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Omics data pack v1

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@ariharrisonlab ariharrisonlab released this 04 Sep 20:11
· 12 commits to main since this release
omics-pack-v1
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Learn about vigilant mode.

Omics evidence packs for the NovoMCP engine. Install them and target_discovery, validate_target, and stratify_patients light up with no database server — the engine routes omics.* reads to the local pack.

Packs

  • omics-core.sqlite.gz (~12.5 MB) — 108,436 target–disease associations (Open Targets / UniProt / Reactome) + 134,940 resistance variants (ClinVar). License: CC-BY-4.0 (see NOTICE-omics-core.md).
  • omics-pgx.sqlite.gz (~6 KB) — 56 pharmacogenes (PharmGKB / CPIC / gnomAD). License: CC-BY-SA-4.0 + ODbL — a separate opt-in pack (ShareAlike terms; see NOTICE-omics-pgx.md).

Install

python scripts/omics-pack/install_omics_pack.py omics-core.sqlite.gz              # target discovery
python scripts/omics-pack/install_omics_pack.py omics-core.sqlite.gz omics-pgx.sqlite.gz   # + patient stratification

Merges into ~/.novo/omics/omics.db. See docs/optional-data-services.md.

Data is compiled from public reference sources; per-source attribution is in the NOTICE files. The perturbation signature-reversal channel is omitted from this release pending clearer per-row licensing.

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