Junior B.
b731478f5d
Set up the project skeleton per PLAN.md §4: - src/ package: identifiers, disease, drugs, scoring, provenance with pydantic schemas and confidence-tier logic (working); data-pull/compute functions stubbed per their build week - 5 starter notebooks (01-05) with PLAN-referenced steps - tests/test_scoring.py: tier-assignment tests pass; scoring reference test xfail until Week 3 - docs/: recovery_test_report, data_sources, known_limitations skeletons - pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README - data/ tree preserved via .gitkeep; raw/processed/results gitignored Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
50 lines
1.3 KiB
Plaintext
50 lines
1.3 KiB
Plaintext
{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# 03 \u2014 Drug profiles\n",
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"\n",
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"Week 2 (PLAN.md \u00a76). Curate the ~300-drug set, pull ChEMBL + LINCS L1000 data, and assemble `drug_profiles_v1.parquet`.\n\nDrug set: 2 ground-truth + ~50 related-mechanism + ~50 negative controls + ~200 random (fixed seed). Document any missing LINCS signatures in `docs/known_limitations.md`."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import sys\n",
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"sys.path.insert(0, '..') # import the src package from notebooks/"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from src import drugs\n",
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"from src import RANDOM_SEED\n",
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"\n",
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"# Step 1: drugs.curate_drug_set(seed=RANDOM_SEED) -> data/processed/drug_set_v1.csv\n",
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"# Step 2: drugs.fetch_chembl_profile(...) for each drug -> data/raw/chembl/\n",
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"# Step 3: drugs.fetch_lincs_signature(...) -> data/raw/lincs/\n",
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"# Step 4: drugs.persist_drug_profiles(...) -> drug_profiles_v1.parquet"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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} |