id: monarch-kg
version: '2026-05-07'
generated_at: '2026-05-07T22:07:34Z'
packages:
  biolink: 4.3.9
  koza: 2.3.0
  monarch-ingest: 0.8.0
artifacts:
- path: monarch-kg.tar.gz
  sha256: 6716b8acee80b30197e8c6352ea87e99b2165c57e99dc253588ce32c6a7fa161
- path: merged_graph_stats.yaml
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- path: qc_report.yaml
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sources:
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  version: 9.0.0
  transform_version: 3d9d654f
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  build_version: alliance-ingest_9.0.0_3d9d654f_4.3.6
  generated_at: '2026-05-07T04:56:21Z'
  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: '2026-05-07T04:56:20Z'
  artifacts:
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  - path: alliance_allele_nodes.tsv
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  - path: alliance_disease_edges.tsv
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  - path: alliance_gene_nodes.tsv
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  - path: alliance_gene_to_expression_edges.tsv
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  - path: alliance_genotype_edges.tsv
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  - path: alliance_genotype_nodes.tsv
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  - path: alliance_phenotype_edges.tsv
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  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: 4.3.9
  build_version: bgee-ingest_15.2_040fbaf8_4.3.9
  generated_at: '2026-05-07T04:57:43Z'
  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: '2026-05-07T04:57:42Z'
  artifacts:
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    sha256: 259a5051ff3e1d118eb84a900050ec6ae3b1243640b5be7491954829b1fb2b61
  tools:
    koza: 2.4.0
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- 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: '2026-05-07T04:54:21Z'
  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: '2026-05-07T04:54:21Z'
  artifacts:
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    sha256: ac4ae558fe386d2742c007b406b69f96f81304ec8b1cf3757548e40f788908f5
  tools:
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- id: clingen-ingest
  version: '2026-05-06'
  transform_version: 5af4af58
  biolink_version: 4.3.6
  build_version: clingen-ingest_2026-05-06_5af4af58_4.3.6
  generated_at: '2026-05-07T04:55:15Z'
  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: '2026-05-06'
    version_method: max_published_date
    retrieved_at: '2026-05-07T04:55:15Z'
  - id: infores:hgnc
    name: HUGO Gene Nomenclature Committee
    urls:
    - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
    version: '2026-05-05'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:55:15Z'
  artifacts:
  - path: clingen_gene_disease_edges.tsv
    sha256: d286061a385e69becc45653024bf54eedb0f894d70d94e5b8502feb01c030e2f
  - path: clingen_variant_edges.tsv
    sha256: a7ebe93c6141e62cecc056bb2a10cdb1176508d8067e7d7d925e50554a3582e5
  - path: clingen_variant_nodes.tsv
    sha256: 4727d85aea681303bd224bd6a7331ffc643265f0efee4fb4551b4a6c836891c8
  tools:
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- id: clinvar-ingest
  version: '2026-05-05'
  transform_version: 53c243d5
  biolink_version: 4.3.6
  build_version: clinvar-ingest_2026-05-05_53c243d5_4.3.6
  generated_at: '2026-05-07T04:55:32Z'
  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: '2026-05-05'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:55:32Z'
  - id: infores:medgen
    name: MedGen
    urls:
    - https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz
    version: '2026-05-06'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:55:32Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-05-03'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:55:32Z'
  artifacts:
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  - path: clinvar_variant_nodes.tsv
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  tools:
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- id: ctd-ingest
  version: '2026-04-30'
  transform_version: 9855dc58
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  build_version: ctd-ingest_2026-04-30_9855dc58_4.3.9
  generated_at: '2026-05-07T04:53:00Z'
  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: '2026-05-07T04:53:00Z'
  artifacts:
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    sha256: fe3f3486ffbebba6847b700c755c4f8a292d36c3d32f85315a0ca23703e31d10
  tools:
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- id: cureid-ingest
  version: '2025-12-18'
  transform_version: 7ce72810
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  build_version: cureid-ingest_2025-12-18_7ce72810_4.3.9
  generated_at: '2026-05-07T04:52:13Z'
  sources:
  - id: infores:cureid
    name: "CureID \u2014 Drug Repurposing Database"
    urls:
    - https://opendata.ncats.nih.gov/public/cureid/cureid_data.tsv
    version: '2025-12-18'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:52:13Z'
  artifacts:
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  - path: cureid_nodes.tsv
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  tools:
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- id: dictybase-ingest
  version: unknown
  transform_version: d01bb330
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  build_version: dictybase-ingest_unknown_d01bb330_4.3.9
  generated_at: '2026-05-07T04:52:14Z'
  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: '2026-05-07T04:52:14Z'
  - id: infores:ddpheno
    name: Dicty Phenotype Ontology (BBOP SQLite)
    urls:
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    version: '2022-10-17'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:52:14Z'
  artifacts:
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  - path: dictybase_gene_to_phenotype_edges.tsv
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- id: go-ingest
  version: '2026-03-28'
  transform_version: ae3e5c3d
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  build_version: go-ingest_2026-03-28_ae3e5c3d_4.3.6
  generated_at: '2026-05-07T04:55:37Z'
  sources:
  - id: infores:goa
    name: GO Annotations (GOA)
    urls:
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    - 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: '2026-03-28'
    version_method: file_header
    retrieved_at: '2026-05-07T04:55:35Z'
  - id: infores:eco
    name: Evidence & Conclusion Ontology (gaf-eco-mapping)
    urls:
    - https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/gaf-eco-mapping.txt
    version: 269fa799
    version_method: github_branch_head
    retrieved_at: '2026-05-07T04:55:35Z'
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- id: hgnc-ingest
  version: '2026-05-05'
  transform_version: 425c6c6d
  biolink_version: 4.3.9
  build_version: hgnc-ingest_2026-05-05_425c6c6d_4.3.9
  generated_at: '2026-05-07T04:52:46Z'
  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: '2026-05-05'
    version_method: rest_info_api
    retrieved_at: '2026-05-07T04:52:46Z'
  - 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: '2026-05-07T04:52:46Z'
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  - path: hgnc_gene_nodes.tsv
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- id: medic-ingest
  version: 1.3.0
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  build_version: medic-ingest_1.3.0_92b44a82_4.3.9
  generated_at: '2026-05-07T04:52:57Z'
  sources:
  - id: infores:medic
    name: "MeDIC \u2014 Medicines, Diseases, Indications and Contraindications"
    urls:
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    version: 1.3.0
    version_method: local_name_regex
    retrieved_at: '2026-05-07T04:52:57Z'
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- id: mmrrc-ingest
  version: '2026-05-03'
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  build_version: mmrrc-ingest_2026-05-03_bcfb4af4_4.2.5
  generated_at: '2026-05-07T04:53:26Z'
  sources:
  - id: infores:mmrrc
    name: Mutant Mouse Resource & Research Centers (MMRRC)
    urls:
    - https://www.mmrrc.org/about/mmrrc_catalog_data.csv
    version: '2026-05-03'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:53:26Z'
  artifacts:
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- id: monarch-phenotype-profile-ingest
  version: '2026-02-16'
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  build_version: monarch-phenotype-profile-ingest_2026-02-16_33bc017d_4.3.6
  generated_at: '2026-05-07T04:53:58Z'
  sources:
  - id: infores:hpoa
    name: HPO Annotations (HPOA)
    urls:
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    - 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: '2026-05-07T04:53:58Z'
  - 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: '2026-05-07T04:53:58Z'
  - id: infores:mondo
    name: Mondo Disease Ontology (SSSOM)
    urls:
    - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv
    version: '2026-05-03'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:53:58Z'
  artifacts:
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  - path: hpoa_disease_to_phenotype_edges.tsv
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    sha256: 323fef72bed09aedc08d2aa8fd8e0402d70e079a6f142261f359f398b7ca780a
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- id: ncbi-gene
  version: '2026-05-06'
  transform_version: 9fc4ca75
  biolink_version: 4.3.6
  build_version: ncbi-gene_2026-05-06_9fc4ca75_4.3.6
  generated_at: '2026-05-07T05:15:40Z'
  sources:
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
    version: '2026-05-06'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T05:15:39Z'
  artifacts:
  - path: ncbi_gene.nt.gz
    sha256: 72ee3e0a9e96813055a22d0494bb51bd1402120ded2c2dc4899199995bf8c6b8
  - path: ncbi_gene_nodes.tsv
    sha256: abbb989d79fb19c57e52f48dd3ff5a3be62d33b6ce0cc44419a9712710ef4f45
  tools:
    koza: 2.2.0
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    kghub_downloader: 0.4.4
- id: omim-ingest
  version: '2026-05-06'
  transform_version: b617a53b
  biolink_version: 4.3.6
  build_version: omim-ingest_2026-05-06_b617a53b_4.3.6
  generated_at: '2026-05-07T04:53:33Z'
  sources:
  - id: infores:omim
    name: OMIM (Online Mendelian Inheritance in Man)
    urls:
    - https://data.omim.org/downloads/{MONARCH_OMIM_DOWNLOAD_KEY}/morbidmap.txt
    version: '2026-05-06'
    version_method: file_header
    retrieved_at: '2026-05-07T04:53:33Z'
  artifacts:
  - path: omim_gene_to_disease_edges.tsv
    sha256: af479ef21f46daecc5ed1f0dcd9be652f1c4e77b52238a9b4f7b45143703d9d6
  tools:
    koza: 2.1.1
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- 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: '2026-05-07T05:05:34Z'
  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: '2026-05-07T05:05:33Z'
  - id: infores:ncbi-gene
    name: NCBI Gene
    urls:
    - https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
    version: '2026-05-06'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T05:05:33Z'
  artifacts:
  - path: panther_genome_orthologs_edges.tsv
    sha256: 89f71dabbbcf388faff529d90f94341d336a0592768d04023104fc5596fc98c2
  tools:
    koza: 2.1.1
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- id: phenopacket-ingest
  version: 0.1.26
  transform_version: 33a8b263
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  build_version: phenopacket-ingest_0.1.26_33a8b263_4.3.6
  generated_at: '2026-05-07T04:53:46Z'
  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: '2026-05-07T04:53:46Z'
  artifacts:
  - path: phenopacket_ingest_edges.tsv
    sha256: 4a86ccd8f9ba5354609ec6771b29784c25cf1a60dd24b427f491d0574a4bcaa4
  - path: phenopacket_ingest_nodes.tsv
    sha256: b14b0badec30409da5b0a1ad01f9dd6ece20de40c24ae9094d5f1408eb459104
  tools:
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- id: pombase-ingest
  version: '2026-05-07'
  transform_version: be65ca88
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  build_version: pombase-ingest_2026-05-07_be65ca88_4.3.9
  generated_at: '2026-05-07T04:52:42Z'
  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: '2026-05-07'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:52:42Z'
  artifacts:
  - path: pombase_gene_nodes.tsv
    sha256: 8bf7c01878efc78068594b8bc8efc1e31056145fa9a429bff15f86aa7e1ff797
  - path: pombase_gene_to_phenotype_edges.tsv
    sha256: e9525dcbac2aa2ea445b228e3983e9cdfe773e17f2e09c2a012056cf48b2304b
  tools:
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- id: reactome-ingest
  version: '96'
  transform_version: b244eb83
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  build_version: reactome-ingest_96_b244eb83_4.3.9
  generated_at: '2026-05-07T04:52:39Z'
  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: '2026-05-07T04:52:39Z'
  artifacts:
  - path: reactome_chemical_to_pathway_edges.tsv
    sha256: b64ca096793fe909b5a4b7a3a04d4df95e204cba53d8cacb70bbfc7c2b9dd2ed
  - path: reactome_gene_to_pathway_edges.tsv
    sha256: 28c20af7bf96320ce691295d00a2798b379929c62974997fc9f0982f33dfae0e
  - path: reactome_pathway_nodes.tsv
    sha256: 9fd4b15a6b68a24f6ea341de97c8c4e3baa45f0fe8cee6c896ebca72df6615c4
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- id: string-ingest
  version: '12.0'
  transform_version: f96320f0
  biolink_version: 4.3.9
  build_version: string-ingest_12.0_f96320f0_4.3.9
  generated_at: '2026-05-07T05:05:37Z'
  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: '2026-05-07T05:05:36Z'
  artifacts:
  - path: string_protein_links_edges.tsv
    sha256: a407688b8d558cad20d5661ac840f010a8bfccb74bcbab88a3bd00d7bba9fe7a
  tools:
    koza: 2.4.0
    biolink_model: 4.3.9
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- id: upheno-cross-species-ingest
  version: 531e30c7
  transform_version: 5761f211
  biolink_version: 4.4.0rc2
  build_version: upheno-cross-species-ingest_531e30c7_5761f211_4.4.0rc2
  generated_at: '2026-05-07T04:53:42Z'
  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: '2026-05-07T04:53:42Z'
  artifacts:
  - path: upheno_phenotype_to_phenotype_edges.tsv
    sha256: e673aaabbe8c8bc69bfe0c570b83b50fab36dc3c7df160fcc78e6270ec10f163
  - path: upheno_phenotype_to_phenotype_nodes.tsv
    sha256: 6d64b989b8dd52cf74ae157634931cada329d9e57c7c89132ca866b322a27c81
  tools:
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- id: xenbase-ingest
  version: '2026-05-06'
  transform_version: 8c8d0fe6
  biolink_version: 4.3.9
  build_version: xenbase-ingest_2026-05-06_8c8d0fe6_4.3.9
  generated_at: '2026-05-07T16:08:38Z'
  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: '2026-05-06'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T16:08:37Z'
  - 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: '2026-05-07T16:08:37Z'
  artifacts:
  - path: xenbase_gene_to_phenotype_edges.tsv
    sha256: e2c2bceb5d7722630c401f3907565ee7d21be35987444cd5ebdbd7e2a2d20443
  - path: xenbase_gene_to_phenotype_nodes.tsv
    sha256: 2bed91c8b666008748233133166d7ca895f164261eacd107b4e3c5ae288509c5
  - path: xenbase_non_entrez_orthologs_edges.tsv
    sha256: 8a348f27a76864b6a06d7b2025d24de564666d50c6ee08b03cea7d109a8e528e
  - path: xenbase_orthologs_edges.tsv
    sha256: f1104eb93b367569849e8c68f49ee51ab47c2d484910f4841b4066c864f3c3b6
  tools:
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- id: zfin-ingest
  version: '2026-05-06'
  transform_version: 15c3cda5
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  build_version: zfin-ingest_2026-05-06_15c3cda5_4.3.9
  generated_at: '2026-05-07T04:53:47Z'
  sources:
  - id: infores:zfin
    name: Zebrafish Information Network (ZFIN)
    urls:
    - https://zfin.org/downloads/phenoGeneCleanData_fish.txt
    - https://zfin.org/downloads/phenotype_fish.txt
    - https://zfin.org/downloads/pheno_environment_fish.txt
    - https://zfin.org/downloads/pub_to_pubmed_id_translation.txt
    - https://zfin.org/downloads/fly_orthos.txt
    - https://zfin.org/downloads/human_orthos.txt
    - https://zfin.org/downloads/mouse_orthos.txt
    version: '2026-05-06'
    version_method: http_last_modified
    retrieved_at: '2026-05-07T04:53:47Z'
  - 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: '2026-05-07T04:53:47Z'
  artifacts:
  - path: zfin_gene_to_phenotype_edges.tsv
    sha256: b8de7ab285f59117aad027fabfd15875e2cda7b3ae814d0b27a297d4704fb448
  - path: zfin_genotype_to_phenotype_edges.tsv
    sha256: 0d56fb0624476f4e3aba4f3bcda6e1961f2ac00205e890ba7606c95a0b51489f
  - path: zfin_orthology_edges.tsv
    sha256: 41f5c914aadd99f694a08fe0997e9becace04ff32f0e08ad31e62edcf2578836
  tools:
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    biolink_model: 4.3.9
    kghub_downloader: 0.4.5
disagreements: []
version_drift: []
