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"schema_version": "1.0.0",
"sources": [
{
"id": "dog10k",
"name": "Dog10K 2K canid variation release",
"role": "Later population, breed-frequency, consequence, and structural-variant evidence",
"homepage": "https://dog10k.kiz.ac.cn/",
"access_url": "https://zenodo.org/records/8084059",
"citation_url": "https://doi.org/10.5281/zenodo.8084059",
"pinning_strategy": "Pin Zenodo record version and verify published MD5 checksums",
"redistribution": "source-link-only",
"assembly": "UU_Cfam_GSD_1.0",
"notes": "Do not mirror the 51.6 GB release. Produce only a compact, scientifically useful derived index after confirming redistribution terms."
},
{
"id": "ensembl-compara",
"name": "Ensembl Compara",
"role": "Dog-human-mouse orthology",
"homepage": "https://www.ensembl.org/",
"access_url": "https://ftp.ensembl.org/pub/release-116/tsv/ensembl-compara/homologies/",
"citation_url": "https://www.ensembl.org/info/about/publications/index.html",
"pinning_strategy": "Pin release 116 dog, human, and mouse genome-specific protein_default exports with MD5, SHA-256, byte counts, assemblies, and expected normalized row counts",
"redistribution": "attribution",
"assembly": null,
"notes": "The three genome-specific files must be unioned because Ensembl deliberately partitions pairwise homologies across them. The normalized snapshot uses stable gene IDs and preserves ambiguous cardinalities."
},
{
"id": "hgnc",
"name": "HUGO Gene Nomenclature Committee",
"role": "Stable HGNC-to-NCBI-Gene-to-Ensembl identifier crosswalk for human evidence",
"homepage": "https://www.genenames.org/",
"access_url": "https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt",
"citation_url": "https://www.genenames.org/about/guidelines/",
"pinning_strategy": "Record retrieval timestamp, upstream Last-Modified value, byte count, and SHA-256 for the complete-set export",
"redistribution": "attribution",
"assembly": null,
"notes": "HGNC IDs, NCBI Gene IDs, and Ensembl gene IDs are join keys. Symbols remain display-only and symbol disagreements fail the Monarch transform."
},
{
"id": "hpo",
"name": "Human Phenotype Ontology",
"role": "Human phenotype hierarchy and disease annotations",
"homepage": "https://hpo.jax.org/",
"access_url": "https://github.com/obophenotype/human-phenotype-ontology/releases/tag/v2026-09-01",
"citation_url": "https://hpo.jax.org/app/about",
"pinning_strategy": "Pin the v2026-09-01 ontology and matching annotation assets by GitHub release asset ID, byte count, and SHA-256",
"redistribution": "attribution",
"assembly": null,
"notes": "The ontology is dated 2026-09-01 and phenotype.hpoa declares annotation version 2026-09-02. Asset API URLs are used because name-based browser download URLs can drift when release assets are replaced."
},
{
"id": "mgi",
"name": "Mouse Genome Informatics",
"role": "Mouse gene-phenotype, genotype, disease-model, and homology evidence",
"homepage": "https://www.informatics.jax.org/",
"access_url": "https://www.informatics.jax.org/downloads/reports/index.html",
"citation_url": "https://www.informatics.jax.org/mgihome/other/citation.shtml",
"pinning_strategy": "Pin the 2026-09-12 retrieval using Last-Modified timestamps, byte counts, and SHA-256 for each report; verify the embedded MP 2026-08-25 release",
"redistribution": "attribution",
"assembly": null,
"notes": "The first direct ingest uses MGI_GenePheno.rpt, MGI_Gene_Model_Coord.rpt, MGI_EntrezGene.rpt, and MPheno_OBO.ontology. Conflicting or unresolved stable IDs are retained for audit and excluded from ranking."
},
{
"id": "monarch-kg",
"name": "Monarch Knowledge Graph",
"role": "Human disease-phenotype and gene-disease associations",
"homepage": "https://monarchinitiative.org/",
"access_url": "https://data.monarchinitiative.org/monarch-kg/2026-09-02/",
"citation_url": "https://monarch-app.monarchinitiative.org/",
"pinning_strategy": "Pin the dated 2026-09-02 metadata and human/mouse association TSVs by byte count and SHA-256; pin a matching stable-ID HGNC crosswalk separately",
"redistribution": "processed-only",
"assembly": null,
"notes": "Only the human gene-disease and mouse gene-phenotype subsets are materialized. Aggregated MGI evidence retains primary-source provenance and must not be double-counted with direct MGI ingest."
},
{
"id": "omia",
"name": "Online Mendelian Inheritance in Animals",
"role": "Canine disease-gene, breed, causal-variant, and publication evidence",
"homepage": "https://omia.org/",
"access_url": "https://omia.org/static/omia.sql.gz",
"citation_url": "https://omia.org/citing/",
"pinning_strategy": "Pin the 2026-09-12 retrieval of the complete SQL dump and official internal-to-NCBI Gene export by byte count and SHA-256",
"redistribution": "processed-only",
"assembly": null,
"notes": "The processed canine subset retains unresolved internal gene IDs but excludes them from ranking. Contact OMIA about publications relying on the MySQL dump or extended data. Cite DOI 10.25910/2AMR-PV70 and retain stated reference assemblies."
},
{
"id": "phenio",
"name": "PHENIO / uPheno",
"role": "Cross-species phenotype mappings and ontology backbone",
"homepage": "https://monarch-initiative.github.io/phenio/",
"access_url": "https://github.com/monarch-initiative/phenio/releases/tag/v2026-09-01",
"citation_url": "https://monarch-app.monarchinitiative.org/Sources/phenio/",
"pinning_strategy": "Pin v2026-09-01, its source commit, and immutable relation-graph and upstream-version asset IDs by byte count and SHA-256",
"redistribution": "attribution",
"assembly": null,
"notes": "The processed snapshot retains only the entailed reflexive HP/MP/UPHENO subclass closure and the complete upstream version table; the 340 MB integrated relation graph is not redistributed."
},
{
"id": "pubmed",
"name": "PubMed (NCBI E-utilities)",
"role": "Clinical phenotype text for the publications OMIA cites, read to curate HPO terms",
"homepage": "https://pubmed.ncbi.nlm.nih.gov/",
"access_url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
"citation_url": "https://www.ncbi.nlm.nih.gov/home/about/policies/",
"pinning_strategy": "PubMed publishes no release identifier, so the snapshot pins the exact set of identifiers it was built from by SHA-256 over that set, plus the retrieval date. Re-running can legitimately differ if NCBI revises a record.",
"redistribution": "source-link-only",
"assembly": null,
"notes": "Only the abstracts of publications cited by rank-eligible OMIA phenes are retrieved. Text stays in dist/ and is never committed or published; only derived HPO term identifiers reach the browser package. Requests carry a tool and contact string as NCBI asks, and stay under the published rate limit."
}
]
}
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