zotero-cli

Zotero CLI Skill for Claude Code

Two complementary tools for Zotero:

Tool	Purpose	Speed
zot	CRUD, reading, export, PDF, stats — local SQLite	Instant
rak	Semantic/hybrid search, Q&A — vector + BM25	~2s

Always use --json when processing results programmatically.

Routing Rules

User Intent	Command	Why
Search by title/author/tag	zot --json search "transformer"	Fast metadata match
Search paper content / fulltext	rak --json search "query" --hybrid	zot fulltext is word-level LIKE only; rak has BM25 + vector
Semantic search ("papers about cell fate")	rak --json search "cell fate" --hybrid	Needs semantic understanding
Similarity search ("papers like this one")	rak --json similar KEY	Dedicated command, uses embeddings
Keyword-only search (no model needed)	rak --json search "query" --bm25	Fast, no embedding model required
Read/view a paper	zot --json read KEY	Direct lookup
Export citation	zot export KEY	Local data
Add/delete/tag/note	zot ...	All write ops
PDF full text extraction	zot --json pdf KEY	Local file access
Library stats	zot --json stats	Local aggregation
Open PDF/URL	zot open KEY or zot open --url KEY	System open
Ask question about papers	rak ask "question" --hybrid	Needs RAG pipeline

Rule of thumb: Use zot for metadata lookup and all CRUD. Use rak for any search that involves paper content, semantic meaning, or Q&A. When in doubt about search, prefer rak --hybrid — it covers both keyword and semantic matching.

If rak is not installed, fall back to zot for everything. Check with which rak.

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zot — Zotero CLI (Core Tool)

Search & Browse

zot --json search "transformer attention"
zot --json search "BERT" --collection "NLP"
zot --json list --collection "Machine Learning" --limit 10
zot --json read ITEMKEY
zot --json relate ITEMKEY

Notes & Tags

zot --json note ITEMKEY
zot note ITEMKEY --add "Key finding: ..."
zot --json tag ITEMKEY
zot tag ITEMKEY --add "important"
zot tag ITEMKEY --remove "to-read"

Citation Export

zot export ITEMKEY                    # BibTeX
zot export ITEMKEY --format csl-json  # CSL-JSON
zot export ITEMKEY --format json      # Raw JSON

Item Management (Write Ops)

zot add --doi "10.1038/s41586-023-06139-9"
zot add --url "https://arxiv.org/abs/2301.00001"
zot --no-interaction delete ITEMKEY

Collections

zot --json collection list
zot --json collection items COLLECTIONKEY
zot collection create "New Project"
zot collection move ITEMKEY COLLECTIONKEY
zot collection rename COLLECTIONKEY "New Name"
zot collection delete COLLECTIONKEY

PDF & Summarization

zot --json pdf ITEMKEY
zot pdf ITEMKEY --pages 1-5
zot --json summarize ITEMKEY
zot summarize-all

Utilities

zot --json stats                     # Library statistics
zot open ITEMKEY                     # Open PDF in system viewer
zot open --url ITEMKEY               # Open URL/DOI in browser

Configuration

zot config init
zot config profile list
zot config profile set lab
zot config cache stats
zot config cache clear

Global Flags

Flag	Purpose
--json	JSON output (ALWAYS use for programmatic processing)
--limit N	Limit results (default: 50)
--detail minimal	Only key/title/authors/year — saves tokens
--detail full	Include extra fields
--no-interaction	Suppress prompts (for automation)
--profile NAME	Use a specific config profile
--verbose	Verbose/debug output

---

rak — Zotero RAG Search (Semantic Search)

Prerequisites

# Check if rak is available
which rak

# Index must be built before first search
rak index

Search

# Hybrid search (recommended — vector + BM25)
rak --json search "cell fate determination" --hybrid

# Pure keyword search (no embedding model needed)
rak --json search "CRISPR knockout" --bm25

# With filters
rak --json search "CRISPR" --hybrid --limit 5 --collection "Methods" --tag "review"

# Find similar papers by item key
rak --json similar K853PGUG --limit 5

Q&A (RAG)

# Single question
rak ask "What are the main clustering methods for single-cell?" --hybrid

# Interactive chat
rak chat --hybrid

Export Search Results

rak export "single cell" --format csv
rak export "CRISPR" --format bibtex --output refs.bib

Index Management

rak index              # Incremental index (new items only)
rak index --full       # Full rebuild
rak reindex            # Clear + rebuild (useful after changing pdf_provider)
rak status             # Show index status
rak clear --yes        # Delete all indexes

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Workflow Patterns

Pattern 1: Find and Read a Paper

# Step 1: Search (use zot for keyword, rak for semantic)
zot --json search "single cell RNA sequencing"

# Step 2: Read details
zot --json read K853PGUG

# Step 3: Full PDF text if needed
zot --json pdf K853PGUG

Pattern 2: Semantic Literature Discovery

# Step 1: Semantic search with rak
rak --json search "mechanisms of drug resistance in cancer" --hybrid --limit 10

# Step 2: Read promising results with zot
zot --json --detail full read KEY1
zot --json pdf KEY1 --pages 1-5

Pattern 3: AI-Powered Library Reorganization

# Step 1: Export all abstracts
zot --json summarize-all > abstracts.json

# Step 2: AI analyzes and generates classification plan
# Step 3: Create collections and move items
zot collection create "Category A"
zot collection move ITEMKEY COLLECTIONKEY

Pattern 4: Q&A Over Library

# Ask a question — rak retrieves relevant papers + generates answer
rak ask "Compare attention mechanisms in transformer variants" --hybrid --context 10

Important Notes

• zot read operations work offline with zero config
• zot write operations need API credentials via zot config init
• rak requires rak index before first search
• PDF cache — zot caches PDF extractions automatically
• Item keys are 8-character alphanumeric strings like K853PGUG
• After writes — Zotero desktop needs to sync, then rak index to update search index