zotero-cli

zotero-cli is a skill for Claude Code, Codex from 54yyyu/zotero-mcp. It costs 93 tokens per session (2,398 once invoked), scanned A, original, MIT.

A command-line interface for Zotero, a tool for organizing research papers and references. It lets you search a library, read PDF text, manage metadata and collections, add sources, and export bibliographies.

In plain words
What is it for?
Use it to find papers, inspect PDFs, update tags and notes, add items by DOI or URL, manage collections, and generate bibliographies.
Why use it?
It lets you work with research references from scripts or the shell without manually navigating the Zotero application for every task.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it to find papers, inspect PDFs, update tags and notes, add items by DOI or URL, manage collections, and generate bibliographies.

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Install with agentmods
npx agentmods add skills/54yyyu/zotero-mcp/zotero-cli
About the project

zotero-mcp connects a Zotero research library to AI assistants through the Model Context Protocol, allowing them to search papers, retrieve content, summarize research, and work with citations or annotations. It is for people who want to discuss and analyze their research library with an AI assistant. The catalogue skill and MCP entry provide that connection.

54yyyu/zotero-mcp · 5,567 stars · on GitHub · stevenyuyy.com

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.

Any agent
npx skills add 54yyyu/zotero-mcp --skill zotero-cli
Clone the repo
git clone --depth 1 https://github.com/54yyyu/zotero-mcp

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for zotero-cli

README.md
[![agentmods](https://agentmods.dev/badge/skills/54yyyu/zotero-mcp/zotero-cli/github.svg)](https://agentmods.dev/skills/54yyyu/zotero-mcp/zotero-cli)
Your own site
<a href="https://agentmods.dev/skills/54yyyu/zotero-mcp/zotero-cli"><img src="https://agentmods.dev/badge/skills/54yyyu/zotero-mcp/zotero-cli/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for zotero-cli

Your own site · 80×15
<a href="https://agentmods.dev/skills/54yyyu/zotero-mcp/zotero-cli"><img src="https://agentmods.dev/badge/skills/54yyyu/zotero-mcp/zotero-cli.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 93 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,398 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00093 $0.02398
Opus 5.5 $0.00037 $0.00959
Sonnet 5.5 $0.00019 $0.00480
Haiku 4.5 $0.00009 $0.00240

Measured 18d ago against content hash 24822998c0fe, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

zotero-cli 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 18d ago.

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.

src/zotero_mcp/skills/zotero-cli/SKILL.md · 205 lines

How it starts

The opening of the file, as written. The whole thing — 205 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Zotero from the shell

zotero-cli reaches a Zotero library directly. Prefer it over the Zotero MCP server when you have shell access: the MCP server's tool schemas cost ~14k tokens of context on every request whether or not you use them, while this costs only what you actually run.

Check it is set up before the first real call:

zotero-cli config          # prints the resolved Zotero settings

If that fails, Zotero is not reachable. Local mode needs the Zotero desktop app running with its local API enabled; web mode needs ZOTERO_API_KEY and ZOTERO_LIBRARY_ID. Say so rather than guessing at library contents.

Always pass --json when you will read the output

Default output is markdown for humans. --json gives you one object per invocation with a stable shape, so you never parse prose:

{"ok": true, "command": "search", "schema": 1, "data": {...}}
{"ok": false, "command": "search", "schema": 1, "error": {"message": "...", "code": "..."}}

Both go to stdout; [INFO]/[WARN] diagnostics go to stderr. Check ok before using data. Run zotero-cli --json-schema for the full contract.

The core loop

Almost every task is: find keys → act on keys. Item keys are 8 characters and are the currency of every command.

# 1. find - use --detail keys_only to keep the result small while browsing
zotero-cli --json search "attention mechanisms" --limit 10 --detail keys_only

# 2. act - metadata, full text, or a page range
zotero-cli --json get metadata ABCD1234
zotero-cli --json get fulltext ABCD1234
zotero-cli --json read ABCD1234 --start-page 3 --end-page 8

Pipe keys straight into the next call:

zotero-cli --json search "diffusion models" --limit 5 --detail keys_only \
  | jq -r '.data.items[].key' \
  | while read -r key; do zotero-cli --json get metadata "$key"; done

Choosing a search mode

Mode Use it for Command
items (default) a title, author or phrase you know search "Vaswani attention"
semantic a topic or idea, no exact wording search --mode semantic "why transformers scale"
tag items you filed under a tag search --mode tag "to-read,important"
advanced structured field conditions search --mode advanced --conditions '[...]'
citekey a BibTeX citation key search --mode citekey smith2020
notes text inside your notes, not item fields search --mode notes "research question"

Read the full file on GitHub · 205 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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. 18d ago Changed · +18 lines 24822998c0fe
  2. 1mo ago Changed · +2 lines e2e932c4a2a6
  3. 1mo ago Changed · +39 lines 76cb1b2def99
  4. 1mo ago Changed · +1 lines 6620a5835d6c
  5. 1mo ago First seen · 145 lines · 93 tokens per session scan A 4e8177843b3b

Subscribe to this mod's changes

zotero-cli is a skill published in the GitHub repository 54yyyu/zotero-mcp (5,567 stars, last pushed 9d ago), licensed MIT. It adds 93 tokens to every session and 2,398 once invoked, about $0.0004 per session on Opus 5.5. 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 2026-08-30.

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