# pubmed-database

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

- skill · `type=skill` · Claude Code · 149 installs
- Author: davila7
- License: not stated · policy=link-only · description only; the file stays with the author
- Source: https://github.com/davila7/claude-code-templates/tree/HEAD/cli-tool/components/skills/scientific/pubmed-database
- Updated: 2026-10-24
- HTML: https://affpapa.org/en/nevibecode/skills/pubmed-database

## What it 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.

## Install

### Claude Code (native platform)

1. **claude-code-templates**
```bash
npx claude-code-templates@latest --skill scientific/pubmed-database
```

2. **Skills CLI (Vercel)**
```bash
npx skills add davila7/claude-code-templates --skill pubmed-database -a claude-code
```

3. **Manually: put the files in place**
- File: `~/.claude/skills/pubmed-database/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/pubmed-database/

### Codex

**Manually: put the files in place**
- File: `.agents/skills/pubmed-database/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

**Manually: put the files in place**
- File: `.cursor/skills/pubmed-database/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install davila7/claude-code-templates pubmed-database
```

2. **Manually: put the files in place**
- File: `.github/skills/pubmed-database/SKILL.md`

### Gemini CLI

**Platform CLI**
```bash
gemini skills install https://github.com/davila7/claude-code-templates --path cli-tool/components/skills/scientific/pubmed-database
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/pubmed-database/SKILL.md` — The legacy .windsurf/skills/ path still works

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/davila7/claude-code-templates/tree/HEAD/cli-tool/components/skills/scientific/pubmed-database

## When to use it
- 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
- 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

## Similar
- [pubmed-mcp-server](https://affpapa.org/en/nevibecode/mcp/pubmed-mcp-server.md) — MCP server · ★ 163
- [nature-academic-search](https://affpapa.org/en/nevibecode/skills/nature-academic-search.md) — skill · 15300 installs
- [PubMed Search](https://affpapa.org/en/nevibecode/mcp/pubmed-search.md) — MCP server · ★ 28
- [pubmed-search](https://affpapa.org/en/nevibecode/skills/pubmed-search.md) — skill · 706 installs
- [quickgo-database](https://affpapa.org/en/nevibecode/skills/quickgo-database.md) — skill · 2100 installs
- [embl-ebi-ols](https://affpapa.org/en/nevibecode/skills/embl-ebi-ols.md) — skill · 2100 installs

## Other versions with the same name
- [pubmed-database · google-deepmind](https://affpapa.org/en/nevibecode/skills/google-deepmind-pubmed-database.md) — 2700 installs

From the same set: [davila7/claude-code-templates](https://affpapa.org/en/nevibecode/by/davila7/claude-code-templates.md) — 495 cards

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