paper-rag

paper-ragRAG over your PubMed library

Hybrid dense + BM25 retrieval over ingested papers, packaged as a Claude Code plugin.

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Commands
Workflows
paper-rag

Auto-resolving ingest

Ingest by PMID, URL, or local file. PMIDs resolve PMC open-access full text automatically, falling back to metadata-only.

Reproducible PubMed search

/paper-rag:pubmed-search compiles a deterministic Boolean query from structured concepts, validated against a local MeSH index, before you ingest anything.

Hybrid retrieval

Dense embeddings (Chroma) fused with BM25 lexical search via Reciprocal Rank Fusion, filterable with --where.

Cited answers

/paper-rag:ask writes a grounded answer with a BibTeX References block from your own library.

Where to go ​

Start hereGet StartedInstall the plugin, create a home, ingest your first paper, and ask it a question.VisualWorkflowsDiagrams of ingest, hybrid retrieval, cite/mine, and the on-disk home layout.ReferenceCommandsAll `/paper-rag:*` commands: syntax, flags, and a worked example each.ModelConceptsHomes, doc_key identity, chunk types, embedding models, and tags.

Design commitments ​

RuleWhat it means for you
doc_key is identityEvery paper's key is its PMID, or a sha256 of the file if there's none — the same key tags its directory, every Chroma chunk, and its BM25 entries, so re-ingest is delete-then-reinsert by key, not by search.
Index stays in syncAny ingest that touches Chroma triggers a full BM25 rebuild for that collection — the two never drift apart.
Metadata never touches the indexcite and mine read metadata.json straight off disk; neither ever opens Chroma or BM25.
Models don't mixEach embedding model gets its own Chroma collection and BM25 file — switching models means a fresh index, never a blend.
Homes are fully separateA home's chroma/, bm25/, papers/, and config.json never cross into another home.
Answers are groundedquery.py only ranks and returns JSON — it never writes prose. Claude cites every claim by PMID and appends real BibTeX from your own library.

See Concepts for the reasoning behind each of these.