feat(olink): data-driven per-disease effect-size catalog - #4
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Ships synthlab/data/olink_disease_effects.csv — a curated, source-cited per-disease protein effect-size catalog covering 7 diseases × 43 rows (Alzheimer, BRCA_hereditary, CAD, CKD, Cancer_broad, IBD, T2D). Every row cites a real DOI (Sun et al. 2023 UKB-PPP, Williams et al. 2022 Sci Transl Med, Eldjarn et al. 2023 deCODE, Cohen et al. 2018 CancerSEEK, Dubin et al. 2023 Nat Comm CRIC, Guo et al. 2024 Nat Aging, Hu et al. 2025 Nat Comm UKB-PPP, Ahn et al. 2021 Cancers). Public API in synthlab.olink: - DiseaseEffectCatalog (frozen dataclass wrapping the loaded frame with .diseases(), .proteins_for(), .effects_for(noise_sd, seed)) - load_disease_effect_catalog(path=None) — importlib.resources-based ship-in-wheel loader Both re-exported from synthlab/__init__.py. Tests (tests/test_olink_disease_catalog.py, 15 tests): - schema, minimum disease coverage, DOI shape, defensible magnitudes - effects_for shape, KeyError paths, noise determinism / perturbation - end-to-end round-trip: catalog → effects_for → simulate_olink_npx, assert per-disease mean NPX shift matches catalog within 3 SE at 500 samples/arm × 44 rows Demo notebook (notebooks/olink_demo.ipynb) gains Section 10 — disease-conditional generation — with loading, inspection, 3-group cohort simulation (T2D/CAD/baseline, 300 samples each), top-5 grouped-bar chart, and a catalog-vs-empirical scatter. Rebuilt via notebooks/_build_olink_demo.py; executed outputs embedded. Cell count goes from 24 → 34. Docs: - README.md gains a "Disease-conditional effect catalog" subsection with per-disease row-range citations. - docs/olink_disease_catalog.md — full schema, unit-conversion guidance, SE guidance, evidence-strength rubric, PR checklist for adding a new disease. Ship-in-wheel plumbing: - synthlab/data/__init__.py + data/*.csv in [tool.setuptools.package-data] - .gitignore carve-out so synthlab/data/*.csv are tracked while other data/ and *.csv remain ignored. Stacks on PR #2 (feat/olink-npx-simulator). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Replaces closed PR #3 (base branch was the now-deleted
feat/olink-npx-simulatorafter #2 merged — rebased onto current main as a single cherry-picked commit).Content unchanged from #3: 7-disease × 43-row catalog,
DiseaseEffectCatalogclass, extended demo notebook §10, docs rubric. See PR #3 for full description.🤖 Generated with Claude Code