pubmed

pubmed is a skill for Claude Code, Codex from ai4protein/VenusFactory2. It costs 71 tokens per session (991 once invoked), scanned A, original, no licence file.

A search and retrieval tool for PubMed, the U.S. National Library of Medicine database of biomedical research citations. It can search by keywords or retrieve titles, structured abstracts, authors, and DOI links for known PubMed identifiers.

In plain words
What is it for?
Use it for medical and biological literature searches, resolving citations, retrieving paper abstracts, or building a collection of abstracts for natural-language processing.
Why use it?
It helps you find biomedical papers and collect consistent citation details for research or text analysis. PubMed contains citations rather than being a general-purpose web search engine.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it for medical and biological literature searches, resolving citations, retrieving paper abstracts, or building a collection of abstracts for natural-language processing.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/ai4protein/venusfactory2/pubmed
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 ai4protein/VenusFactory2 --skill pubmed
Clone the repo
git clone --depth 1 https://github.com/ai4protein/VenusFactory2

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 pubmed

README.md
[![agentmods](https://agentmods.dev/badge/skills/ai4protein/venusfactory2/pubmed/github.svg)](https://agentmods.dev/skills/ai4protein/venusfactory2/pubmed)
Your own site
<a href="https://agentmods.dev/skills/ai4protein/venusfactory2/pubmed"><img src="https://agentmods.dev/badge/skills/ai4protein/venusfactory2/pubmed/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 pubmed

Your own site · 80×15
<a href="https://agentmods.dev/skills/ai4protein/venusfactory2/pubmed"><img src="https://agentmods.dev/badge/skills/ai4protein/venusfactory2/pubmed.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 71 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 991 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.
Origin unknown 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 $0.00071 $0.00991
Opus 5 $0.00036 $0.00495
Sonnet 5 $0.00014 $0.00198
Haiku 4.5 $0.00007 $0.00099

Measured 9d ago against content hash b141edd71a64, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

pubmed 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 9d 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/agent/skills/pubmed/SKILL.md · 73 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

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. 9d ago First seen · 73 lines · 71 tokens per session scan A b141edd71a64

Subscribe to this mod's changes

pubmed is a skill published in the GitHub repository ai4protein/VenusFactory2 (248 stars, last pushed 1mo ago), with no licence file. It adds 71 tokens to every session and 991 once invoked, about $0.0004 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.

Related

Other skills, from other repositories

esm

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel…

synthetic-sciences/openscience · 86 tokens

omnisci

Run OmniScientist end to end in the OmniScientist CLI using DeepSeek V4 Flash. Turn raw research data (images, signals, audio, video, 3-D, tables, or graphs) and an open direction into perceived evidence, a falsifiable hypothesis, recorded analysis, real citations, a gated candidate paper, PDF, and Overleaf bundle.…

Omni-Scientist/OmniScientist · 145 tokens

Protein Structures — AlphaFold & PDB

Obtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a novel sequence with ColabFold — and visualise them in the Mol desktop app.

aristoteleo/PantheonOS · 63 tokens

math-skill

A comprehensive mathematical reasoning skill for AI assistants — handles arithmetic to research-level problems with rigorous step-by-step reasoning, systematic verification, and transparent uncertainty handling.

Wholiver/Math.Skill · 33 tokens

arxiv-paper-search

A paper-search skill that uses arXiv's official public API, a free service for finding research papers, to retrieve academic publications without a token.

johnson7788/skill-ppt-agents · 107 tokens

design-taste-frontend

Anti-slop frontend skill for landing pages, portfolios, and redesigns. The agent reads the brief, infers the right design direction, and ships interfaces that do not look templated. Real design systems when applicable, audit-first on redesigns, strict pre-flight check.

Leonxlnx/taste-skill · 61 tokens