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pubmed-database · davila7 — Claude Code skill: query PubMed via API

A Claude skill for PubMed access over the E-utilities REST API: MeSH queries, batch fetches, citation matching by PMID or DOI.

Install into Claude Code · claude-code-templates All methods and platforms ↓ 
npx claude-code-templates@latest --skill scientific/pubmed-database
Open on GitHub

What pubmed-database does

The skill teaches the agent to talk to PubMed through NCBI's E-utilities. Five endpoints are covered: ESearch returns PMIDs for a query, EFetch pulls full records, ESummary gives short document info, EPost uploads identifiers for batch work, and ELink finds related articles. Queries combine Boolean operators, field tags and MeSH terms, subheadings included.

For Python code the author points to biopython (Bio.Entrez) instead, leaving this skill for raw HTTP calls and custom API clients. Rate limits matter here: 3 requests per second without an NCBI key, 10 with one. Every request should carry a User-Agent header.

Two reference files ship alongside: search_syntax.md for field tags and operators, api_reference.md for endpoint parameters. Typical work is systematic reviews, tracking new publications, or resolving a citation from journal, year, volume and page.

What it helps with

  • pull a set of articles on a topic filtered by publication type
  • resolve a PMID from a partial citation
  • fetch abstracts for many records in one batch
  • build a query with MeSH terms and subheadings
  • set up recurring monitoring of an author's new papers

Example prompts for the agent

  • Find systematic reviews on type 2 diabetes from 2023–2024
  • Fetch the abstracts for these PMIDs with EFetch
  • Build a query using a MeSH term and the /drug therapy subheading

How to install pubmed-database

1claude-code-templates

npx claude-code-templates@latest --skill scientific/pubmed-database

2Skills CLI (Vercel)

npx skills add davila7/claude-code-templates --skill pubmed-database -a claude-code

3Manually: put the files in place

~/.claude/skills/pubmed-database/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/pubmed-database/

Step by step, with commands for each platform: How to install skills in Claude Code: five ways

Questions about pubmed-database

How do I install pubmed-database in Claude Code?

Run npx claude-code-templates@latest --skill scientific/pubmed-database. Or use npx skills add davila7/claude-code-templates --skill pubmed-database -a claude-code.

What does pubmed-database do?

It helps the agent compose PubMed searches and call the E-utilities API: find articles, download records, match citations by identifier.

Do I need an API key for PubMed?

NCBI allows 3 requests per second without a key and 10 with one. The key is optional, but bulk fetches hit the limit fast without it.

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pubmed-database by other authors comes first.

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