zot — A Zotero CLI for Any AI Agent

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zotero-cli is a Zotero CLI for any AI agent.

• Reads — direct local SQLite, zero-config, offline, millisecond response

• Writes — safe via Zotero Web API, Zotero stays in sync

• PDF + ranked search — extract full text with caching; index-free ranked retrieval scored with FTS5 bm25 against Zotero 10's own full-text index (fulltext.sqlite), library-wide or scoped to a collection

• Agent-native — stable JSON envelope, typed exit codes, zot schema, --dry-run, --idempotency-key, NDJSON streaming

• MCP server — exposes 39 tools to Claude Desktop / LM Studio / Cursor via zot mcp serve

You never need to learn these commands. Install the bundled skill once, and the AI does the rest: ask in natural language — "summarize this collection", "what have I read about X?", "organize these papers" — and the skill maps each request to the right zot calls, chains multi-step workflows, and writes per-paper summaries for you. The commands in this README are what happens under the hood, not what you have to type. → Install the skill

Architecture

Related MCP server: zotero-mcp

Install

uv tool install zotero-cli-ai      # recommended
pipx install zotero-cli-ai         # or
pip install zotero-cli-ai          # or

Note: the PyPI package is zotero-cli-ai (zotero-cli is an unrelated older project); the installed command is zot.

60-second quickstart

# Reads work out of the box — no API key, Zotero data dir auto-detected
zot search "transformer attention"
zot read ABC123
zot export ABC123                  # BibTeX

# Writes need a Web API key (https://www.zotero.org/settings/keys)
zot config init
zot add --doi "10.1038/s41586-023-06139-9"

One install, then just talk to your AI (Claude Code or any skill-aware agent):

cp -r skill/zotero-cli ~/.claude/skills/

Make it yours. The skill is plain Markdown — edit your installed copy or write your own skill on top of it: swap in your own workflows (skill/zotero-cli/references/workflows.md) and adapt the per-type summary templates to your discipline (skill/zotero-cli/references/summary-templates.md). Everything the AI does is readable, modifiable text; nothing is hidden in a binary.

When stdout is not a TTY, zot automatically emits a stable JSON envelope so agents never need --json:

{ "ok": true, "data": { ... }, "meta": { "schema_version": "1.11.0", "cli_version": "0.14.0", "request_id": "..." } }

Workflow: topic → collection → summary & QA

You never run any of this by hand. With the skill installed, describe the goal in natural language and the AI drives these commands for you. They are documented here so you can see — or run manually, if you prefer — what happens under the hood.

From a keyword or topic to a curated collection with grounded summaries and cited Q&A:

# 1. Collect literature — import by DOI list, or rank what the library already has
zot add --from-file dois.txt                            # Crossref-resolved metadata per DOI
zot search "T cell metabolic reprogramming" --ranked    # or score what is already in the library

# 2. Build a collection and file the items into it
zot collection create "T-cell metabolism"               # returns the collection key
zot collection move ITEMKEY COLLECTIONKEY               # repeat per item

# 3. Summary — one item, or export abstracts for triage
zot summarize ITEMKEY                                   # structured summary of one item
zot summarize-all > abstracts.json                      # key + title + abstract, library-wide

# 4. QA scoped to the collection
zot search "checkpoint resistance" --ranked --collection "T-cell metabolism"
zot ask "which studies report exhausted T cell states?" --collection "T-cell metabolism"

zot ask runs ranked retrieval over the collection and returns a citation-keyed evidence pack; your agent (Claude Code, Codex, Gemini CLI, ...) synthesizes the grounded answer. In Claude Code, the bundled skill runs this whole pipeline from a single natural-language request.

Documentation

Full docs live at https://agents365-ai.github.io/zotero-cli-ai/.

Why zotero-cli? The only actively maintained Python CLI that reads Zotero's local SQLite database directly, with a clean read/write split: SQLite for fast offline reads, Web API for safe writes that Zotero stays aware of. See the comparison page for a feature-by-feature breakdown against similar tools.

Support

If zot helps you, consider supporting the author:

Author

Agents365-ai

• Bilibili: https://space.bilibili.com/441831884

• GitHub: https://github.com/Agents365-ai

License

zotero-cli is dual-licensed:

• Open source: GNU AGPL-3.0-or-later (see LICENSE).

• Commercial: a separate commercial license is available for use in closed-source or commercial products without the AGPL's copyleft obligations (see LICENSE-COMMERCIAL).

Contributions are accepted under the project's Developer Certificate of Origin.