id: monarch-kg version: '2026-11-03' generated_at: '2026-11-03T04:19:11Z' packages: biolink: 4.4.2 koza: 2.7.0.post20.dev0+24399bf monarch-ingest: 0.8.0 artifacts: - path: monarch-kg.tar.gz sha256: f9aeecac42cc93c8444abd652b5973767fd19b63573d338b1788db5d37514f8c - path: merged_graph_stats.yaml sha256: 16de2e79c2f9281404c484dc07d76ee82f59b0bf54a22756339fd48ae4b1353a - path: qc_report.yaml sha256: a282825ba7775083aebcb1b019cffe5d9dec4e179e9a544db0a40010272161a6 - path: connectivity_summary.yaml sha256: e7afc212b0997a3a2233b23987ecebf031257206c54afc07492244e5e3ce124c - path: monarch-kg_schema_report.yaml sha256: 8fd94763b7f727906bfe8d99335b6b5c5a02d1a7f05d7c86af2e3e93426d6fe4 sources: - id: alliance-ingest version: 9.2.0 transform_version: b0d7654e biolink_version: 4.3.6 build_version: alliance-ingest_9.2.0_b0d7654e_4.3.6 generated_at: '2026-11-01T04:56:52Z' 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: 9.2.0 version_method: alliance_fms_api retrieved_at: '2026-11-01T04:56:50Z' 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: '2026-11-01T04:56:50Z' - 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: '2026-07-06' version_method: alliance_fms_submission retrieved_at: '2026-11-01T04:56:50Z' - 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: '2026-07-07' version_method: alliance_fms_submission retrieved_at: '2026-11-01T04:56:50Z' - 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: '2026-07-09' version_method: alliance_fms_submission retrieved_at: '2026-11-01T04:56:50Z' - 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: '2026-11-01T04:56:50Z' - 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: '2026-11-01T04:56:50Z' - 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: '2026-09-15' version_method: alliance_fms_submission retrieved_at: '2026-11-01T04:56:50Z' artifacts: - path: alliance_allele_edges.tsv sha256: b5e4015e03585088bd36766520dd3adea46103676f375c1186bbf378bc79968b - path: alliance_allele_nodes.tsv sha256: 449a1168e5105d3af7dbdc5a1b03eed66889d2759cf8b4fcfdb235d4f96320c4 - path: alliance_disease_edges.tsv sha256: be37083d0883564e9144fb0b52cc34b6043455b26eb9ca15a54cbe628fcaa7b3 - path: alliance_gene_nodes.tsv sha256: 42b8af0563e53b9a48accb3f30b5933437f19c72018bff5abe4f50af3f763a20 - path: alliance_gene_to_expression_edges.tsv sha256: 88458865f22e1f628cd97b237dd4baafefe87b0e3037eb42b71b36cbb3d849cf - path: alliance_genotype_edges.tsv sha256: 48ae40b4ea6b3583fe759e39b557e816916f1fdc950459ab596fa22dad344ed9 - path: alliance_genotype_nodes.tsv sha256: 4740a5693e85d01fdaa9d2762d7135c6666c7a18df3fae6d1726644a5f9027b4 - path: alliance_phenotype_edges.tsv sha256: ca599acad6543ddbd556c5ca3ac64f375878d171acf93afdf2c13783b571238c tools: koza: 2.1.1 biolink_model: 4.3.6 kghub_downloader: 0.4.4 - id: bgee-ingest version: '15.2' transform_version: b1611c8f biolink_version: 4.4.6 build_version: bgee-ingest_15.2_b1611c8f_4.4.6 generated_at: '2026-11-01T05:36:46Z' sources: - id: infores:bgee name: "BGee \u2014 Gene Expression" urls: - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Homo_sapiens_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Bos_taurus_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Canis_lupus_familiaris_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Gallus_gallus_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Sus_scrofa_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Rattus_norvegicus_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Mus_musculus_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Danio_rerio_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Xenopus_laevis_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Drosophila_melanogaster_expr_simple.tsv.gz - https://www.bgee.org/ftp/bgee_v15_2/download/calls/expr_calls/Caenorhabditis_elegans_expr_simple.tsv.gz version: '15.2' version_method: ftp_index_probe retrieved_at: '2026-11-01T05:36:46Z' artifacts: - path: bgee_gene_to_expression_edges.tsv sha256: e72c2a0eb3bc5401875423e96996d21e1d79f82240b3aca383841ef1639ad4f8 tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 - id: biogrid-ingest version: 4.4.226 transform_version: 181c6cf7 biolink_version: 4.3.6 build_version: biogrid-ingest_4.4.226_181c6cf7_4.3.6 generated_at: '2026-11-01T05:12:16Z' 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: '2026-11-01T05:12:14Z' artifacts: - path: biogrid_gene_to_gene_edges.tsv sha256: 7a8c779f31c135078fffa4b40c7512dcd679201ccc1a3565953abd35e8d37944 tools: koza: 2.1.1 biolink_model: 4.3.6 kghub_downloader: 0.4.4 - id: clingen-ingest version: '2026-08-31' transform_version: 5af4af58 biolink_version: 4.3.6 build_version: clingen-ingest_2026-08-31_5af4af58_4.3.6 generated_at: '2026-09-01T03:29:32Z' sources: - id: infores:clingen name: "ClinGen \u2014 Clinical Genome Resource" urls: - http://erepo.clinicalgenome.org/redmine/projects/evrepo/pcer/api/classifications/all?format=tabbed version: '2026-08-31' version_method: max_published_date retrieved_at: '2026-09-01T03:29:31Z' - id: infores:hgnc name: HUGO Gene Nomenclature Committee urls: - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt version: '2026-08-28' version_method: http_last_modified retrieved_at: '2026-09-01T03:29:31Z' artifacts: - path: clingen_gene_disease_edges.tsv sha256: f03a332f62a919ed63510baa8c5a9411ad46ebef906b7e8e214b0f6e34964ad3 - path: clingen_variant_edges.tsv sha256: d7dc64d9199ec227df6ab5a045ddae6b5b90f28823adb331f5d63bb13066feb3 - path: clingen_variant_nodes.tsv sha256: 2fcd225024bfc914e75d761e36d0a58e8977210f84b33bf4760e35e69dc72de1 tools: koza: 2.1.1 biolink_model: 4.3.6 kghub_downloader: 0.4.4 - id: clinvar-ingest version: '2026-10-26' transform_version: bf8e652e biolink_version: 4.3.6 build_version: clinvar-ingest_2026-10-26_bf8e652e_4.3.6 generated_at: '2026-11-01T02:58:03Z' sources: - id: infores:clinvar name: ClinVar urls: - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz version: '2026-10-26' version_method: http_last_modified retrieved_at: '2026-11-01T02:58:02Z' - id: infores:medgen name: MedGen urls: - https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz version: '2026-10-28' version_method: http_last_modified retrieved_at: '2026-11-01T02:58:02Z' - id: infores:mondo name: Mondo Disease Ontology (SSSOM) urls: - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv version: '2026-10-04' version_method: http_last_modified retrieved_at: '2026-11-01T02:58:02Z' artifacts: - path: clinvar_variant_edges.tsv sha256: b3e1a194d504e8ad0cefee4ff41197bd829780ead2cf49582a25e1c7913d1987 - path: clinvar_variant_nodes.tsv sha256: 6930f437ae9600516fe1c9d189762ad4fb09d13df3fda087403cefdee94a73e3 tools: koza: 2.1.1 biolink_model: 4.3.6 kghub_downloader: 0.4.5 - id: cureid-ingest version: '2026-05-28' transform_version: 7ce72810 biolink_version: 4.4.6 build_version: cureid-ingest_2026-05-28_7ce72810_4.4.6 generated_at: '2026-11-01T03:54:57Z' 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: '2026-11-01T03:54:57Z' artifacts: - path: cureid_edges.tsv sha256: cc0be147c492cf36717cb9b69602307d53e97be64d2956b911af3a26fd525a49 - path: cureid_nodes.tsv sha256: f008f6f85d8023921ecc8d61989e82a4d0c9c61eacb2cb91095c0810f731db4c tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 - id: dictybase-ingest version: unknown transform_version: d01bb330 biolink_version: 4.4.4 build_version: dictybase-ingest_unknown_d01bb330_4.4.4 generated_at: '2026-09-02T03:20:17Z' sources: - id: infores:dictybase name: dictyBase urls: - http://dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=general&ID=gene_information.txt - http://dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=mutant_phenotypes&ID=all-mutants-ddb_g.txt version: unknown version_method: unavailable retrieved_at: '2026-09-02T03:20:17Z' artifacts: - path: dictybase_gene_nodes.tsv sha256: 068c66340828b45e9643f65196fecdd0ff61bcd685ebd78c098c057ad07a24d1 - path: dictybase_gene_to_phenotype_edges.tsv sha256: def17621d9f2fb94c5fe696cd5c8152d9159d03eac49af78153a08646370e380 tools: koza: 2.6.2 biolink_model: 4.4.4 kghub_downloader: 0.5.0 - id: go-ingest version: '2026-08-04' transform_version: a7cd768d biolink_version: 4.3.6 build_version: go-ingest_2026-08-04_a7cd768d_4.3.6 generated_at: '2026-11-01T05:37:07Z' 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: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' sources: - id: infores:dictybase name: dictyBase urls: - http://current.geneontology.org/annotations/gaf/DICDI-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:flybase name: FlyBase urls: - http://current.geneontology.org/annotations/gaf/DROME-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:goa-chicken name: GOA Chicken (UniProt) urls: - http://current.geneontology.org/annotations/gaf/CHICK-uniprot.gaf.gz version: '2026-07-28' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:goa-cow name: GOA Cow (UniProt) urls: - http://current.geneontology.org/annotations/gaf/BOVIN-uniprot.gaf.gz version: '2026-07-28' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:goa-dog name: GOA Dog (UniProt) urls: - http://current.geneontology.org/annotations/gaf/CANLF-uniprot.gaf.gz version: '2026-07-28' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:goa-human name: GOA Human (UniProt) urls: - http://current.geneontology.org/annotations/gaf/HUMAN-uniprot.gaf.gz version: '2026-07-28' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:goa-pig name: GOA Pig (UniProt) urls: - http://current.geneontology.org/annotations/gaf/PIG-uniprot.gaf.gz version: '2026-07-28' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:mgi name: Mouse Genome Informatics urls: - http://current.geneontology.org/annotations/gaf/MOUSE-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:pombase name: PomBase urls: - http://current.geneontology.org/annotations/gaf/SCHPO-mod.gaf.gz version: '2026-07-28' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:rgd name: Rat Genome Database urls: - http://current.geneontology.org/annotations/gaf/RAT-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:sgd name: Saccharomyces Genome Database urls: - http://current.geneontology.org/annotations/gaf/YEAST-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:wormbase name: WormBase urls: - http://current.geneontology.org/annotations/gaf/CAEEL-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - id: infores:zfin name: ZFIN urls: - http://current.geneontology.org/annotations/gaf/DANRE-mod.gaf.gz version: '2026-08-04' version_method: file_header retrieved_at: '2026-11-01T05:37:06Z' - 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: '2026-11-01T05:37:06Z' artifacts: - path: go_annotation_edges.tsv sha256: ba7a20943d57c6e124d096ad3c459e5bd6398f2e3ecf3c145a0993f4836288d7 tools: koza: 2.6.1 biolink_model: 4.3.6 kghub_downloader: 0.4.4 - id: hgnc-ingest version: '2026-08-28' transform_version: 425c6c6d biolink_version: 4.4.4 build_version: hgnc-ingest_2026-08-28_425c6c6d_4.4.4 generated_at: '2026-09-01T02:23:33Z' sources: - id: infores:hgnc name: HUGO Gene Nomenclature Committee urls: - http://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt version: '2026-08-28' version_method: rest_info_api retrieved_at: '2026-09-01T02:23:33Z' - id: infores:agr name: Alliance of Genome Resources urls: - https://fms.alliancegenome.org/download/BGI_HUMAN.json.gz version: 9.1.0 version_method: alliance_fms_api retrieved_at: '2026-09-01T02:23:33Z' artifacts: - path: hgnc_gene.nt.gz sha256: ba855fe23fec6bd333a7729d9ed905d4d03503bef68b5ff6d2d3d38fa58f4d36 - path: hgnc_gene_nodes.tsv sha256: d0c4661cabfd60d8fb1ae1e9969d81e8ab404603b72f3edcdc97c8137b6b7d45 tools: koza: 2.6.2 biolink_model: 4.4.4 kghub_downloader: 0.5.0 - id: kg-phenio version: v2026-10-07 transform_version: eaa738d3 biolink_version: 4.2.5 build_version: kg-phenio_v2026-10-07_eaa738d3_4.2.5 generated_at: '2026-10-08T09:30:44Z' sources: - id: phenio name: PHENIO urls: - https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.json version: v2026-10-07 version_method: github_release_api retrieved_at: '2026-10-08T09:30:44Z' sources: - id: infores:bfo name: BFO urls: - http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl version: '2019-08-26' version_method: owl_version_iri - id: infores:bspo name: BSPO urls: - http://purl.obolibrary.org/obo/bspo/releases/2023-05-27/bspo-base.owl version: '2023-05-27' version_method: owl_version_iri - id: infores:chebi name: CHEBI urls: - http://purl.obolibrary.org/obo/chebi/obophenotype/releases/2026-08-28/chebi_slim.owl version: '2026-08-28' version_method: owl_version_iri - id: infores:eco name: ECO urls: - http://purl.obolibrary.org/obo/eco/releases/2026-07-10/eco.owl version: '2026-07-10' version_method: owl_version_iri - id: infores:fbdv name: FBDV urls: - http://purl.obolibrary.org/obo/fbdv/releases/2026-09-30/fbdv-base.owl version: '2026-09-30' version_method: owl_version_iri - id: infores:foodon name: FOODON urls: - http://purl.obolibrary.org/obo/foodon/releases/2026-09-20/foodon.owl version: '2026-02-02' version_method: owl_version_iri - id: infores:hgnc name: HGNC urls: [] version: unknown version_method: owl_version_iri - id: infores:monochrom name: MONOCHROM urls: - http://purl.obolibrary.org/obo/chr/releases/2025-10-15/chr-base.owl version: '2025-10-15' version_method: owl_version_iri - id: infores:mpath name: MPATH urls: - http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl version: '2020-05-19' version_method: owl_version_iri - id: infores:nbo name: NBO urls: - http://purl.obolibrary.org/obo/nbo/releases/2023-07-04/nbo.owl version: '2023-07-04' version_method: owl_version_iri - id: infores:ncbigene name: NCBIGENE urls: [] version: unknown version_method: owl_version_iri - id: infores:ncbitaxon-taxslim name: NCBITAXON-TAXSLIM urls: - http://purl.obolibrary.org/obo/ncbitaxon/releases/2026-07-12/subsets/taxslim.owl version: '2026-07-12' version_method: owl_version_iri - id: infores:pato name: PATO urls: - http://purl.obolibrary.org/obo/pato/releases/2026-10-01/pato-base.owl version: '2026-10-01' version_method: owl_version_iri - id: infores:pr name: PR urls: - http://purl.obolibrary.org/obo/pr/obophenotype/releases/2026-09-15/pr_slim.owl version: '2026-09-15' version_method: owl_version_iri - id: infores:ro name: RO urls: - http://purl.obolibrary.org/obo/ro/releases/2026-09-04/ro-base.owl version: '2026-09-04' version_method: owl_version_iri - id: infores:so name: SO urls: - http://purl.obolibrary.org/obo/so/2026-08-07/so.owl version: '2026-08-07' version_method: owl_version_iri - id: infores:upheno-alignments name: UPHENO-ALIGNMENTS urls: - http://purl.obolibrary.org/obo/upheno/releases/2025-10-12/components/upheno-alignments.owl version: '2025-10-12' version_method: owl_version_iri - id: infores:upheno-bridge name: UPHENO-BRIDGE urls: - http://purl.obolibrary.org/obo/upheno/releases/2025-10-08/components/upheno-bridge.owl version: '2025-10-08' version_method: owl_version_iri - id: infores:wbls name: WBLS urls: - http://purl.obolibrary.org/obo/wbls/releases/2026-04-16/wbls-base.owl version: '2026-04-16' version_method: owl_version_iri - id: infores:zfs name: ZFS urls: - http://purl.obolibrary.org/obo/zfa/releases/2026-07-16/zfa.owl version: '2026-07-16' version_method: owl_version_iri - id: infores:cl name: CL urls: - http://purl.obolibrary.org/obo/cl/releases/2026-06-08/cl-base.owl version: '2026-06-08' version_method: owl_version_iri - id: infores:ddanat name: DDANAT urls: [] version: '2026-10-06' version_method: owl_version_iri - id: infores:ddpheno name: DDPHENO urls: - http://purl.obolibrary.org/obo/ddpheno/releases/2023-08-26/ddpheno-base.owl version: '2023-08-26' version_method: owl_version_iri - id: infores:dpo name: DPO urls: - http://purl.obolibrary.org/obo/dpo/releases/2026-10-01/dpo-base.owl version: '2026-10-01' version_method: owl_version_iri - id: infores:emapa name: EMAPA urls: - http://purl.obolibrary.org/obo/emapa/releases/2026-10-02/emapa.owl version: '2026-10-06' version_method: owl_version_iri - id: infores:fbbt name: FBBT urls: - http://purl.obolibrary.org/obo/fbbt/releases/2026-10-01/fbbt.owl version: '2026-10-01' version_method: owl_version_iri - id: infores:fypo name: FYPO urls: - http://purl.obolibrary.org/obo/fypo/releases/2026-09-08/fypo-base.owl version: '2026-09-08' version_method: owl_version_iri - id: infores:go name: GO urls: - http://purl.obolibrary.org/obo/go/releases/2026-07-26/go-base.owl version: '2026-07-26' version_method: owl_version_iri - id: infores:hp name: HP urls: - http://purl.obolibrary.org/obo/hp/releases/2026-09-01/hp-base.owl version: '2026-09-01' version_method: owl_version_iri - id: infores:hsapdv name: HSAPDV urls: - http://purl.obolibrary.org/obo/life-stages/releases/2025-01-23/components/hsapdv.owl version: '2025-01-23' version_method: owl_version_iri - id: infores:mondo name: MONDO urls: - http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mondo-base.owl version: '2026-10-06' version_method: owl_version_iri - id: infores:mp name: MP urls: - http://purl.obolibrary.org/obo/mp/releases/2026-09-23/mp-base.owl version: '2026-09-23' version_method: owl_version_iri - id: infores:oba name: OBA urls: - http://purl.obolibrary.org/obo/oba/releases/2026-07-14/oba-base.owl version: '2026-07-14' version_method: owl_version_iri - id: infores:uberon name: UBERON urls: - http://purl.obolibrary.org/obo/uberon/releases/2026-10-01/uberon-base.owl version: '2026-10-01' version_method: owl_version_iri - id: infores:upheno name: UPHENO urls: - http://purl.obolibrary.org/obo/upheno/releases/2025-10-12/upheno-base.owl version: '2025-10-12' version_method: owl_version_iri - id: infores:wbbt name: WBBT urls: - http://purl.obolibrary.org/obo/wbbt/releases/2025-08-19/wbbt.owl version: '2026-10-06' version_method: owl_version_iri - id: infores:wbphenotype name: WBPHENOTYPE urls: - http://purl.obolibrary.org/obo/wbphenotype/releases/2026-04-15/wbphenotype-base.owl version: '2026-04-15' version_method: owl_version_iri - id: infores:xao name: XAO urls: - http://purl.obolibrary.org/obo/xao/releases/2024-09-03/xao.owl version: '2026-10-06' version_method: owl_version_iri - id: infores:xpo name: XPO urls: - http://purl.obolibrary.org/obo/xpo/releases/2025-07-25/xpo-base.owl version: '2025-07-25' version_method: owl_version_iri - id: infores:zfa name: ZFA urls: - http://purl.obolibrary.org/obo/zfa/releases/2026-07-16/zfa.owl version: '2026-07-16' version_method: owl_version_iri - id: infores:zp name: ZP urls: - http://purl.obolibrary.org/obo/zp/releases/2024-04-18/zp-base.owl version: '2024-04-18' version_method: owl_version_iri - id: infores:doid name: DOID urls: - http://purl.obolibrary.org/obo/doid/releases/2026-08-31/doid.owl version: '2026-08-31' version_method: owl_version_iri - id: infores:icd10cm name: ICD10CM urls: - https://data.bioontology.org/ontologies/ICD10CM/submissions/27/icd10cm.owl version: 2024ab version_method: owl_version_iri - id: infores:icd11foundation name: ICD11FOUNDATION urls: [] version: '2025-01-26' version_method: owl_version_iri - id: infores:ncit name: NCIT urls: - http://purl.obolibrary.org/obo/ncit/releases/2026-03-19/ncit.owl version: 26.02d version_method: owl_version_iri - id: infores:omim name: OMIM urls: - http://purl.obolibrary.org/obo/mondo/releases/2026-09-16/omim.owl version: '2026-09-16' version_method: owl_version_iri - id: infores:omo name: OMO urls: - http://purl.obolibrary.org/obo/omo/releases/2026-03-16/omo.owl version: '2026-03-16' version_method: owl_version_iri - id: infores:ordo name: ORDO urls: - https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.7.owl version: '4.7' version_method: owl_version_iri - id: infores:upheno-cross-species name: UPheno cross-species mappings urls: - https://data.monarchinitiative.org/mappings/latest/upheno-cross-species.sssom.tsv version: '2026-10-04' version_method: http_last_modified retrieved_at: '2026-10-08T09:30:44Z' - id: infores:upheno-species-independent name: UPheno species-independent mappings urls: - https://data.monarchinitiative.org/mappings/latest/upheno-species-independent.sssom.tsv version: '2026-10-04' version_method: http_last_modified retrieved_at: '2026-10-08T09:30:44Z' artifacts: - path: merged-kg.tar.gz tools: koza: 1.0.0 biolink_model: 4.2.5 kghub_downloader: 0.4.5 - id: loinc-ingest version: '2.80' transform_version: 56d78bb1 biolink_version: 4.4.6 build_version: loinc-ingest_2.80_56d78bb1_4.4.6 generated_at: '2026-11-01T03:44:38Z' 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: '2026-11-01T03:44:38Z' - id: infores:omop2obo name: OMOP2OBO Measurement Mappings urls: - https://doi.org/10.5281/zenodo.6949858 version: V1.1 version_method: static retrieved_at: '2026-11-01T03:44:38Z' - 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: '2026-11-01T03:44:38Z' 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: eb0dff7a1ae7d2d17e31fdf20199645ed948af0d771b064c3899e426009b7c79 - path: loinc_hierarchy_edges.tsv sha256: 1be892ca50c9a9e37b9138522025773a610251a0d7a6f231ede9e2dffe286a85 - path: loinc_nodes_nodes.tsv sha256: 246623447b1e63d9cbb5f53a3a9bdf1462630884c8613d1f0698abd6c79e4cf3 - path: loinc_parts_nodes.tsv sha256: 51d4624c34967ac5db59a295a7d93d6d2c9e37e1bdad0d0fee0618ae7581e733 - path: loinc_phenotype_edges.tsv sha256: 6123450d5bf01d4cac165be1b5ef0e4943b4e52fbfba8579fbd6fa6f1bd99fa8 tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 - id: mmrrc-ingest version: '2026-10-25' transform_version: 56303fc8 biolink_version: 4.2.5 build_version: mmrrc-ingest_2026-10-25_56303fc8_4.2.5 generated_at: '2026-11-01T04:42:29Z' sources: - id: infores:mmrrc name: Mutant Mouse Resource & Research Centers (MMRRC) urls: - https://www.mmrrc.org/about/mmrrc_catalog_data.csv version: '2026-10-25' version_method: http_last_modified retrieved_at: '2026-11-01T04:42:29Z' artifacts: - path: mmrrc_allele_to_genotype_edges.tsv sha256: 0aea3e3f2a1690431e7390fb62456204d36e3030598bc54a82f386ae9cead560 - path: mmrrc_genotype_nodes.tsv sha256: d5346a65e35fcc2ee796928c9c2316568642ca3640f6e260bd49c6e52dc68fb1 - path: mmrrc_genotype_to_gene_edges.tsv sha256: ba3f14b16ce471894ccdbdc703d779dd6845d21a58b45a7ccbfa98bbde183789 - path: mmrrc_genotype_to_phenotype_edges.tsv sha256: c156d8395e6ec77f9f524c1b991469574e1ae6f81c96d89af40fd8ac0b1426d7 tools: koza: 2.0.0 biolink_model: 4.2.5 kghub_downloader: 0.4.2 - id: monarch-phenotype-profile-ingest version: '2026-09-02' transform_version: eeb42f6b biolink_version: 4.3.6 build_version: monarch-phenotype-profile-ingest_2026-09-02_eeb42f6b_4.3.6 generated_at: '2026-10-03T03:01:12Z' sources: - id: infores:hpoa name: HPO Annotations (HPOA) urls: - http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt - http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa version: '2026-09-02' version_method: file_header retrieved_at: '2026-10-03T03:01:11Z' sources: - id: infores:omim name: OMIM urls: - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa version: '2026-08-27' version_method: hpoa_biocuration_max retrieved_at: '2026-10-03T03:01:11Z' - id: infores:orphanet name: Orphanet urls: - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa version: '2026-09-02' version_method: hpoa_biocuration_max retrieved_at: '2026-10-03T03:01:11Z' - id: infores:decipher name: DECIPHER urls: - http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa version: '2013-05-29' version_method: hpoa_biocuration_max retrieved_at: '2026-10-03T03:01:11Z' - id: infores:hp name: Human Phenotype Ontology (HP) urls: - http://purl.obolibrary.org/obo/hp.obo version: '2026-09-02' version_method: http_last_modified retrieved_at: '2026-10-03T03:01:11Z' - id: infores:mondo name: Mondo Disease Ontology (SSSOM) urls: - https://data.monarchinitiative.org/mappings/latest/mondo.sssom.tsv version: '2026-09-09' version_method: http_last_modified retrieved_at: '2026-10-03T03:01:11Z' artifacts: - path: hpoa_disease_mode_of_inheritance_edges.tsv sha256: d0107f1d62a1c14ec7316bb49e8bb3aa84d6a92661debc36e1dad867942f4037 - path: hpoa_disease_to_phenotype_edges.tsv sha256: ea89c38c162ab7d3b5c8cedf5f4978781df9028fd2bd2fb9c51f16f12e94a104 - path: hpoa_gene_to_disease_edges.tsv sha256: 20931de25212df95ac289d8c4c1fb8ff17cfa41a8fdda1715e612e5fc68946ff - path: hpoa_gene_to_phenotype_edges.tsv sha256: f81cca70b4de73334a7e68d02d91a774a9efbf58bae968bd075252de67de780a tools: koza: 2.1.1 biolink_model: 4.3.6 kghub_downloader: 0.4.4 - id: ncbi-gene version: '2026-10-02' transform_version: 9fc4ca75 biolink_version: 4.3.6 build_version: ncbi-gene_2026-10-02_9fc4ca75_4.3.6 generated_at: '2026-10-03T03:55:42Z' sources: - id: infores:ncbi-gene name: NCBI Gene urls: - https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz version: '2026-10-02' version_method: http_last_modified retrieved_at: '2026-10-03T03:55:41Z' artifacts: - path: ncbi_gene.nt.gz sha256: df9b3e91c3fa19ce1067158cf46f04b13057638ea81a5a81c7895fa553c79ebb - path: ncbi_gene_nodes.tsv sha256: 5f56ae919dd1401b9e415c5fcc07559b2a1fbb822fd3fa72772454e43c99d236 tools: koza: 2.2.0 biolink_model: 4.3.6 kghub_downloader: 0.4.4 - id: omim-ingest version: '2026-10-31' transform_version: b617a53b biolink_version: 4.3.6 build_version: omim-ingest_2026-10-31_b617a53b_4.3.6 generated_at: '2026-11-01T05:18:20Z' sources: - id: infores:omim name: OMIM (Online Mendelian Inheritance in Man) urls: - https://data.omim.org/downloads/{MONARCH_OMIM_DOWNLOAD_KEY}/morbidmap.txt version: '2026-10-31' version_method: file_header retrieved_at: '2026-11-01T05:18:20Z' artifacts: - path: omim_gene_to_disease_edges.tsv sha256: ab83e29098658da94b6764e3329f6a3979727421c5efdd014e3e7658cac9cf29 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: '2026-11-01T03:01:10Z' 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: '2026-11-01T03:01:09Z' - id: infores:ncbi-gene name: NCBI Gene urls: - https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz version: '2026-10-30' version_method: http_last_modified retrieved_at: '2026-11-01T03:01:09Z' artifacts: - path: panther_genome_orthologs_edges.tsv sha256: c55de9e6eeffa2dbbfe8085431a6b5df92494bf64df94f33632f14ecf8f05105 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: '2026-11-01' transform_version: be65ca88 biolink_version: 4.4.6 build_version: pombase-ingest_2026-11-01_be65ca88_4.4.6 generated_at: '2026-11-01T03:01:26Z' 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: '2026-11-01' version_method: http_last_modified retrieved_at: '2026-11-01T03:01:26Z' artifacts: - path: pombase_gene_nodes.tsv sha256: c09365df8e8933bda7918f97f11047bcc1fc4fdb2e46443616a4ef6146e00eb8 - path: pombase_gene_to_phenotype_edges.tsv sha256: a4ecef77642dd16f5578cf30e634588bf9bacc53bde0c0a06953f87e6d23dd81 tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 - id: reactome-ingest version: '97' transform_version: b244eb83 biolink_version: 4.4.5 build_version: reactome-ingest_97_b244eb83_4.4.5 generated_at: '2026-10-01T05:28:41Z' sources: - id: infores:reactome name: Reactome urls: - https://reactome.org/download/current/ReactomePathways.txt - https://reactome.org/download/current/NCBI2Reactome.txt - https://reactome.org/download/current/ChEBI2Reactome.txt version: '97' version_method: reactome_content_service retrieved_at: '2026-10-01T05:28:41Z' artifacts: - path: reactome_chemical_to_pathway_edges.tsv sha256: 14650bc3325c6cf5755a10bfef95aca2f2940730aef100456dc2b2ce4f20f831 - path: reactome_gene_to_pathway_edges.tsv sha256: 5af3fb58f335f83f9d4b61f39c19b08f03fde621908ff4c54dff25d7735e74db - path: reactome_pathway_nodes.tsv sha256: 7882c3ae1fd3ef21ee941481cc6c903b46ef6b9e49f683a59f28bd76cf791ac7 tools: koza: 2.6.2 biolink_model: 4.4.5 kghub_downloader: 0.5.0 - id: string-ingest version: '12.0' transform_version: f96320f0 biolink_version: 4.4.4 build_version: string-ingest_12.0_f96320f0_4.4.4 generated_at: '2026-09-01T02:18:17Z' sources: - id: infores:string name: "STRING \u2014 Functional Protein Interaction Networks" urls: - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9606.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/10116.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/10090.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9615.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9913.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9031.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/8364.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/7955.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/7227.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/6239.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/44689.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/227321.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/284812.protein.links.detailed.v12.0.txt.gz - https://stringdb-downloads.org/download/protein.links.detailed.v12.0/4932.protein.links.detailed.v12.0.txt.gz - https://string-db.org/mapping_files/entrez/all_organisms.entrez_2_string.tsv version: '12.0' version_method: url_path retrieved_at: '2026-09-01T02:18:17Z' artifacts: - path: string_protein_links_edges.tsv sha256: 0fba6fbf3bfd7cd2cd1e92e34ea9024fb6c83e5feacdc818dc3f5f7f9ae92d21 tools: koza: 2.6.2 biolink_model: 4.4.4 kghub_downloader: 0.5.0 - id: upheno-cross-species-ingest version: 531e30c7 transform_version: 71415b00 biolink_version: 4.4.6 build_version: upheno-cross-species-ingest_531e30c7_71415b00_4.4.6 generated_at: '2026-11-01T04:51:48Z' 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: '2026-11-01T04:51:48Z' artifacts: - path: upheno_phenotype_to_phenotype_edges.tsv sha256: b5ffb756b430efa37744856a87b20e6c789bb1b4e411c9be823d7da1fa3d4258 - path: upheno_phenotype_to_phenotype_nodes.tsv sha256: 6d64b989b8dd52cf74ae157634931cada329d9e57c7c89132ca866b322a27c81 tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 - id: xenbase-ingest version: '2026-10-28' transform_version: 8c8d0fe6 biolink_version: 4.4.6 build_version: xenbase-ingest_2026-10-28_8c8d0fe6_4.4.6 generated_at: '2026-11-01T05:45:11Z' 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: '2026-10-28' version_method: http_last_modified retrieved_at: '2026-11-01T05:45:10Z' - 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: '2026-11-01T05:45:10Z' artifacts: - path: xenbase_gene_to_phenotype_edges.tsv sha256: eda0395bd4f829b1c04b430876572954798ceac30d60bb2fc0017f65c2b814be - path: xenbase_gene_to_phenotype_nodes.tsv sha256: 2bed91c8b666008748233133166d7ca895f164261eacd107b4e3c5ae288509c5 - path: xenbase_non_entrez_orthologs_edges.tsv sha256: b50d2f1ebb1673ffa122ba29a3744d2229ebc5743fe11da600b50788d67d30cc - path: xenbase_orthologs_edges.tsv sha256: 68db5122095635d9a30788dbec0ec275d1d9fe39e0767cb69c203e23ed805d32 tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 - id: zfin-ingest version: '2026-10-31' transform_version: 15c3cda5 biolink_version: 4.4.6 build_version: zfin-ingest_2026-10-31_15c3cda5_4.4.6 generated_at: '2026-11-01T03:23:57Z' 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: '2026-10-31' version_method: http_last_modified retrieved_at: '2026-11-01T03:23:57Z' - 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: cf37a0e1 version_method: github_branch_head retrieved_at: '2026-11-01T03:23:57Z' artifacts: - path: zfin_gene_to_phenotype_edges.tsv sha256: f4a2365bfbe4e096b2d185f1cf52450252fbc5642b580a3ef68c3a43b395e6c0 - path: zfin_genotype_to_phenotype_edges.tsv sha256: d36eaeb5d1a5e6d89d4ef594d4a2b9d484c96a364f8ba4e7d7131899afa5ca59 - path: zfin_orthology_edges.tsv sha256: 25f35e74ff20905871a79994c0af382a2506bdaf692e85bd32a9c37edde71ce8 tools: koza: 2.7.0 biolink_model: 4.4.6 kghub_downloader: 0.5.0 disagreements: - id: infores:agr versions_observed: - 9.1.0 - 9.2.0 by_ingest: alliance-ingest: 9.2.0 hgnc-ingest: 9.1.0 version_drift: - id: infores:mondo versions_observed: - '2026-09-09' - '2026-10-04' by_ingest: clinvar-ingest: '2026-10-04' monarch-phenotype-profile-ingest: '2026-09-09' - id: infores:ncbi-gene versions_observed: - '2026-10-02' - '2026-10-30' by_ingest: ncbi-gene: '2026-10-02' pantherdb-orthologs-ingest: '2026-10-30' attributions: - ingest: medic source: MeDIC version: 2.0.0 notice: "Contains data from the European Medicines Agency (\xA9 EMA), the Pharmaceuticals\ \ and Medical Devices Agency of Japan (PMDA, https://www.pmda.go.jp), the Central\ \ Drugs Standard Control Organisation of India (CDSCO), EveryCure (drug-list and\ \ disease-list, CC BY 4.0) and the Mondo Disease Ontology (CC BY 4.0). Data has\ \ been edited: source records were parsed, translated, normalised, and mapped\ \ to ontology identifiers by the MeDIC pipeline. None of these bodies endorses\ \ this derived work." terms: https://data.monarchinitiative.org/medic/v2.0.0/LICENSING.md