zoty

Lightweight Zotero MCP server for AI agents.

What it does

MCP server that connects AI agents to your local Zotero library. Provides 8 tools: BM25-ranked search over titles, abstracts, and indexed attachment full text, within-item passage search, collection browsing, item lookup, BibTeX plus formatted citation export for item keys returned by search, and paper ingestion by arXiv ID or DOI with automatic PDF attachment.

Requirements

• Python 3.10+
• Zotero desktop running (Zotero 8 is the default target; Zotero 7 is also supported)
• Zotero local API enabled: Zotero Settings > Advanced > Config Editor > set extensions.zotero.httpServer.localAPI.enabled to true
• Zoty Bridge plugin installed (for PDF attachment and collection assignment)

Add to Your Agent

Claude Code

Add from the command line:

claude mcp add zoty -- uvx zoty

Add to your .mcp.json or ~/.claude/settings.json:

{
  "mcpServers": {
    "zoty": {
      "command": "uvx",
      "args": ["zoty"]
    }
  }
}

Codex

Add from the command line:

codex mcp add zoty -- uvx zoty

Add to your ~/.codex/config.toml:

[mcp_servers.zoty]
command = "uvx"
args = ["zoty"]

Installation

Requires uv.

Run without installing (recommended for MCP setups):

uvx zoty

Install persistently:

uv tool install zoty

Upgrade an installed copy:

uv tool upgrade zoty

If you run zoty with uvx instead of installing it, refresh to the latest published version with:

uvx --refresh zoty

From a local checkout:

uv run zoty

# Or install from source as a tool
uv tool install .

PDF Reading Advice for Agents

For best results when coding agents open attachment filepaths from zoty, make sure poppler and the associated Poppler utilities are installed on the machine. In practice this usually means tools like pdftotext, pdfinfo, and pdftoppm are available on PATH.

This is especially important for Claude Code, which uses these utilities to read PDF pages efficiently. Without them, agents may still be able to open the PDF files themselves, but page extraction tends to be slower and less reliable.

Typical installs:

# macOS
brew install poppler

# Ubuntu / Debian
sudo apt-get install poppler-utils

Zoty Bridge Plugin

A tiny Zotero 7/8 plugin that lets zoty execute JavaScript inside Zotero's privileged context. This is needed for operations that can't go through the REST API: PDF attachment and collection assignment both require writing to Zotero's SQLite database, which locks out external processes. The bridge sidesteps this by running JS inside Zotero itself.

Install the plugin

1. Download zoty-bridge.xpi from releases, or build it yourself:

   make build

2. In Zotero: Tools > Add-ons > gear icon > Install Add-on From File > select the .xpi
3. Restart Zotero

The bridge runs an HTTP server on localhost:24119 when Zotero is open. No configuration needed.

Tools

Tool	Description
search_library	Find which items in your Zotero library match a keyword query, ranked by BM25 over title, abstract, and indexed attachment full text, with optional plain-text snippets, attachment counts, collection filtering, collection key/name pairs, and case-insensitive item type values like journalArticle, preprint, conferencePaper, book, bookSection, thesis, report, and webpage
search_within_item	Find which passages within one or more known items match a keyword query, using search_library results to drill into a specific paper or compare several papers; top-level item summaries carry parent titles, and per-match parent key is only repeated for multi-item ranking
list_collections	List all collections with keys, names, and item counts
list_collection_items	List items in a specific collection, including collection key/name pairs on each item
get_item	Full metadata for a single item_key or batch item_keys; use the key field from search_library, list_collection_items, or get_recent_items results. Single-key requests keep the detailed item payload, while batch requests return compact item records with items plus optional per-item errors
get_bibtex_and_citation_for_items	BibTeX plus formatted citation and bibliography text for a single item_key or batch item_keys; use the key field from search_library, list_collection_items, or get_recent_items results. Both can be combined and at least one must be provided
get_recent_items	Recently added items, sorted by date, with collection key/name pairs on each item
add_paper	Add a paper by arXiv ID or DOI with automatic PDF download and collection-scoped duplicate prevention

Attachment payloads include linkMode as a descriptive string (imported_file, imported_url, linked_file, or linked_url) instead of Zotero's internal numeric codes.

How it works

Read operations still use pyzotero for collection/item APIs, but search now runs off a persistent sidecar index under ~/.cache/zoty/fulltext-index. zoty reads Zotero metadata from zotero.sqlite in immutable mode, reuses Zotero's extracted attachment text caches (.zotero-ft-cache) for PDF/EPUB/HTML full text, chunks that text locally, and rebuilds immutable BM25 snapshots in the background. At startup zoty loads the active snapshot synchronously if one exists, then queues a refresh when Zotero content changed.

Write operations use the Zotero connector endpoint (/connector/saveItems) to create metadata items. PDF attachment and collection assignment go through the zoty-bridge plugin, which executes JavaScript in Zotero's privileged context. The same bridge is used as a thin control plane to ask Zotero to generate missing full-text caches when needed; zoty does not add plugin-owned tables to zotero.sqlite or transfer raw attachment text through the bridge. This two-path design exists because Zotero's SQLite database uses exclusive locking -- external processes can read it (immutable mode) but not write to it while Zotero is running.

arXiv traffic is throttled internally to respect arXiv's access policy. Concurrent add_paper calls queue transparently: metadata requests serialize with a 3-second gap, and arXiv PDF downloads are rate-limited separately.

Development

make build   # build zotero-plugin/dist/zoty-bridge.xpi
make test    # run Python unit tests

License

MIT

Rate Limiting Across Sessions

zoty rate-limits arXiv traffic inside the running MCP server process. If several add_paper calls reach the same server at once, zoty queues them and drains metadata requests at arXiv-safe speed.

That limiter is not shared across separate zoty processes. If you start one zoty instance per agent, session, or editor window, each process will enforce its own limit and the combined request rate can still exceed arXiv policy.

If you expect multiple sessions to pull papers at the same time, start one long-lived zoty server and point all clients at that same instance.

Start one shared local server:

zoty --transport streamable-http --host 127.0.0.1 --port 8000

The shared MCP endpoint will be:

http://127.0.0.1:8000/mcp

If you want a different endpoint path:

zoty \
  --transport streamable-http \
  --host 127.0.0.1 \
  --port 8000 \
  --streamable-http-path /zoty-mcp

Then point every client at the same URL:

http://127.0.0.1:8000/zoty-mcp

For clients that support remote MCP servers by URL, the config should look like this:

{
  "mcpServers": {
    "zoty": {
      "url": "http://127.0.0.1:8000/mcp"
    }
  }
}

Avoid this pattern when multiple sessions may import papers in parallel, because it starts a separate zoty process per client:

{
  "mcpServers": {
    "zoty": {
      "command": "zoty"
    }
  }
}

Recommended boot sequence:

1. Boot Zotero and make sure the Zotero connector and zoty-bridge plugin are available.
2. Start one shared zoty server with --transport streamable-http.
3. Configure each agent or MCP client to connect to that existing server URL instead of launching its own copy.
4. Let the shared server serialize arXiv metadata lookups and rate-limit arXiv PDF downloads for everyone.

This keeps the agent-side behavior simple: tool calls may take a bit longer under load, but they will queue naturally instead of hammering export.arxiv.org.