opencite

opencite is a skill for Claude Code from neuromechanist/research-skills. It costs 111 tokens per session (1,285 once invoked), scanned A, original, BSD-3-Clause.

A command-line research tool for finding academic papers, managing citations, retrieving PDFs, and converting PDFs to Markdown. It searches sources such as Semantic Scholar, OpenAlex, PubMed, arXiv, and bioRxiv, a website where researchers share biology and medical studies before formal publication.

In plain words
What is it for?
Use it for literature reviews, citation searches, DOI and BibTeX lookups, citation-graph exploration, paper downloads, and batch PDF conversion.
Why use it?
It reduces the manual work of searching several research databases, removing duplicate results, downloading papers, and formatting references.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the opencite plugin — 1 skill shipped together

Good fit Use it for literature reviews, citation searches, DOI and BibTeX lookups, citation-graph exploration, paper downloads, and batch PDF conversion.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/neuromechanist/research-skills/opencite
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 neuromechanist/research-skills --skill opencite
Clone the repo
git clone --depth 1 https://github.com/neuromechanist/research-skills

Made for: Claude Code.

Or install opencite, the plugin that ships this one along with the rest of its 1 skill.

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 opencite

README.md
[![agentmods](https://agentmods.dev/badge/skills/neuromechanist/research-skills/opencite/github.svg)](https://agentmods.dev/skills/neuromechanist/research-skills/opencite)
Your own site
<a href="https://agentmods.dev/skills/neuromechanist/research-skills/opencite"><img src="https://agentmods.dev/badge/skills/neuromechanist/research-skills/opencite/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 opencite

Your own site · 80×15
<a href="https://agentmods.dev/skills/neuromechanist/research-skills/opencite"><img src="https://agentmods.dev/badge/skills/neuromechanist/research-skills/opencite.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 111 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,285 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 warn 7 Sept 2026
SkillSpector: 11 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium MCP Rug Pull · line 18
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 36
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 37
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 38
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 50
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 51
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 66
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 78
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 101
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium MCP Rug Pull · line 102
    uvx/uv tool run commands without ==version create a rug-pull risk.
    Fix: Pin the version: uvx package-name==1.2.3
  • medium Rogue Agent · line 101
    Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.
    Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
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 $0.00111 $0.01285
Opus 5 $0.00056 $0.00642
Sonnet 5 $0.00022 $0.00257
Haiku 4.5 $0.00011 $0.00128

Measured 12d ago against content hash ede5275d562b, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

opencite 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 12d 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.

plugins/opencite/skills/opencite/SKILL.md · 125 lines

How it starts

The opening of the file, as written. The whole thing — 125 lines — stays where its author put it; the contents beside it link to each section on GitHub.

OpenCite CLI

OpenCite is a CLI tool for academic literature search and citation management. It aggregates results from Semantic Scholar, OpenAlex, PubMed, arXiv, and bioRxiv/medRxiv, deduplicates them, and outputs formatted results. It also supports PDF retrieval, PDF-to-markdown conversion, and batch operations.

Installation

# Recommended
uv pip install opencite

# Alternative: run without installing
uvx opencite --version

PDF conversion support (markitdown and markit-mistral) is included by default. When MISTRAL_API_KEY is set, markit-mistral handles math, tables, and complex layouts. Otherwise, markitdown (free, local) is the fallback.

For development:

uv sync --extra dev

Research Workflow

Follow this end-to-end workflow for literature research, paper retrieval, or reading material on a topic.

1. Search for relevant papers

Choose the search strategy based on the request:

  • Canonical/foundational papers: uvx opencite canonical "topic" --max 10
  • Recent or specific papers: uvx opencite search "query" --max 20 --sort citations
  • Citation graph exploration: uvx opencite cite "DOI" --direction both
  • Combine strategies when appropriate (e.g., canonical for background + search for recent work)

2. Evaluate and select papers

Review results considering citation count, relevance, recency, and open access availability. Present a summary and confirm which papers to retrieve.

3. Download and convert

For multiple papers (preferred): Save search results as JSON and use batch-fetch:

uvx opencite search "topic" --max 10 -f json -o results.json
uvx opencite batch-fetch --from-json results.json --convert -o ./papers --summary report.json

batch-fetch --convert automatically creates this directory structure:

papers/
├── pdf/          # downloaded PDFs
└── markdown/     # converted markdown files
    └── img/      # per-paper image directories (mistral only)

For individual papers:

Read the full file on GitHub · 125 lines

Files

What ships with it

3 files 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. 12d ago First seen · 125 lines · 111 tokens per session scan A ede5275d562b

Subscribe to this mod's changes

opencite is a skill published in the GitHub repository neuromechanist/research-skills (45 stars, last pushed 9d ago), licensed BSD-3-Clause. It adds 111 tokens to every session and 1,285 once invoked, about $0.0006 per session on Opus 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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