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: '2026-02-16'
    version_method: file_header
    retrieved_at: '2026-06-03T02:53:21Z'
    sources:
    - id: infores:omim
      name: OMIM
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2026-02-16'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-06-03T02:53:21Z'
    - id: infores:orphanet
      name: Orphanet
      urls:
      - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa
      version: '2026-02-16'
      version_method: hpoa_biocuration_max
      retrieved_at: '2026-06-03T02:53:21Z'
    - 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: '2026-06-03T02:53:21Z'
  - id: infores:hp
    name: Human Phenotype Ontology (HP)
    urls:
    - http://purl.obolibrary.org/obo/hp.obo
    version: '2026-02-16'
    version_method: http_last_modified
    retrieved_at: '2026-06-03T02:53:21Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-05-26'
    version_method: http_last_modified
    retrieved_at: '2026-06-03T02:53:21Z'
  artifacts:
  - path: hpoa_disease_mode_of_inheritance_edges.tsv
    sha256: ba61b8e49ac252081ee6d549cc3398039e06f900c2bee08a852acf1b4cdda577
  - path: hpoa_disease_to_phenotype_edges.tsv
    sha256: 5cb588ec8f8dae21b46cb71a03250b4fae1dc1df1e0dff17e5f36e3837485340
  - path: hpoa_gene_to_disease_edges.tsv
    sha256: 5a9c3c0d7bffbfe348e0c09f78ed295c742d41fca697b2ab74b3507df572800c
  - path: hpoa_gene_to_phenotype_edges.tsv
    sha256: 5f88d963f4d5e9b8d25765ab341be86d4e5354790a4d6d41bdbd7abb6b6a8e25
  tools:
    koza: 2.1.1
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: ncbi-gene
  version: '2026-06-02'
  transform_version: 9fc4ca75
  biolink_version: 4.3.6
  build_version: ncbi-gene_2026-06-02_9fc4ca75_4.3.6
  generated_at: '2026-06-03T04:01:46Z'
  sources:
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
    version: '2026-06-02'
    version_method: http_last_modified
    retrieved_at: '2026-06-03T04:01:45Z'
  artifacts:
  - path: ncbi_gene.nt.gz
    sha256: a0295c7e3c4ceac682fe86a24b907f372cb2c87cb9112a988f8d2c1354d27a7c
  - path: ncbi_gene_nodes.tsv
    sha256: fd597b146dc4e1bd6ab4165cb86ac57e3050a95a508e1f8d69ec5027b1a2ad04
  tools:
    koza: 2.2.0
    biolink_model: 4.3.6
    kghub_downloader: 0.4.4
- id: omim-ingest
  version: '2026-05-31'
  transform_version: b617a53b
  biolink_version: 4.3.6
  build_version: omim-ingest_2026-05-31_b617a53b_4.3.6
  generated_at: '2026-06-01T04:46:14Z'
  sources:
  - id: infores:omim
    name: OMIM (Online Mendelian Inheritance in Man)
    urls:
    - https://data.omim.org/downloads/{MONARCH_OMIM_DOWNLOAD_KEY}/morbidmap.txt
    version: '2026-05-31'
    version_method: file_header
    retrieved_at: '2026-06-01T04:46:14Z'
  artifacts:
  - path: omim_gene_to_disease_edges.tsv
    sha256: eac5846d8f1afb95f632d691fb8089f15ef6576226942b949dc272ee5e56d82c
  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: '2026-06-01T02:24:15Z'
  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: '2026-06-01T02:24:14Z'
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
    version: '2026-05-31'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:24:14Z'
  artifacts:
  - path: panther_genome_orthologs_edges.tsv
    sha256: ced6b674377e07fb8d3b29b5bbe38ddb084f4bc4477fd18384d7a4ec2cee109d
  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: '2026-05-31'
  transform_version: be65ca88
  biolink_version: 4.4.2
  build_version: pombase-ingest_2026-05-31_be65ca88_4.4.2
  generated_at: '2026-06-01T02:36:09Z'
  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: '2026-05-31'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:36:09Z'
  artifacts:
  - path: pombase_gene_nodes.tsv
    sha256: 29eb7b086621da180368f217a293f9ab0c7e5a04a8a4765bd9fbe8ca0abee692
  - path: pombase_gene_to_phenotype_edges.tsv
    sha256: c7c510f2bcea5bd1cca593dec0af4a33f231cd4ad7520c7f0abe000678dd1a74
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: reactome-ingest
  version: '96'
  transform_version: b244eb83
  biolink_version: 4.4.2
  build_version: reactome-ingest_96_b244eb83_4.4.2
  generated_at: '2026-06-01T05:02:46Z'
  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: '96'
    version_method: reactome_content_service
    retrieved_at: '2026-06-01T05:02:45Z'
  artifacts:
  - path: reactome_chemical_to_pathway_edges.tsv
    sha256: cae807f2206c3b0ab506a87e569af8e15261ca957251b10f5027d81243a333d6
  - path: reactome_gene_to_pathway_edges.tsv
    sha256: f5740f3e7e13a9cec7cf8f4b82e1ab2f93f0036724e66c1a5311fbb52c21d43b
  - path: reactome_pathway_nodes.tsv
    sha256: 9fd4b15a6b68a24f6ea341de97c8c4e3baa45f0fe8cee6c896ebca72df6615c4
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: string-ingest
  version: '12.0'
  transform_version: f96320f0
  biolink_version: 4.4.2
  build_version: string-ingest_12.0_f96320f0_4.4.2
  generated_at: '2026-06-01T02:16:22Z'
  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: '2026-06-01T02:16:22Z'
  artifacts:
  - path: string_protein_links_edges.tsv
    sha256: 25ab40c507e2c8e52f4d02800b106069b1cb11a47cf693ae2cb47cb6d96c7061
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: upheno-cross-species-ingest
  version: 531e30c7
  transform_version: 71415b00
  biolink_version: 4.4.2.post9.dev0+b0d9ef649
  build_version: upheno-cross-species-ingest_531e30c7_71415b00_4.4.2.post9.dev0+b0d9ef649
  generated_at: '2026-06-01T04:15:36Z'
  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: '2026-06-01T04:15:36Z'
  artifacts:
  - path: upheno_phenotype_to_phenotype_edges.tsv
    sha256: 361d3e98b388b6b2782509b2810af2b36331e99a62f53d4c3e26c09a88ca7eb6
  - path: upheno_phenotype_to_phenotype_nodes.tsv
    sha256: 6d64b989b8dd52cf74ae157634931cada329d9e57c7c89132ca866b322a27c81
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2.post9.dev0+b0d9ef649
    kghub_downloader: 0.4.5
- id: xenbase-ingest
  version: '2026-05-27'
  transform_version: 8c8d0fe6
  biolink_version: 4.4.2
  build_version: xenbase-ingest_2026-05-27_8c8d0fe6_4.4.2
  generated_at: '2026-06-01T05:05:41Z'
  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: '2026-05-27'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T05:05:40Z'
  - 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: '2026-06-01T05:05:40Z'
  artifacts:
  - path: xenbase_gene_to_phenotype_edges.tsv
    sha256: c835388e1ec00c60ee41641385da55b5971b55343301abe43a72f880fc4e8bd5
  - path: xenbase_gene_to_phenotype_nodes.tsv
    sha256: 2bed91c8b666008748233133166d7ca895f164261eacd107b4e3c5ae288509c5
  - path: xenbase_non_entrez_orthologs_edges.tsv
    sha256: 0180fe6760dee780f4eb5f6ae864d5b953537ba190a2886ebf0080b22e650ec0
  - path: xenbase_orthologs_edges.tsv
    sha256: 0e24a3b8f90aaf05b0b6cb5b2b45f35e4761d85da6487c6bbe2822395ce93ebf
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
- id: zfin-ingest
  version: '2026-05-31'
  transform_version: 15c3cda5
  biolink_version: 4.4.2
  build_version: zfin-ingest_2026-05-31_15c3cda5_4.4.2
  generated_at: '2026-06-01T02:48:02Z'
  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: '2026-05-31'
    version_method: http_last_modified
    retrieved_at: '2026-06-01T02:48:01Z'
  - 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: '2026-06-01T02:48:01Z'
  artifacts:
  - path: zfin_gene_to_phenotype_edges.tsv
    sha256: fd3f2fbc24930b499669f8a34279c462bdf9ed1a221cf123de56831d61f8e89a
  - path: zfin_genotype_to_phenotype_edges.tsv
    sha256: 8ae7787b3902373722d2745eff606aab3a60a99d28400ea9edcd76daec366c13
  - path: zfin_orthology_edges.tsv
    sha256: 03bf3ae4e0446c57d69e12fd8ed4b1233922ef09d22cabb2a3c7e4f976621a62
  tools:
    koza: 2.4.0
    biolink_model: 4.4.2
    kghub_downloader: 0.4.5
disagreements: []
version_drift:
- id: infores:ncbi-gene
  versions_observed:
  - '2026-05-31'
  - '2026-06-02'
  by_ingest:
    ncbi-gene: '2026-06-02'
    pantherdb-orthologs-ingest: '2026-05-31'
