POPPy is a reproducible pipeline for building a phytotherapy ontology / knowledge graph.
It ingests CMAUP/ChEMBL/SQL sources, validates plants (NCBI/POWO), enriches compounds
(SMILES, MACCS via RDKit), and exports OWL/RDF (TTL/RDF/XML). A static site in web/
publishes build stats and downloads.
See
INTEGRATION_NOTES.mdfor a deeper tour of the structure and CSV/SQL mappings.
# 1) Create env
python -m venv .venv && source .venv/bin/activate
# 2) Install (dev tools included: ruff/black/pytest)
pip install -e ".[dev]"
# 3) Build ontology from config (see configs/ontology.yaml)
python scripts/build_ontology.py --config configs/ontology.yaml
---
## Build commands (Makefile)
Run these from the repo root:
```bash
make -C build ontology # build ontology via configs/ontology.yaml
make -C build figures # optional example figure(s) -> docs/figures
make -C build web-data # copy processed TTL + stats into web/data/
make -C build all # ontology + figures + web-data
- [Ontology data ingest guide](docs/recipes/ontology-data-ingest.md)
- [Recipes index](docs/recipes/README.md)
- [Ontology data ingest guide](docs/recipes/ontology-data-ingest.md)