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Datasets:
jang1563
/
NegBioDB

Tasks:
Text Classification
Text Generation
Tabular Classification
Modalities:
Tabular
Text
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
Libraries:
Datasets
pandas
Polars
License:
Dataset card Data Studio Files
xet
 Community
1
NegBioDB
File size: 5,146 Bytes
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# NegBioDB Pipeline Makefile

.PHONY: setup db test clean \
        ge-db ge-download-depmap ge-load-depmap ge-load-rnai ge-export ge-all ge-clean ge-test

# === Week 1: Scaffolding ===

setup:
	uv venv
	uv sync --all-extras
	mkdir -p data exports

db: setup
	uv run python -c "from negbiodb.db import create_database; create_database()"

test: setup
	uv run pytest tests/ -v

clean:
	rm -f data/negbiodb.db
	rm -rf exports/* __pycache__ .pytest_cache
	find . -name "*.pyc" -delete 2>/dev/null || true

# === Week 2: Data Download ===

.PHONY: download download-pubchem download-chembl download-bindingdb download-davis

download-pubchem: setup
	uv run python scripts/download_pubchem.py

download-chembl: setup
	uv run python scripts/download_chembl.py

download-bindingdb: setup
	uv run python scripts/download_bindingdb.py

download-davis: setup
	uv run python scripts/download_davis.py

download: download-pubchem download-chembl download-bindingdb download-davis

# === ETL: Load Sources ===

.PHONY: load-davis load-chembl load-pubchem load-bindingdb load-all

load-davis: db download-davis
	uv run python scripts/load_davis.py

load-chembl: db download-chembl
	uv run python scripts/load_chembl.py

load-pubchem: db download-pubchem
	uv run python scripts/load_pubchem.py

load-bindingdb: db download-bindingdb
	uv run python scripts/load_bindingdb.py

load-all: load-davis load-chembl load-pubchem load-bindingdb

# ============================================================
# Clinical Trial Failure Domain
# ============================================================

.PHONY: ct-db ct-download ct-load-aact ct-classify ct-resolve ct-outcomes ct-all ct-clean

ct-db: setup
	uv run python -c "from negbiodb_ct.ct_db import create_ct_database; create_ct_database()"

ct-download-aact: setup
	uv run python scripts_ct/download_aact.py

ct-download-opentargets: setup
	uv run python scripts_ct/download_opentargets.py

ct-download-cto: setup
	uv run python scripts_ct/download_cto.py

ct-download-shi-du: setup
	uv run python scripts_ct/download_shi_du.py

ct-download: ct-download-opentargets ct-download-cto ct-download-shi-du
	@echo "NOTE: AACT requires --url flag. Run: make ct-download-aact"

ct-load-aact: ct-db
	uv run python scripts_ct/load_aact.py

ct-classify: ct-load-aact
	uv run python scripts_ct/classify_failures.py

ct-resolve: ct-load-aact
	uv run python scripts_ct/resolve_drugs.py

ct-outcomes: ct-classify
	uv run python scripts_ct/load_outcomes.py

ct-all: ct-db ct-load-aact ct-classify ct-resolve ct-outcomes
	@echo "CT pipeline complete."

ct-clean:
	rm -f data/negbiodb_ct.db
	@echo "CT database removed."

ct-test: setup
	uv run pytest tests/test_ct_db.py tests/test_etl_aact.py tests/test_etl_classify.py tests/test_drug_resolver.py tests/test_etl_outcomes.py -v

# ============================================================
# Protein-Protein Interaction Negative Domain
# ============================================================

.PHONY: ppi-db ppi-download ppi-load-huri ppi-load-intact ppi-load-humap ppi-load-string ppi-all ppi-clean ppi-test

ppi-db: setup
	uv run python -c "from negbiodb_ppi.ppi_db import create_ppi_database; create_ppi_database()"

ppi-download-huri: setup
	uv run python scripts_ppi/download_huri.py

ppi-download-intact: setup
	uv run python scripts_ppi/download_intact.py

ppi-download-humap: setup
	uv run python scripts_ppi/download_humap.py

ppi-download-string: setup
	uv run python scripts_ppi/download_string.py

ppi-download-biogrid: setup
	uv run python scripts_ppi/download_biogrid.py

ppi-download: ppi-download-huri ppi-download-intact ppi-download-humap ppi-download-string ppi-download-biogrid

ppi-load-huri: ppi-db ppi-download-huri
	uv run python scripts_ppi/load_huri.py

ppi-load-intact: ppi-db ppi-download-intact
	uv run python scripts_ppi/load_intact.py

ppi-load-humap: ppi-db ppi-download-humap
	uv run python scripts_ppi/load_humap.py

ppi-load-string: ppi-db ppi-download-string
	uv run python scripts_ppi/load_string.py

ppi-all: ppi-db ppi-load-huri ppi-load-intact ppi-load-humap ppi-load-string
	@echo "PPI pipeline complete."

ppi-clean:
	rm -f data/negbiodb_ppi.db
	@echo "PPI database removed."

ppi-test: setup
	uv run pytest tests/test_ppi_db.py tests/test_protein_mapper.py tests/test_etl_huri.py tests/test_etl_intact.py tests/test_etl_humap.py tests/test_etl_string.py -v

# === GE/DepMap Domain ===

ge-db:
	uv run python -c "from negbiodb_depmap.depmap_db import init_db; init_db()"
	@echo "GE database initialized."

ge-download-depmap:
	uv run python scripts_depmap/download_depmap.py

ge-load-depmap: ge-db ge-download-depmap
	uv run python scripts_depmap/load_depmap.py

ge-load-rnai: ge-db ge-download-depmap
	uv run python scripts_depmap/load_rnai.py

ge-export: ge-db
	uv run python scripts_depmap/export_ge_ml_dataset.py

ge-all: ge-db ge-load-depmap ge-load-rnai ge-export
	@echo "GE pipeline complete."

ge-clean:
	rm -f data/negbiodb_depmap.db
	@echo "GE database removed."

ge-test: setup
	uv run pytest tests/test_ge_db.py tests/test_ge_features.py tests/test_etl_depmap.py tests/test_etl_rnai.py tests/test_ge_export.py -v