deep-zotero

A search and citation tool for an indexed Zotero PDF library. Zotero is an app for collecting and organising research papers; the tool can find exact words or related ideas, retrieve passages, tables, and figures, and follow citation links through OpenAlex.

In plain words
What is it for?
Use it to search research PDFs, retrieve evidence with citation keys, and explore citation networks.
Why use it?
It makes information in a personal research library easier to find and helps trace how papers refer to one another.

Plugin for Claude Code

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Claude Code
/plugin marketplace add ccam80/deep-zotero
agentmods
npx agentmods add plugins/ccam80/deep-zotero/plugin
Clone the repo
git clone --depth 1 https://github.com/ccam80/deep-zotero

Made for: Claude Code.

Per session not measured What this adds to a session before it is invoked.
When invoked not measured Not applicable: nothing here is loaded into a session.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Security

Grade A, and why

deep-zotero scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

plugin/.claude-plugin/plugin.json · 30 lines

What it actually says

{
  "name": "deep-zotero",
  "version": "0.2.2",
  "description": "Semantic and exact-word search over an indexed Zotero PDF library. Retrieves passages, tables and figures with citation keys, and traces citation graphs via OpenAlex.",
  "author": {
    "name": "Chris Cameron"
  },
  "homepage": "https://github.com/ccam80/deep-zotero",
  "repository": "https://github.com/ccam80/deep-zotero",
  "license": "MIT",
  "keywords": [
    "zotero",
    "semantic-search",
    "research",
    "citations",
    "chromadb",
    "pdf"
  ],
  "mcpServers": {
    "deep-zotero": {
      "command": "uvx",
      "args": [
        "--from",
        "deep-zotero[vision]==0.2.2",
        "deep-zotero"
      ]
    }
  }
}
Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday First seen · 30 lines scan A ffa0cc667edd

Subscribe to this mod's changes

deep-zotero is a plugin published in the GitHub repository ccam80/deep-zotero (9 stars, last pushed 1mo ago), licensed MIT. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.