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0db04e6 c0a7163 0db04e6 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | # RAG Knowledge Base
Drop reference documents here (`.md`, `.txt`, or `.pdf`). They are ingested by
`python -m src.rag.ingest` at Docker build time and surfaced to the orchestrator
agent via the `retrieve_context` tool. The container entrypoint also rebuilds
the index at startup when a mounted `data/` volume does not already contain
`data/processed/faiss_index/`.
## Recommended seed set
For a clinical-ML / NeuroBridge demo:
- **BBB / molecules**: Lipinski's Rule of Five (1997, 2001), Pajouhesh & Lenz
CNS multiparameter optimization (2005)
- **MRI / harmonization**: Fortin et al. ComBat for cortical thickness (2017),
Fortin et al. ComBat for diffusion (2018), Johnson et al. original ComBat
(2007, gene expression)
- **EEG / artifacts**: Hyvärinen ICA primer (1999), MNE-Python overview
(Gramfort 2013)
## Format notes
- PDFs work via `pypdf`. OCR-only PDFs (scanned images) won't extract text;
pre-OCR them first.
- Markdown is preferred — full text + headers chunk cleanly.
- Files are gitignored by default. Mount them via Docker volume in
production, or COPY them in via a sub-path before the `RUN` ingest line.
## Re-indexing
After adding/removing files, re-run:
python -m src.rag.ingest
This rewrites `data/processed/faiss_index/` from scratch (no incremental
update — the index is small enough to rebuild in seconds).
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