Zotero Agent

Zotero Agent

> English | [中文](./README-zh.md)

Zotero Agent is a Zotero plugin that embeds an MCP (Model Context Protocol) server, turning your local Zotero library into a workspace an AI agent can fully operate — not just read.

It exposes 46 tools spanning library search & retrieval, metadata enrichment, identifier-based import (DOI / arXiv / ISBN / PMID), bulk bibliography import (BibTeX / RIS / CSL-JSON), preprint→published-version upgrade, DOI repair, grey-source PDF download (Sci-Hub / Anna's Archive), duplicate detection & merge, batch tagging, citation-graph expansion, annotation synthesis, and companion-plugin bridges (jasminum, Linter) — plus an escape-hatch run_javascript for arbitrary in-process automation beyond the built-in tools.

In practice, an AI assistant (Claude, Codex, …) talking to this server can search your library in natural language, clean up metadata and tags in bulk, import and de-duplicate papers, fetch missing PDFs, expand a topic through its citation graph, and synthesize your annotations — with dry-run-by-default safety on every write.

How to Use

Step 1: Install the Zotero Plugin

1. Download the latest zotero-agent.xpi from the Releases Page.
2. Install it in Zotero through Tools -> [gear icon] -> Install Plugin From File....
3. Open Editor -> Settings -> Zotero Agent and enable these permissions:
4. Allow Remote Access
5. Enable Write Operations
6. Run JavaScript (eval)

> Note: Run JavaScript (eval) is used to run JavaScript inside Zotero so it can handle tasks that go beyond the built-in MCP tools. Enable it only when you need it.

Step 2: Configure Your AI Client

Get your token from Zotero -> Editor -> Settings -> Zotero Agent -> PSK.

Codex App

Go to Setting -> MCP Servers -> Add server, then use this configuration:

| Field | Value | | --- | --- | | MCP server name | zotero-mcp | | Transport | Streamable HTTP | | URL | http://127.0.0.1:23120/mcp | | Header Key: Authorization | Bearer | | Header Key: Content-Type | application/json |

Codex CLI

Edit %USERPROFILE%/.codex/config.toml or ~/.codex/config.toml:

[mcp_servers.zotero-mcp]
enabled = true
url = "http://127.0.0.1:23120/mcp"
http_headers = { Authorization = "Bearer ", "Content-Type" = "application/json" }

Claude Code

$env:ZOTERO_MCP_BEARER_TOKEN = "YOUR TOKEN"

claude mcp add --transport http zotero-mcp http://127.0.0.1:23120/mcp `
  --scope user `
  --header "Authorization: Bearer $env:ZOTERO_MCP_BEARER_TOKEN" `
  --header "Content-Type: application/json"

> Note: If you install it inside this project and run it from this project directory, do not use --scope user.

Step 3 (Optional): Recommended Companion Plugins

These plugins run alongside Zotero Agent — they're not bundled in, but once installed, the AI agent can drive them through the run_javascript tool (Zotero's privileged context can reach any installed plugin's API). Install the ones that match your workflow:

| Plugin | What it does | How it pairs with this plugin / the agent | | --- | --- | --- | | jasminum 茉莉花 | Scrapes Chinese-database metadata (CNKI / Wanfang / VIP) for Chinese literature with incomplete fields. | This plugin's built-in enrichment targets Western sources (CrossRef / OpenAlex); jasminum fills the Chinese gap. After importing Chinese PDFs, the agent can trigger its scrape / filename-match via run_javascript. | | zotero-updateifsE 绿青蛙 | Writes impact factor, JCR / CAS quartiles, and other journal metrics into items. | After import_by_identifier / enrich_item_metadata fills the core metadata, the agent can batch-update metrics per collection via run_javascript. | | zotero-format-metadata | 50+ metadata linters: title case, dates, pages, LTWA journal abbreviations, Chinese name / pinyin cleanup. | Complements enrich_item_metadata (fills fields) with format normalization — the agent can run its lint rules as a post-enrichment cleanup step. | | zotero-zotadata | Multi-source metadata fill + multi-provider PDF discovery (Unpaywall / arXiv / CORE / …). | A heavier alternative to find_missing_pdfs when you need broader PDF sources; the agent can invoke its retrieval pipeline via run_javascript. |

Let the agent install them for you. With run_javascript (eval) enabled, paste a prompt like this — trim the list to what you need:

> Please install these Zotero companion plugins via run_javascript. For each repo: fetch https://api.github.com/repos//releases/latest, pick the asset whose name ends in .xpi, install it with AddonManager.getInstallForURL(url) then install.install(), and report each plugin's id / version / active state. Drop any I don't need: > - jasminum (Chinese metadata: CNKI / Wanfang / VIP) — l0o0/jasminum > - Green Frog / updateifsE (impact factor & quartiles) — redleafnew/zotero-updateifsE > - Linter / format-metadata (format cleanup & journal abbreviations) — northword/zotero-format-metadata > - Zotadata (multi-source fill + PDF discovery) — ydeng11/zotero-zotadata

Some plugins may need a Zotero restart to fully activate. Note: most of these are also searchable in the community Zotero Add-on Market plugin (e.g. format-metadata appears there as "Linter for Zotero"); a few (like zotadata) are GitHub-release-only.

> See the Built on Open Source — Integration Status & Roadmap section below for how each is called today and which interactions we plan to promote into dedicated MCP tools.

Grey-source PDF Download (Sci-Hub / Anna's Archive)

On top of Zotero's built-in open-access resolvers, the plugin can use Sci-Hub / Anna's Archive as fallback PDF download sources.

Enable in the preferences panel. In Editor -> Settings -> Zotero Agent, turn on the Sci-Hub / Anna's Archive toggle. A source list appears pre-filled with sensible defaults (several Sci-Hub mirrors + Anna's Archive); you can add or remove sources, or restore the defaults. Sources register as manual-only resolvers — used only when you explicitly trigger a download, never in the background. Everything stays off by default.

Download. Once enabled, Zotero's native right-click Find Available PDF automatically includes these sources: Zotero tries free sources first (arXiv / open access) and falls back to the grey sources only when needed. You can also drive it through the MCP tools manage_pdf_resolvers (enable/disable and manage the source list) and find_missing_pdfs (audit which items lack a PDF, then fetch).

Compliance. Sci-Hub / Anna's Archive are grey-area sources. Legal compliance in your jurisdiction is your responsibility.

Development Setup

Clone the repository:

git clone https://github.com/psiQAQ/zotero-agent.git
cd zotero-agent

Set up the plugin development environment:

npm install
npm run build

Load the plugin in Zotero:

# For development with auto-reload
npm run start

# Or install the built .xpi file manually
# The xpi file will be generated at "./.scaffold/build/zotero-agent.xpi"
npm run build

MCP Tools

The table below is based on the actual tool definitions in src/modules/streamableMCPServer.ts.

| Tool Name | Purpose | | --- | --- | | get_libraries | List the Zotero libraries available in the current client. | | search_library | Search the Zotero library with filters such as title, year, full text, item type, and relevance scoring. | | search_libraries | Search libraries by name. | | search_annotations | Search highlights, notes, and comments by query, color, tag, or item scope. | | get_item_details | Get detailed metadata for a specific Zotero item. | | get_annotations | Get annotations and notes for a specific item or annotation ID. | | get_content | Read full-text content from PDFs, attachments, notes, and abstracts. | | get_collections | List collections in the library, including recursive tree output when needed. | | search_collections | Search collections by name. | | get_collection_details | Get detailed information for a specific collection. | | get_collection_items | List items inside a specific collection. | | get_subcollections | Get child collections under a specific collection. | | create_collection | Create a new collection, optionally under a parent collection. | | update_collection | Rename or move an existing collection. | | delete_collection | Delete a collection, with optional item deletion. | | add_items_to_collection | Add one or more items to a collection. | | remove_items_from_collection | Remove one or more items from a collection without deleting them from the library. | | search_fulltext | Search across cached full-text document content and return matching passages. | | get_item_abstract | Get the abstract or summary of a specific item. | | semantic_search | Run embedding-based semantic search to find conceptually related content. | | find_similar | Find items that are semantically similar to a given item. | | semantic_status | Show the status and index statistics of the semantic search service. | | fulltext_database | Access the cached full-text database with list, search, get, and stats actions. | | write_note | Create, update, or append Zotero notes. | | write_tag | Add, remove, or replace tags on Zotero items. | | write_metadata | Update item metadata such as title, abstract, DOI, date, or creators. | | write_item | Create items, re-parent attachments, or import local files as attachments. | | run_javascript | Execute JavaScript inside the Zotero process for advanced automation. | | reload_plugin | Reload an installed Zotero plugin for development workflows. | | install_plugin_from_url | Install or upgrade a plugin XPI from a reachable URL or file path. | | import_by_identifier | Import an item by DOI, arXiv ID, ISBN, or PMID. | | import_bibliography | Bulk-import BibTeX / RIS / CSL-JSON (auto-detected); idempotent dedup by DOI / title similarity; dry-run plan by default. | | find_missing_pdfs | Report items without PDFs or fetch open-access PDFs for them. | | manage_pdf_resolvers | Register Sci-Hub / Anna's Archive into Zotero's native PDF resolver pref (grey sources default automatic=false, manual-only); actual download is via findmissingpdfs. | | extract_identifier_from_pdf | Mine DOI or arXiv ID from a PDF's fulltext cache using frequency voting. Read-only. | | find_doi | Reverse-lookup a DOI via CrossRef title-similarity (≥0.86 threshold), or mode:"repair" to validate a dead DOI (Handle System API) and propose a replacement; dry-run default, confirm write requires write.enabled. | | enrich_item_metadata | Fill missing fields (abstract/venue/volume/issue/pages/ISSN/publisher/date) from a DOI via doi.org CSL-JSON + OpenAlex; dry-run default, confirm write requires write.enabled. | | upgrade_preprints | Find the published version of arXiv-style preprints via OpenAlex title search and upgrade DOI/venue/date/itemType; old values backed up into Extra; dry-run default. | | check_retractions | Check items against scite.ai editorial notices such as retractions or corrections. | | find_related_papers | Traverse the citation graph through OpenAlex to find citing or referenced papers. | | synthesize_annotations | Aggregate highlights and notes into a literature-review-oriented markdown bundle. | | find_duplicates | Detect duplicate items using Zotero's native duplicates engine. | | merge_duplicates | Merge duplicate items into a chosen master item. | | batch_update_tags | Run bulk tag operations such as add, remove, or rename. | | fetch_chinese_metadata | Scrape CNKI/Wanfang/VIP metadata for top-level Chinese attachments & CNKI snapshots via the jasminum companion plugin (eligibility classification, hang-proof watchdog). | | lint_metadata | Run zotero-format-metadata (Linter) rules over items — title case, dates, journal abbreviations, Chinese name splitting; unknown rule ids rejected with the valid list. |

Built on Open Source — Integration Status & Roadmap

This plugin stands on the shoulders of several open-source projects: it forks a writable in-process MCP base and folds in the best ideas from ~17 reference projects (archived read-only as submodules under refs/). Full technical comparisons live in:

• [AI / MCP integration approaches](./docs/benchmarking/ai-plugins-mcp.md) — 5 projects
• [Metadata enrichment plugins](./docs/benchmarking/metadata-enrichment.md) — 8 projects
• [PDF download approaches](./docs/benchmarking/pdf-download.md) — 4 projects

1. What this fork adds on top of the base

Forked from cookjohn/zotero-mcp — a clean, in-process, locally-writable MCP server (27 tools, direct saveTx/eraseTx). Our additions:

| Area | cookjohn base | This fork adds | | --- | --- | --- | | Auth | loopback only | PSK Bearer auth + Origin validation (DNS-rebind defense) | | Eval | none | run_javascript privileged eval tool (timeout + 100 KB cap) | | Tools | 27 | 46 — +19 tools (identifier & bulk-bibliography import, missing-PDF audit, citation graph, dedup, batch tags, metadata enrich, DOI reverse-lookup & repair, preprint upgrade, grey-source download, companion-plugin bridges, …) | | Search | keyword | + RRF hybrid semantic search, 0-result fallback ladder | | Testing | none | 31-scenario in-process selfTest + node unit tests (91 cases) | | Deploy | manual | one-shot deploy-live (base64 ship + self-upgrade) + reload_plugin / install_plugin_from_url | | i18n | zh / en | + de / es / fr / ja | | CJK | — | byte-level HTTP read fix (dense CJK bodies no longer mojibake) |

2. Capabilities absorbed from reference projects (integrated)

Ideas were re-implemented (not vendored) into native tools:

AI / MCP — see [comparison](./docs/benchmarking/ai-plugins-mcp.md)

| Source | Absorbed into | Status | TODO | | --- | --- | --- | --- | | 54yyyu/zotero-mcp | import_by_identifier, import_bibliography (BibTeX / RIS / CSL-JSON), find_missing_pdfs, find_related_papers (OpenAlex), check_retractions (scite), synthesize_annotations | ✅ | batch OA indexing | | introfini/ZotSeek | RRF hybrid semantic_search | ✅ | WebGPU acceleration; Matryoshka dim truncation | | introfini/mcp-server-zotero-dev | run_javascript, reload_plugin, install_plugin_from_url | ✅ | screenshot / DOM-inspection tools for UI debugging |

Metadata — see [comparison](./docs/benchmarking/metadata-enrichment.md)

| Source | Absorbed into | Status | TODO | | --- | --- | --- | --- | | zotero-metadata-hunter | enrich_item_metadata (field-level fill from DOI CSL-JSON + OpenAlex), upgrade_preprints (published-version upgrade via OpenAlex title search) | ✅ | — | | zotero-doi-fix | find_doi (title-similarity fusion + mode:"repair": Handle-System validation → replace w/ backup), extract_identifier_from_pdf | ✅ | — |

PDF — see [comparison](./docs/benchmarking/pdf-download.md)

| Source | Absorbed into | Status | TODO | | --- | --- | --- | --- | | pdferret, zotero-scipdf | manage_pdf_resolvers (native findPDFs.resolvers read/write) + grey-source download | ✅ | multi-mirror rotation; stronger DOI extraction (scipdf's 5-regex + attachment scrape) |

3. Not integrated, but callable via `

…

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: psiQAQ
• Source: psiQAQ/zotero-agent
• License: MIT

Install and usage instructions live in the source repository linked above.