Build the drug profile dataset (PLAN §6 Week 2):
- week2_curate_drugset.py: 300-drug set (2 ground-truth + 32 related-
mechanism + 26 negative-control + 240 random), restricted to
LINCS-scorable compounds, seed=42
- week2_chembl.py: InChIKey->ChEMBL match (145/300), MoA + targets
- week2_lincs_extract.py: cmapPy-slice both Level-5 GCTX phases to 978
landmark genes, mean-aggregate per drug to one consensus signature
- week2_assemble.py: join into drug_profiles_v1.parquet, Tier B (LINCS
single-source), scored flag per PLAN §6 Week 3 task 2
- docs/data_sources.md: drug set composition + LINCS/ChEMBL provenance
Results (all gitignored data): 300/300 drugs scored, both ground-truth
drugs present (hydroxyurea Phase II = CHEMBL467, L-glutamine Phase I).
Key caveat recorded: only 56/477 (12%) of the disease signature genes
are LINCS landmarks, so Week-3 scoring uses a 30-up/26-down query.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
