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   "source": [
    "# 02 \u2014 Disease signature\n",
    "\n",
    "Week 1 (PLAN.md \u00a76). Pull Open Targets + a GEO expression study, run differential expression, and build `sickle_cell_signature_v1.json` (Tier A) with full provenance.\n\nSteps: (1) Open Targets associations, (2) choose + download GEO dataset, (3) differential expression, (4) build + persist signature.\n\n**Pitfall to document:** whole-blood expression is partly driven by cell-composition differences, not disease state (PLAN.md \u00a79.1)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.insert(0, '..')  # import the src package from notebooks/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from src import disease\n",
    "from src.provenance import ConfidenceTier\n",
    "\n",
    "# Step 1: Open Targets associations for MONDO:0011382  -> data/raw/open_targets/\n",
    "# Step 2: choose + download GEO study (GSE53441 / GSE35007 / newer) -> data/raw/geo/\n",
    "# Step 3: disease.compute_differential_expression(...)\n",
    "# Step 4: disease.build_signature(...) then disease.persist_signature(...)"
   ]
  }
 ],
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