Zotero MCP — Your Library

Access Zotero libraries (local or web API), retrieve items/notes/attachments, and run semantic search.

Codex CLI Notes

• •Stdio transport (codex-cli via dotter) via $HOME/mcp/mcp-zotero-matlab-tools/bin/zotero-mcp serve --transport stdio (exposed as zotero-mcp in PATH).
• •Local: ZOTERO_LOCAL=true with Zotero desktop running.
• •Web API: set ZOTERO_API_KEY, ZOTERO_LIBRARY_ID, ZOTERO_LIBRARY_TYPE.
• •Semantic (optional): OPENAI_API_KEY or GEMINI_API_KEY.

Tools and When to Call (selection)

• •Search: zotero_search_items(query, qmode?, item_type?, limit?, tag?), zotero_search_by_tag(tag[], item_type?, limit?), zotero_semantic_search(query, filters?, limit?)
• •Items: zotero_get_item_metadata(item_key, include_abstract?, format?), zotero_get_item_fulltext(item_key)
• •Collections: zotero_get_collections(limit?), zotero_get_collection_items(collection_key, limit?)
• •Children/Notes/Annotations: zotero_get_item_children(item_key), zotero_get_notes(item_key?), zotero_search_notes(query), zotero_get_annotations(item_key?)
• •Batch/Recent/Tags: zotero_batch_update_tags(add_tags?, remove_tags?, query, limit?), zotero_get_recent(limit?), zotero_get_tags(limit?)
• •Advanced: zotero_advanced_search(conditions[], join_mode?, sort_by?, sort_direction?, limit?), DB status: zotero_get_search_database_status, update: zotero_update_search_database(force_rebuild?, limit?)

Examples (codex-cli)

• •Items by tag: zotero_search_by_tag {"tag":["RAG||Retrieval","-draft"],"limit":20}
• •Full text: zotero_get_item_fulltext {"item_key":"ABCD1234"}

Security

• •Local mode accesses your local Zotero; avoid exposing library content unintentionally.
• •Web API mode requires ZOTERO_API_KEY; keep it in environment variables.
• •Semantic search may call external embedding providers; set keys (OPENAI_API_KEY/GEMINI_API_KEY) securely.