What is pubmed-search?

A natural-language search tool for finding biomedical research in PubMed, a large database of medical and life-science papers. It can return full article text and links to figures when available.

Use it to find papers, read their available full text, and inspect figures about biomedical topics such as gene editing or disease research.

It lets users search by describing a research question instead of constructing detailed database filters or keywords.

pubmed-search — Skill for Claude Code by yorkeccak

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 yorkeccak/scientific-skills --skill pubmed-search

Clone the repo

git clone --depth 1 https://github.com/yorkeccak/scientific-skills

Made for: Claude Code.

Or install scientific-skills, the plugin that ships this one along with the rest of its 13 skills.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/yorkeccak/scientific-skills/pubmed-search/github.svg)](https://agentmods.dev/skills/yorkeccak/scientific-skills/pubmed-search)

Your own site

<a href="https://agentmods.dev/skills/yorkeccak/scientific-skills/pubmed-search"><img src="https://agentmods.dev/badge/skills/yorkeccak/scientific-skills/pubmed-search/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/yorkeccak/scientific-skills/pubmed-search"><img src="https://agentmods.dev/badge/skills/yorkeccak/scientific-skills/pubmed-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 30 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,445 The whole file, excluding the scripts and references it only reads on demand.

Security scan B 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

Socket pass 18 Mar 2026
Snyk fail 15 Feb 2026

How audits are shown

Origin 86% copy Near-identical to another mod 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.

Model	Per session	Once invoked
Fable 5.1	$0.00030	$0.01445
Opus 5	$0.00015	$0.00723
Sonnet 5	$0.00006	$0.00289
Haiku 4.5	$0.00003	$0.00145

Measured 12d ago against content hash 9cfc8fea968a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade B, and why

pubmed-search scanned grade B with 1 finding 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.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/search.mjs), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Reads agent configuration directoriesmediumAgent snooping

.claude/, .codex/, .gemini/ hold keys, settings and other credentials a mod has no legitimate need for.

PUBMED_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/pubmed-search/*/scripts/*" -type f 2>/dev/null | head -1)

Origin

This is a copy

86% identical to biorxiv-search — 109 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

skills/pubmed-search/SKILL.md · 245 lines

How it starts

The opening of the file, as written. The whole thing — 245 lines — stays where its author put it; the contents beside it link to each section on GitHub.

PubMed Search

Search the complete PubMed database of biomedical literature using natural language queries powered by Valyu's semantic search API.

Why This Skill is Powerful

No API Parameter Parsing: Just pass natural language queries directly - no need to construct complex search parameters
Semantic Search: Understands the meaning of your query, not just keyword matching
Full-Text Access: Returns complete article content, not just abstracts
Image Links: Includes figures and images from papers
Comprehensive Coverage: Access to all of PubMed's biomedical literature

Requirements

Node.js 18+ (uses built-in fetch)
Valyu API key from https://platform.valyu.ai ($10 free credits)

CRITICAL: Script Path Resolution

The scripts/search commands in this documentation are relative to this skill's installation directory.

Before running any command, locate the script using:

PUBMED_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/pubmed-search/*/scripts/*" -type f 2>/dev/null | head -1)

Then use the full path for all commands:

$PUBMED_SCRIPT "CRISPR gene editing" 15

API Key Setup Flow

When you run a search and receive "setup_required": true, follow this flow:

Ask the user for their API key: "To search PubMed, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
Once the user provides the key, run:
```
scripts/search setup <api-key>
```
Retry the original search.

Example Flow:

User: Search PubMed for CAR-T cell therapy advances
→ Response: {"success": false, "setup_required": true, ...}
→ Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
→ User: "val_abc123..."
→ Claude runs: scripts/search setup val_abc123...
→ Response: {"success": true, "type": "setup", ...}
→ Claude retries: scripts/search "CAR-T cell therapy advances" 10
→ Success!

Usage

Basic Search

scripts/search "your natural language query" [maxResults]

Read the full file on GitHub · 245 lines

Files

What ships with it

2 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.

12d ago First seen · 245 lines · 30 tokens per session scan B 9cfc8fea968a

Subscribe to this mod's changes

pubmed-search is a skill published in the GitHub repository yorkeccak/scientific-skills (61 stars, last pushed 7mo ago), licensed MIT. It adds 30 tokens to every session and 1,445 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it B with 1 finding (reads agent configuration directories). It is 86% identical to biorxiv-search, differing in 109 lines, and is treated as a copy.

Research Scientific biomedical-literature full-text-search medical-research natural-language-queries pubmed research-integration semantic-search

pubmed-search

Getting it into your agent

Wrote this? Show the measurements

What it costs to keep this loaded

Grade B, and why

Reads agent configuration directoriesmediumAgent snooping

This is a copy

How it starts

PubMed Search

Why This Skill is Powerful

Requirements

CRITICAL: Script Path Resolution

API Key Setup Flow

Example Flow:

Usage

Basic Search

What ships with it

What this file has done since we first saw it

Other skills, from other repositories

pubmed-search

pubmed-search

pubmed-search

biomedical-search

biomedical-search

biomedical-search