zotero-mcp

MCP server that lets AI assistants search, create, organize, and cite from a Zotero library. Produces Word documents with live Zotero field codes. Checks for retractions, finds duplicates, maps citation graphs, and builds a knowledge graph with paper recommendations.

Quickstart

Add to your MCP client config (Claude Code, Claude Desktop, etc.):

{
  "zotero": {
    "command": "uvx",
    "args": ["zotero-mcp-plus"],
    "env": {
      "ZOTERO_API_KEY": "your-api-key",
      "ZOTERO_USER_ID": "your-user-id"
    }
  }
}

Get your API key and user ID at zotero.org/settings/keys.

OPENALEX_API_KEY is also required for the analysis tools (check_retractions, get_citation_graph, check_published_versions). To enable those plus the knowledge graph and full-text search tools, add the extras and an OpenAlex key:

{
  "zotero": {
    "command": "uvx",
    "args": ["zotero-mcp-plus[graph,fulltext]"],
    "env": {
      "ZOTERO_API_KEY": "your-api-key",
      "ZOTERO_USER_ID": "your-user-id",
      "OPENALEX_API_KEY": "your-openalex-key"
    }
  }
}

Free OpenAlex key at openalex.org/users/me.

Operating modes

All 36 tools work with just API credentials — Zotero desktop does not need to be running. Two diagnostic tools (check_ssl_health, audit_local_keys) require no credentials at all.

Mode	What it provides	Requirements
Cloud (primary)	All reads, writes, citations, attachments, analysis, fulltext, entities	ZOTERO_API_KEY + ZOTERO_USER_ID env vars
Local (optional)	Faster reads via Zotero desktop's local API (no rate limits)	Zotero 7 desktop running with local API enabled

When Zotero desktop is running, reads automatically use the faster local API. When it is not, reads fall back to the Web API transparently.

Call server_status to check which modes are available.

Tools

Read tools

Tool	Description
server_status	Check which modes are available
search_items	Search library items by keyword
get_item	Fetch item metadata or BibTeX
get_collections	List all collections
get_collection_items	List items in a collection
get_notes	List child notes on an item
get_item_attachments	List attachments with availability status
get_pdf_content	Find best path to a paper's full text (PMCID, local PDF, or web download). Pass extract_text=true for inline text

Write tools

Tool	Description
create_item	Create item from DOI, PMID, or URL (with duplicate detection)
create_item_manual	Create item with manual metadata (with duplicate detection)
create_note	Attach a note to an item
create_collection	Create a collection
batch_organize	Bulk-add tags/collection to items
add_to_collection	Add item to a collection
update_item	Patch metadata fields
attach_pdf	Attach a local or auto-downloaded PDF
trash_items	Move items to trash (reversible)
empty_trash	Permanently delete all trashed items
manage_tags	List, remove, or rename tags library-wide (action="list|remove|rename")

Citation tools

Tool	Description
write_cited_document	Create new .docx with live Zotero citations
insert_citations	Insert citations into existing .docx

Analysis tools

Tool	Description
check_retractions	Check items for retractions, corrections, and errata via CrossRef + OpenAlex
find_duplicates	Scan library for duplicate items by DOI and title similarity
get_citation_graph	Get citing/referenced works via OpenAlex with in-library flags
check_published_versions	Check if preprints have been formally published; reports journal and in-library status

Knowledge graph tools

Requires the graph extra (uvx "zotero-mcp-plus[graph]" or pip install "zotero-mcp-plus[graph]") and OPENALEX_API_KEY env var.

Tool	Description
build_index	Build or update citation graph and/or fulltext index (type="graph|fulltext|both")
query_knowledge_graph	PageRank, clusters, bridge papers, shortest paths, neighborhood, timeline, topic evolution, citation velocity, trending
find_related_papers	Semantic Scholar recommendations from library seeds (like Connected Papers)
query_authors	Prolific/influential authors, co-author lookup, ego network, author clusters
export_knowledge_graph	Interactive HTML visualization (citations, authors, or full view) with D3.js

Full-text search tools

Requires the fulltext extra (uvx "zotero-mcp-plus[fulltext]" or pip install "zotero-mcp-plus[fulltext]").

Tool	Description
search_fulltext	Search indexed full text with BM25 ranking and highlighted snippets

Use build_index(type='fulltext') to extract text from library PDFs and build the FTS5 search index.

Entity extraction tools

Two-tool pattern: the MCP server provides abstracts, the calling LLM extracts entities, and stores them back.

Tool	Description
get_unextracted_abstracts	Get papers with abstracts not yet entity-extracted
store_entities	Persist typed entities (biomarker, drug, gene, etc.) extracted by the LLM
search_entities	Query entity index: by_name, by_type, paper_entities (by DOI), co_occurrence, shared_entities

Diagnostic tools

These two tools require no API credentials and can be used to debug setup problems.

Tool	Description
check_ssl_health	Diagnose Python SSL/TLS config — cert paths, CA count, env-var overrides, live HTTPS probes. Returns HEALTHY/DEGRADED/BROKEN verdict with remediation steps. Use when any tool reports CERTIFICATE_VERIFY_FAILED.
audit_local_keys	Scan local Zotero SQLite for item/collection keys containing characters (0, 1, O) that the Zotero sync server rejects, halting sync.

MCP Prompts

Pre-built multi-tool workflows that guide the AI through common tasks:

Prompt	Description
literature_audit	Check retractions, verify preprint publication status, scan for duplicates
build_and_explore	Build indexes and explore research landscape (influential papers, clusters, trends)
add_and_verify	Add a paper, check retractions, attach PDF, find related work
extract_entities	Extract biomedical entities from unprocessed abstracts and store them

Writing with live citations

Both document tools use [@ITEM_KEY] markers in content:

Gastric cancer screening reduces mortality [@ABC123]. Multiple studies
support this finding [@DEF456, @GHI789].

• write_cited_document creates a new .docx from markdown
• insert_citations modifies an existing .docx (preserves formatting, including tables)
• Citations are emitted as Vancouver-style superscript numbers
• A References section with a live Zotero bibliography field is appended

After opening in Word with the Zotero plugin: click Refresh to populate the bibliography and switch citation styles.

Architecture

┌─────────────┐  reads+writes  ┌──────────────────┐
│  MCP client │ ──────────────>│ Zotero Web API   │
│             │                │ api.zotero.org   │
│             │  reads (fast)  ├──────────────────┤
│             │ ─ ─ ─ ─ ─ ─ ─>│ Zotero Desktop   │
│             │    (optional)  │ localhost:23119  │
│             │   resolves     ├──────────────────┤
│             │ ──────────────>│ Translation Srv  │
│             │                │ PubMed/CrossRef  │
│             │   analysis     ├──────────────────┤
│             │ ──────────────>│ OpenAlex         │
│             │                │ CrossRef updates │
│             │  knowledge     ├──────────────────┤
│             │  graph + FTS5  │ SQLite + NetworkX│
│             │                │ (local cache)    │
│             │  related       ├──────────────────┤
│             │  papers        │ Semantic Scholar │
└─────────────┘                └──────────────────┘

Setup

1. Create a Zotero Web API key (required)

1. Go to zotero.org/settings/keys
2. Create a key with write access to your library
3. Copy the API key and note your User ID

2. Enable Zotero's local API (optional, for faster reads)

In Zotero Desktop: Settings > Advanced > General > enable Allow other applications on this computer to communicate with Zotero. This is optional — without it, all reads go through the Web API.

3. Install

Option A — uvx (recommended, no clone needed):

Install uv first if you don't have it: astral.sh/uv (one-line install on macOS/Linux). Then use zotero-mcp-plus for the base install or zotero-mcp-plus[graph,fulltext] for the full feature set (see Quickstart above). Your MCP client runs uvx directly — no separate install step.

Option B — local install:

git clone https://github.com/alisoroushmd/zotero-mcp.git
cd zotero-mcp
pip install -e ".[graph,fulltext]"

Then configure your MCP client to run python -m zotero_mcp.

4. Set up OpenAlex API key (required for analysis and knowledge graph tools)

OPENALEX_API_KEY is required for: check_retractions, get_citation_graph, check_published_versions, build_index(type='graph'), query_knowledge_graph, query_authors, and export_knowledge_graph. OpenAlex requires a free API key as of Feb 2026:

1. Register at openalex.org/users/me
2. Set OPENALEX_API_KEY in your MCP client config

5. Install knowledge graph support (optional)

With uvx (add to your MCP client config args):

zotero-mcp-plus[graph]

With pip (local install):

pip install "zotero-mcp-plus[graph]"

Adds networkx, numpy, and scipy for build_index(type='graph'), query_knowledge_graph, query_authors, and export_knowledge_graph. find_related_papers works without it (uses Semantic Scholar API directly).

Optionally set SEMANTIC_SCHOLAR_API_KEY for improved rate limits.

6. Install full-text search support (optional)

With uvx (add to your MCP client config args):

zotero-mcp-plus[fulltext]

With pip (local install):

pip install "zotero-mcp-plus[fulltext]"

Adds pypdf for extracting text from PDFs. Used by build_index(type='fulltext') to build a searchable FTS5 index. Without it, search_fulltext and build_index(type='fulltext') return an install prompt.

Environment variables

Variable	Required	Description
ZOTERO_API_KEY	Yes	Zotero Web API key — get at zotero.org/settings/keys
ZOTERO_USER_ID	Yes	Zotero user/group ID — same page as the API key
OPENALEX_API_KEY	For analysis/graph tools	Required for check_retractions, get_citation_graph, check_published_versions, and all knowledge-graph tools — free at openalex.org/users/me
ZOTERO_MCP_EMAIL	No	Your email address. Sent in User-Agent headers to CrossRef/OpenAlex polite pools and required for Unpaywall PDF lookup in attach_pdf. Without it, Unpaywall PDF fetches are skipped.
SEMANTIC_SCHOLAR_API_KEY	No	Improves rate limits for find_related_papers — free at semanticscholar.org
ZOTERO_DATA_DIR	No	Override path to Zotero desktop data directory (default: ~/Zotero). Used by audit_local_keys and the local PDF path resolver in get_pdf_content.
ZOTERO_MCP_GRAPH_DB	No	Override path for the knowledge-graph SQLite database (default: ~/.local/share/zotero-mcp/graph.sqlite or $XDG_DATA_HOME/zotero-mcp/graph.sqlite).
XDG_DATA_HOME	No	Standard XDG override for the default graph DB location.
PARENT_WATCHDOG_DISABLE	No	Set to 1 to disable the orphan-process watchdog that kills the server when the parent process (Claude.app, uvx, etc.) exits.

Troubleshooting

Problem	Cause	Fix
Cloud CRUD mode requires ZOTERO_API_KEY	Missing env vars	Set ZOTERO_API_KEY and ZOTERO_USER_ID in your MCP client config
CERTIFICATE_VERIFY_FAILED on any tool	Python SSL misconfiguration	Run check_ssl_health — it diagnoses the cert bundle and returns remediation steps
attach_pdf never finds a free PDF	ZOTERO_MCP_EMAIL not set	Unpaywall requires a real email address. Set ZOTERO_MCP_EMAIL in your config.
Analysis tools fail without obvious error	OPENALEX_API_KEY missing	check_retractions, get_citation_graph, and check_published_versions all require it
Reads are slow	Zotero desktop not running; reads go through Web API	Start Zotero and enable local API for faster reads (optional)
Item not found after creation	Zotero sync lag	Items created via Web API appear locally after Zotero syncs (usually seconds)
Version conflict for item	Item was modified between read and write	Retry the operation; the server uses optimistic locking
Translation server 503	translate.zotero.org is intermittent	The server falls back to PubMed and CrossRef automatically
Orphan server processes accumulate	Parent exits without closing stdin	Normal behavior is auto-handled by the watchdog. Disable with PARENT_WATCHDOG_DISABLE=1 if it conflicts with your setup.

Development

pip install -e ".[dev,graph,fulltext]"
python -m pytest tests/ -v

License

MIT