Integration Notes (Notebook → Modules)

DB queries live in src/poppy/io/db.py and are configured in configs/ontology.yaml.
CSV loaders live in src/poppy/io/csvs.py and are configured in configs/ontology.yaml.
rdflib enrichment functions live in src/poppy/ontology/enrich.py.
The orchestrated build is src/poppy/ontology/pipeline.py with CLI in scripts/build_ontology.py.

CSV/SQL Mappings

CMAUP:
- CMAUPv2.0_download_Plant_Ingredient_Associations_allIngredients.txt → rename Plant_ID→plant_id, Ingredient_ID→compound_id
- CMAUPv2.0_download_Plants.txt → rename Plant_ID→plant_id, Scientific_Name→scientific_name
- CMAUPv2.0_download_Ingredient_Target_Associations_ActivityValues_References.txt → Ingredient_ID→compound_id, Target_ID→gene_id
NPASS: NPASSv1.0_download_naturalProducts_targetInfo.txt → NP_ID→compound_id, Target→gene_id
ChEMBL mechanisms: ChEMBL_drug_mechanisms.csv → molecule_chembl_id→compound_id, target_chembl_id→gene_id
COCONUT (SQL examples):
- SELECT id AS plant_id, name AS scientific_name FROM coconut.organisms;
- A compound join across coconut.properties, coconut.entries, coconut.structures, coconut.organism_map

python -m venv .venv && source .venv/bin/activate
pip install -e ".[dev]"
python scripts/build_ontology.py --config configs/ontology.yaml