Publish VariantHound dataset 0.8.0 from ac278a1fef6d22e3e6f803449cc71d971ad78117

.gitattributes

@@ -58,3 +58,8 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+data/hpo/disease_annotations.jsonl filter=lfs diff=lfs merge=lfs -text
+data/hpo/gene_phenotypes.jsonl filter=lfs diff=lfs merge=lfs -text
+data/mgi/genotype_phenotypes.jsonl filter=lfs diff=lfs merge=lfs -text
+data/monarch/mouse_gene_phenotype.jsonl filter=lfs diff=lfs merge=lfs -text
+data/orthology_manifest.json filter=lfs diff=lfs merge=lfs -text

DATA_CONTRACT.md

@@ -1,40 +1,68 @@
-# VariantHound Hugging Face data contract
-
-## Package layout
-
-| Path | Purpose |
-|---|---|
-| `data/benchmark_cases.jsonl` | One validated canine benchmark case per line, sorted by case ID |
-| `data/source_manifest.json` | Upstream source access, pinning, redistribution, and attribution policy |
-| `data/orthology_manifest.json` | Release-qualified dog-human-mouse mapping policy or pinned mapping snapshot |
-| `data/ml-readiness-policy.json` | Versioned independent-sample and learned-model promotion thresholds |
-| `schemas/*.schema.json` | Machine-readable contracts used by the source repository |
-| `docs/*.md` | Data provenance, leakage-safe evaluation, and orthology guidance |
-| `release-manifest.json` | Dataset version, source commit, file sizes, and SHA-256 digests |
-
-The release builder uses an explicit source-to-destination allowlist. Files under `data/raw`, `data/processed`, browser build directories, credentials, VCF/BCF files, and complete third-party database exports are never copied implicitly.
-
-## Benchmark case fields
-
-Each line in `data/benchmark_cases.jsonl` contains:
-
-- `id`, `label`, `species`, `breed`, and `expected_gene`;
-- `disease_group_id`, the indivisible split and resampling unit;
-- `phenotypes.present` and `phenotypes.excluded` ontology identifiers;
-- `publication_year`;
-- `evaluation.discovery_mask_evidence_ids` and `evaluation.discovery_mask_disease_ids`;
-- `evaluation.temporal_status` and an exclusion reason when applicable;
-- a literature `reference` with label and URL.
-
-Cases are benchmark inputs, not independent training rows. Disease-level grouping and temporal availability must be preserved in any downstream evaluation.
-
-## Release integrity
-
-`release-manifest.json` is valid only when:
-
-1. every listed payload path exists and no unlisted file is present;
-2. every byte count and lowercase SHA-256 digest matches;
-3. the dataset version and source Git commit are recorded;
-4. the package was built after the repository data validator passed.
-
-The upload script rechecks all four conditions before contacting Hugging Face.
+# VariantHound Hugging Face data contract
+
+## Package layout
+
+| Path | Purpose |
+|---|---|
+| `data/benchmark_cases.jsonl` | One validated canine benchmark case per line, sorted by case ID |
+| `data/source_manifest.json` | Upstream source access, pinning, redistribution, and attribution policy |
+| `data/ensembl-compara-116.json` | Immutable Ensembl 116 artifact checksums, assemblies, and expected row counts |
+| `data/hpo-2026-09-01.json` | Immutable HPO asset IDs, checksums, and expected normalized counts |
+| `data/monarch-kg-2026-09-02.json` | Dated Monarch/HGNC artifacts and exact normalized counts |
+| `data/mgi-2026-09-12.json` | Retrieval-dated MGI/MP artifacts, conflict policy, and exact counts |
+| `data/omia-2026-09-12.json` | Retrieval-dated OMIA dump and official gene-crosswalk checksums |
+| `data/phenio-2026-09-01.json` | Immutable PHENIO relation-graph assets and exact compact-closure counts |
+| `data/orthology_manifest.json` | Release-qualified dog-human-mouse mapping policy or pinned mapping snapshot |
+| `data/hpo/snapshot.json` | HPO release metadata and normalized-file integrity records in full releases |
+| `data/hpo/ontology_terms.jsonl` | HPO term hierarchy, synonyms, alternate IDs, and obsolescence |
+| `data/hpo/gene_phenotypes.jsonl` | NCBI Gene-to-HPO annotations with disease and frequency context |
+| `data/hpo/disease_annotations.jsonl` | Disease-to-HPO annotations with references, evidence, and negation |
+| `data/monarch/snapshot.json` | Monarch release, deduplication, provenance, and output integrity records |
+| `data/monarch/human_gene_disease.jsonl` | Stable-ID human gene-to-MONDO evidence |
+| `data/monarch/mouse_gene_phenotype.jsonl` | MGI gene-to-MP evidence with primary-source attribution |
+| `data/mgi/snapshot.json` | Direct MGI provenance, identifier policies, and output integrity records |
+| `data/mgi/mp_terms.jsonl` | Mammalian Phenotype hierarchy and identifier status |
+| `data/mgi/gene_crosswalk.jsonl` | Phenotype-bearing MGI markers with reconciled NCBI/Ensembl IDs |
+| `data/mgi/genotype_phenotypes.jsonl` | Direct genotype-to-MP evidence and rank-eligibility state |
+| `data/omia/snapshot.json` | Canine OMIA provenance, masking and output-integrity contract |
+| `data/omia/genes.jsonl` | OMIA internal-to-NCBI Gene resolution for canine genes |
+| `data/omia/phenes.jsonl` | Canine phenes, clinical text, inheritance, breeds and ontology links |
+| `data/omia/gene_phene_evidence.jsonl` | Stable-ID canine gene–phene evidence with discovery mask IDs |
+| `data/omia/causal_variants.jsonl` | Variants linked to canine single-locus traits with assemblies and publications |
+| `data/omia/publications.jsonl` | Publications referenced by canine OMIA phenes or variants |
+| `data/phenio/snapshot.json` | PHENIO release, closure semantics, prefix policy, and output integrity |
+| `data/phenio/phenotype_closure.tsv.gz` | Entailed reflexive HP/MP/uPheno subclass closure used for semantic similarity |
+| `data/phenio/upstream_versions.tsv` | Versions of all ontologies integrated into the pinned PHENIO release |
+| `data/browser/manifest.json` | Content-addressed browser collection map, source fingerprints, counts, and limitations |
+| `data/browser/{collection}/*` | Sixteen deterministic gzip buckets per terms, closure, gene-profile, and orthology collection |
+| `data/ml-readiness-policy.json` | Versioned independent-sample and learned-model promotion thresholds |
+| `schemas/*.schema.json` | Machine-readable contracts used by the source repository |
+| `docs/*.md` | Data provenance, leakage-safe evaluation, source-ingestion, and ranking guidance |
+| `release-manifest.json` | Dataset version, source commit, file sizes, and SHA-256 digests |
+
+The release builder uses an explicit source-to-destination allowlist. Files under `data/raw`, `data/processed`, browser build directories, credentials, VCF/BCF files, and complete third-party database exports are never copied implicitly. The complete OMIA SQL dump is excluded; only its verified canine transform can be selected.
+
+## Benchmark case fields
+
+Each line in `data/benchmark_cases.jsonl` contains:
+
+- `id`, `label`, `species`, `breed`, and `expected_gene`;
+- `disease_group_id`, the indivisible split and resampling unit;
+- `phenotypes.present` and `phenotypes.excluded` ontology identifiers;
+- `publication_year`;
+- `evaluation.discovery_mask_evidence_ids` and `evaluation.discovery_mask_disease_ids`;
+- `evaluation.temporal_status` and an exclusion reason when applicable;
+- a literature `reference` with label and URL.
+
+Cases are benchmark inputs, not independent training rows. Disease-level grouping and temporal availability must be preserved in any downstream evaluation.
+
+## Release integrity
+
+`release-manifest.json` is valid only when:
+
+1. every listed payload path exists and no unlisted file is present;
+2. every byte count and lowercase SHA-256 digest matches;
+3. the dataset version and source Git commit are recorded;
+4. the package was built after the repository data validator passed.
+
+The upload script rechecks all four conditions before contacting Hugging Face.

LICENSE

@@ -1,21 +1,21 @@
-                                 Apache License
-                           Version 2.0, January 2004
-                        http://www.apache.org/licenses/
-
-Copyright 2026 VariantHound contributors
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-
-The Apache-2.0 license applies to original VariantHound software only.
-Third-party datasets retain their own licenses, terms, and attribution
-requirements. No third-party raw dataset is redistributed in this repository.
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+Copyright 2026 VariantHound contributors
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+The Apache-2.0 license applies to original VariantHound software only.
+Third-party datasets retain their own licenses, terms, and attribution
+requirements. No third-party raw dataset is redistributed in this repository.

README.md

@@ -1,62 +1,91 @@
----
-pretty_name: VariantHound Research Snapshot
-language:
-- en
-license: other
-size_categories:
-- n<1K
-tags:
-- biology
-- genomics
-- veterinary
-- phenotype
-- tabular
-configs:
-- config_name: benchmark_cases
-  data_files:
-  - split: test
-    path: data/benchmark_cases.jsonl
----
-
-# VariantHound Research Snapshot
-
-VariantHound is an explainable, phenotype-aware research system for ranking candidate genes in canine inherited disease. This dataset repository contains the compact, redistributable artifacts generated from the public [VariantHound source repository](https://github.com/TinyAnts/VariantHound).
-
-> Research and educational use only. This snapshot is not a diagnostic dataset or medical device, and its rankings require expert review and experimental validation.
-
-## Current contents
-
-The initial release is a deliberately small demonstration snapshot:
-
-- three literature-grounded canine benchmark cases;
-- source and orthology provenance manifests;
-- machine-readable schemas for the published contracts;
-- evaluation, data, and orthology documentation;
-- a release manifest containing the source Git commit, byte sizes, and SHA-256 checksums.
-
-`data/benchmark_cases.jsonl` is the viewer-friendly dataset split. The snapshot does not include raw OMIA, HPO, Monarch, MGI, Ensembl, or Dog10K database exports.
-
-## Evaluation safety
-
-The benchmark metadata defines direct evidence and disease masks for discovery simulation. Temporal evaluation is allowed only when a historical source snapshot predating the case publication has been independently materialized. Known-evidence retrieval results must not be reported as discovery performance.
-
-## Orthology status
-
-The initial orthology manifest is `unmaterialized`. That state is intentional: it contains no mapping rows and cannot be used for scoring until an Ensembl release, all three annotation assemblies, a retrieval timestamp, and a source checksum have been pinned and validated.
-
-## Reproducibility
-
-Every uploaded release is built by `pipelines/build_hf_release.py`. Verify `release-manifest.json` before using the data. The manifest records every payload file and its SHA-256 digest.
-
-## Licensing and attribution
-
-Original VariantHound code and documentation are Apache-2.0. Benchmark facts and future processed tables retain their upstream sources' terms and attribution requirements, so the aggregate dataset uses `license: other`. See `docs/DATA.md`, the per-case references, and the source manifest before redistribution or publication.
-
-## Known limitations
-
-- Three demonstration cases are not an adequate performance benchmark.
-- The ontology vocabulary in the demo is intentionally compact and includes internal `VH:*` terms.
-- The current bundle contains no usable production orthology snapshot.
-- A learned ranking model is not supported by the current sample size.
-
-See `DATA_CONTRACT.md` for the package layout and field-level expectations.
+---
+pretty_name: VariantHound Research Snapshot
+language:
+- en
+license: other
+size_categories:
+- 1M<n<10M
+tags:
+- biology
+- genomics
+- veterinary
+- phenotype
+- tabular
+configs:
+- config_name: benchmark_cases
+  data_files:
+  - split: test
+    path: data/benchmark_cases.jsonl
+---
+
+# VariantHound Research Snapshot
+
+VariantHound is an explainable, phenotype-aware research system for ranking candidate genes in canine inherited disease. This dataset repository contains the compact, redistributable artifacts generated from the public [VariantHound source repository](https://github.com/TinyAnts/VariantHound).
+
+> Research and educational use only. This snapshot is not a diagnostic dataset or medical device, and its rankings require expert review and experimental validation.
+
+## Current contents
+
+The release contains:
+
+- three literature-grounded canine benchmark cases;
+- source and orthology provenance manifests;
+- a checksum-pinned Ensembl 116 dog-human-mouse orthology snapshot in releases built by the publication workflow;
+- a checksum pin for HPO 2026-09-01 and its matching human annotations, plus normalized JSONL in publication-workflow releases;
+- a dated Monarch 2026-09-02 evidence snapshot with a checksum-pinned HGNC stable-ID crosswalk;
+- a direct, retrieval-dated MGI genotype/phenotype snapshot with reconciled stable gene IDs;
+- a processed canine OMIA snapshot with phenes, stable-ID gene evidence, causal variants, breeds, and publications;
+- a compact PHENIO HP/MP/uPheno semantic-similarity closure with upstream ontology versions;
+- content-addressed browser shards for terms, phenotype closure, stable-ID gene profiles, and orthology;
+- machine-readable schemas for the published contracts;
+- evaluation, data, orthology, HPO, Monarch, MGI, OMIA, and PHENIO documentation;
+- a release manifest containing the source Git commit, byte sizes, and SHA-256 checksums.
+
+`data/benchmark_cases.jsonl` is the viewer-friendly benchmark split. HPO and OMIA are published as normalized JSONL under their source directories; raw upstream assets are not mirrored. The snapshot does not include raw OMIA, Monarch, MGI, Ensembl, or Dog10K database exports.
+
+## Evaluation safety
+
+The benchmark metadata defines direct evidence and disease masks for discovery simulation. Temporal evaluation is allowed only when a historical source snapshot predating the case publication has been independently materialized. Known-evidence retrieval results must not be reported as discovery performance.
+
+## Orthology status
+
+The publication workflow materializes 41,504 Ensembl 116 protein-tree orthology edges: 20,279 dog-human and 21,225 dog-mouse links. It unions the dog, human, and mouse genome-specific exports because Ensembl partitions pairwise rows arbitrarily between those files. Every artifact is checked against its pinned byte count, official MD5, and SHA-256 before transformation. One-to-many and many-to-many relationships are retained and explicitly marked ambiguous.
+
+## HPO status
+
+The publication workflow verifies three immutable GitHub release assets before materializing 20,482 ontology terms, 333,983 human gene-phenotype annotations, and 286,651 disease-phenotype annotations. Negated disease annotations remain explicit. The snapshot is marked `current-snapshot-only` and cannot be used as a historical temporal-evaluation source.
+
+## Monarch status
+
+The dated Monarch KG subsets materialize 6,965 deduplicated human gene-disease associations and 296,123 mouse gene-phenotype associations. Human HGNC IDs are resolved through a separately pinned HGNC export: 4,799 of 4,800 genes have Ensembl IDs and all 4,800 have a stable NCBI or Ensembl join ID. Primary and aggregator provenance are retained so MGI-derived rows cannot be double-counted when direct MGI data is added.
+
+## Direct MGI status
+
+The direct MGI snapshot contains 15,317 MP terms and 283,119 genotype-phenotype rows. Identifier reconciliation makes 276,606 rows rank-eligible. It retains but excludes 26 rows affected by conflicting NCBI mappings and 6,487 rows whose markers lack stable join IDs. Direct MGI and Monarch's MGI-derived view must be deduplicated by provenance before scoring.
+
+## OMIA status
+
+The retrieval-dated canine transform contains 1,019 phenes, 435 gene-phene edges, and 594 variants linked to single-locus traits. OMIA internal gene IDs are resolved only through the separately pinned official export: 430 gene-phene rows and 591 variant rows are rank-eligible, while unresolved mappings remain available for audit. Each evidence row includes deterministic discovery mask IDs. Because OMIA provides a moving dump rather than historical releases, this snapshot is restricted to current-snapshot evaluation.
+
+## PHENIO status
+
+The pinned PHENIO `v2026-09-01` transform scans 82,128,289 materialized relations and retains 3,972,487 entailed reflexive subclass rows for 20,413 HPO, 15,317 MP, and 54,198 uPheno terms. This compact closure preserves the cross-species paths needed by deterministic semantic similarity while excluding unrelated integrated relations. The full upstream graph is not mirrored.
+
+## Reproducibility
+
+Every uploaded release is built by `pipelines/build_hf_release.py`. Verify `release-manifest.json` before using the data. The manifest records every payload file and its SHA-256 digest.
+
+## Licensing and attribution
+
+Original VariantHound code and documentation are Apache-2.0. Benchmark facts and future processed tables retain their upstream sources' terms and attribution requirements, so the aggregate dataset uses `license: other`. See `docs/DATA.md`, the per-case references, and the source manifest before redistribution or publication.
+
+OMIA data should cite DOI `10.25910/2AMR-PV70` and acknowledge the Sydney Informatics Hub. OMIA asks users to contact its team about publications that rely on the MySQL dump or extended data.
+
+## Known limitations
+
+- Three demonstration cases are not an adequate performance benchmark.
+- The ontology vocabulary in the demo is intentionally compact and includes internal `VH:*` terms.
+- Canonical gene symbols are not present in the Compara bulk export and remain null until a separately pinned identifier-enrichment source is applied; stable Ensembl gene IDs are the join keys.
+- A learned ranking model is not supported by the current sample size.
+
+See `DATA_CONTRACT.md` for the package layout and field-level expectations.

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