zotero-library-mcp 0.8.1

MCP server for searching, reading, annotating, and managing Zotero libraries

zotero-library-mcp

An MCP server that lets Claude, Codex, and ChatGPT add papers and books to your Zotero library by DOI, arXiv ID, or ISBN — and manage your collections, tags, and items.

The server supports both MCP transports used by these clients:

• stdio (default) for Claude Code, Claude Desktop, Codex CLI/IDE, and the ChatGPT desktop app
• Streamable HTTP for a hosted ChatGPT app or any remote MCP client

Tools

Adding papers

• add_paper_by_doi — Resolve a DOI via CrossRef and add the paper to Zotero (with duplicate detection)
• add_papers_by_dois — Batch-add up to 50 papers at once
• add_paper_by_arxiv_id — Add a preprint by arXiv ID (uses DOI when available, falls back to arXiv metadata)
• add_item_from_metadata — Create any supported Zotero item type from validated manual metadata

Adding books

• add_book_by_isbn — Resolve an ISBN via Open Library and add the book to Zotero (with duplicate detection)

Searching & browsing

• search_library — Search your Zotero library by title, author, tag, etc. (falls back to fuzzy matching when the exact search returns no results)
• get_item_details — View full metadata for any item
• get_recent_items — List recently added items
• get_unfiled_items — Get items not in any collection
• search_fulltext — Search Zotero metadata and indexed full text
• find_duplicates — Find duplicate items by DOI, ISBN, or normalized title
• list_attachments — List every attachment and choose a specific PDF key
• health_check — Verify library credentials, access, and storage configuration

Reading & annotating

• get_item_fulltext — Return bounded plain text from Zotero's index or a PDF, without leaking temporary paths
• get_bibtex — Read-only BibTeX/BibLaTeX export for items, a collection, or the full library
• save_bibtex — Save an export to an authorized local path
• get_annotations — List all highlights and annotations on a paper's PDF
• create_annotation — Highlight a text passage in a PDF (searches for the exact text, creates a visible highlight in Zotero's reader, and returns a preview image for verification). Smart overlap handling: exact duplicates update the existing comment; sub-passages get a contrasting highlight color automatically.
• add_note — Add a note to an item
• list_notes, update_note, delete_note — Manage existing notes
• update_annotation, delete_annotation — Edit or remove annotations

File attachments

• attach_file — Attach a local file over stdio or a ChatGPT file input over HTTP
• download_pdf — Return a remote-safe MCP file resource
• save_pdf — Save a PDF to an authorized local path

Collections

• list_collections — List all collections (with nesting)
• create_collection — Create a new collection (optionally nested under a parent)
• get_collection_items — Browse items in a collection
• add_to_collection — Add an existing item to a collection
• remove_from_collection — Remove an item from a collection (keeps it in your library)
• rename_collection, move_collection — Reorganize collections

Tags

• list_tags — List all tags in your library
• add_tags — Add one or more tags to an item (with optional color)
• remove_tags — Remove tags from an item
• delete_tags — Delete tags from the entire library
• set_tag_color — Assign a color to a tag (appears in Zotero's tag selector)
• rename_tag — Rename a tag across all items in your library
• unset_tag_color — Remove a tag color without deleting the tag

Verification

• verify_items — Re-check recent items against CrossRef to catch bad DOIs or title mismatches

Deleting

• delete_item — Permanently delete an item from your library
• delete_collection — Permanently delete a collection
• trash_item, restore_item — Prefer reversible trash operations for ordinary cleanup

The server also exposes the standard read-only search and fetch tool shapes used by ChatGPT company knowledge and deep research.

Prerequisites

1. A Zotero account
2. A Zotero API key with write permissions: https://www.zotero.org/settings/keys
3. Your Zotero library ID (shown on the same page, or in your profile URL)
4. uv installed

Quick Start

Codex and the ChatGPT desktop app

Codex and the ChatGPT desktop app share MCP configuration on the same Codex host. Add the server once:

codex mcp add zotero \
  --env ZOTERO_LIBRARY_ID=your_library_id \
  --env ZOTERO_API_KEY=your_api_key \
  -- uvx --from git+https://github.com/RaulSimpetru/zotero-library-mcp zotero-mcp

Then restart Codex or the ChatGPT desktop app. In Codex, use /mcp to confirm that zotero is connected. In ChatGPT desktop, open Settings → MCP servers to view the same server.

For WebDAV storage, add the three ZOTERO_WEBDAV_* values shown in the WebDAV example. If the desktop app cannot find uvx, replace it with the full path returned by which uvx.

You can also configure the server directly in ~/.codex/config.toml:

[mcp_servers.zotero]
command = "/full/path/to/uvx"
args = ["--from", "git+https://github.com/RaulSimpetru/zotero-library-mcp", "zotero-mcp"]
env_vars = ["ZOTERO_LIBRARY_ID", "ZOTERO_API_KEY", "ZOTERO_LIBRARY_TYPE", "CROSSREF_MAILTO", "ZOTERO_WEBDAV_URL", "ZOTERO_WEBDAV_USER", "ZOTERO_WEBDAV_PASSWORD"]
startup_timeout_sec = 30
tool_timeout_sec = 120

With env_vars, start Codex/ChatGPT from an environment that contains those variables. Use [mcp_servers.zotero.env] instead if you intentionally want to store their values in the config file.

Claude Code

claude mcp add zotero \
  -e ZOTERO_LIBRARY_ID=your_library_id \
  -e ZOTERO_API_KEY=your_api_key \
  -- uvx --from git+https://github.com/RaulSimpetru/zotero-library-mcp zotero-mcp

WebDAV setup

To use WebDAV file storage (e.g. Synology, Nextcloud), include the WebDAV variables:

claude mcp add zotero \
  -e ZOTERO_LIBRARY_ID=your_library_id \
  -e ZOTERO_API_KEY=your_api_key \
  -e ZOTERO_WEBDAV_URL=https://your-webdav-server.com \
  -e ZOTERO_WEBDAV_USER=your_username \
  -e ZOTERO_WEBDAV_PASSWORD=your_password \
  -- uvx --from git+https://github.com/RaulSimpetru/zotero-library-mcp zotero-mcp

Claude Desktop

Add this to your claude_desktop_config.json:

{
  "mcpServers": {
    "zotero": {
      "command": "/full/path/to/uvx",
      "args": ["--from", "git+https://github.com/RaulSimpetru/zotero-library-mcp", "zotero-mcp"],
      "env": {
        "ZOTERO_LIBRARY_ID": "your_library_id",
        "ZOTERO_API_KEY": "your_api_key",
        "ZOTERO_WEBDAV_URL": "https://your-webdav-server.com",
        "ZOTERO_WEBDAV_USER": "your_username",
        "ZOTERO_WEBDAV_PASSWORD": "your_password"
      }
    }
  }
}

Note: Claude Desktop doesn't inherit your shell's PATH, so you need the full path to uvx. Find it with which uvx in your terminal.

ChatGPT on the web (Apps SDK / developer mode)

ChatGPT web connects to an HTTPS Streamable HTTP endpoint. Start the server locally with the HTTP transport, then make it reachable through Secure MCP Tunnel or another authenticated HTTPS deployment:

ZOTERO_LIBRARY_ID=your_id ZOTERO_API_KEY=your_key \
  uvx --from git+https://github.com/RaulSimpetru/zotero-library-mcp zotero-mcp \
  --transport streamable-http \
  --host 127.0.0.1 \
  --port 8000 \
  --allowed-host your-tunnel.example.com

The MCP endpoint is https://your-tunnel.example.com/mcp. Enable developer mode in ChatGPT, create a developer-mode app, and enter that URL as the MCP server URL. See OpenAI's Connect from ChatGPT guide for the current UI flow.

Security: The safest personal setup is OpenAI Secure MCP Tunnel with the MCP server bound to loopback. HTTP mode disables all server-path reads and writes by default. attach_file accepts ChatGPT's authorized file object, while download_pdf returns an opaque MCP resource link. Safety annotations are approval hints, not an authorization boundary.

For a public single-library deployment, configure an external OAuth 2.1 identity provider. The server validates JWT access tokens against its JWKS endpoint:

export ZOTERO_MCP_OAUTH_ISSUER=https://auth.example.com
export ZOTERO_MCP_OAUTH_RESOURCE=https://zotero.example.com
export ZOTERO_MCP_OAUTH_JWKS_URL=https://auth.example.com/.well-known/jwks.json
export ZOTERO_MCP_OAUTH_SCOPES=zotero:read,zotero:write

The authorization server must publish OAuth/OIDC discovery metadata, support the MCP OAuth 2.1 flow with PKCE, issue tokens for ZOTERO_MCP_OAUTH_RESOURCE, and include the configured scopes. See OpenAI's authentication guide. For testing behind an already authenticated gateway only, --allow-unauthenticated-http explicitly acknowledges an unauthenticated non-loopback listener.

This process still uses one server-side Zotero library key. A true multi-user service must map the verified OAuth identity to separate Zotero credentials and enforce per-user authorization; that deployment architecture is intentionally outside this personal-server package.

If an HTTP deployment genuinely needs server paths, enable them only inside confined roots:

zotero-mcp --transport streamable-http \
  --allow-server-files \
  --file-root /srv/zotero-mcp/exports

HTTP launch settings can also be supplied as environment variables:

CLI option	Environment variable	Default
--transport	ZOTERO_MCP_TRANSPORT	stdio
--host	ZOTERO_MCP_HOST	127.0.0.1
--port	ZOTERO_MCP_PORT or PORT	8000
--http-path	ZOTERO_MCP_HTTP_PATH	/mcp
--allowed-host	ZOTERO_MCP_ALLOWED_HOSTS (comma-separated)	local hosts
--allowed-origin	ZOTERO_MCP_ALLOWED_ORIGINS (comma-separated)	local origins
--stateless-http	ZOTERO_MCP_STATELESS_HTTP	false
--allow-unauthenticated-http	ZOTERO_MCP_ALLOW_UNAUTHENTICATED_HTTP	false
--allow-server-files	ZOTERO_MCP_ALLOW_SERVER_FILES	false in HTTP mode
--file-root	ZOTERO_MCP_FILE_ROOTS (comma-separated)	none

Run standalone

ZOTERO_LIBRARY_ID=your_id ZOTERO_API_KEY=your_key \
  uvx --from git+https://github.com/RaulSimpetru/zotero-library-mcp zotero-mcp

Environment Variables

Variable	Required	Description
ZOTERO_LIBRARY_ID	Yes	Your Zotero user or group library ID
ZOTERO_API_KEY	Yes	API key with read/write permissions
ZOTERO_LIBRARY_TYPE	No	user (default) or group
CROSSREF_MAILTO	No	Your email for CrossRef polite pool (faster API access)
UNPAYWALL_EMAIL	No	Contact email for open-access PDF lookup (defaults to CROSSREF_MAILTO)
ZOTERO_WEBDAV_URL	No	WebDAV URL for file storage (e.g. https://dav.example.com)
ZOTERO_WEBDAV_USER	No	WebDAV username
ZOTERO_WEBDAV_PASSWORD	No	WebDAV password
ZOTERO_MCP_OAUTH_ISSUER	No	External OAuth/OIDC issuer URL for protected HTTP deployments
ZOTERO_MCP_OAUTH_RESOURCE	No	Canonical HTTPS MCP resource/audience URL
ZOTERO_MCP_OAUTH_JWKS_URL	No	JWKS URL used to verify JWT access tokens
ZOTERO_MCP_OAUTH_SCOPES	No	Comma-separated required scopes (defaults to read and write)
ZOTERO_MCP_FILE_ROOTS	No	Comma-separated allowed roots when HTTP server paths are enabled

Note: If all three ZOTERO_WEBDAV_* variables are set, file attachments are uploaded to your WebDAV server instead of Zotero's built-in storage. The server automatically appends /zotero to the base URL, matching Zotero Desktop's behavior.

Upgrading to 0.8

Two path-writing operations were split from their read-only counterparts so remote clients can apply correct safety approvals:

• get_bibtex(save_path=...) is now save_bibtex(save_path=...); get_bibtex only returns data.
• download_pdf(save_path=...) is now save_pdf(save_path=...); download_pdf returns an opaque MCP resource link.

Existing read-only calls to get_bibtex and download_pdf continue to work.

0.8.1

• PDF and annotation-preview resources now keep their precise MIME type when read by clients.
• PDF downloads report progress and return a clear WebDAV timeout error.
• health_check reports API-key write permission without modifying the library.
• Server instructions are shorter, reducing repeated client context usage.

How it works

1. You provide a DOI, arXiv ID, or ISBN
2. The server queries the appropriate API to get full metadata:
   • DOI → CrossRef API
   • arXiv ID → arXiv API (with CrossRef fallback when a DOI exists)
   • ISBN → Open Library API
3. Metadata is mapped to Zotero's item format (title, authors, journal/publisher, date, etc.)
4. The item is created in your Zotero library via the Zotero Web API

License

MIT

mcp-name: io.github.RaulSimpetru/zotero-library-mcp