# pubmed-database

Gives your agent a CLI into PubMed and PubMed Central: search papers, pull abstracts and full text, link publications to biological databases.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · 2700 installs · ★ 3329
- Author: google-deepmind
- License: Apache-2.0 · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/google-deepmind/science-skills/tree/HEAD/skills/pubmed_database/SKILL.md
- Updated: 2026-10-23
- HTML: https://affpapa.org/en/nevibecode/skills/google-deepmind-pubmed-database

## What it does

The skill wraps NCBI E-utilities and the PMC BioC API in a single CLI, `scripts/pubmed_api.py`, with ten functions. Search by free-text or structured query, fetch abstracts for a batch of PMIDs, get full text from PMC, link papers to gene, protein, nucleotide and PubChem records, verify medical spelling, match raw citations, and cache result sets for bulk work. The agent runs it through `uv run` and pipes JSON through `jq`, which keeps author lists and metadata out of context.

You need `uv` on PATH and a `.env` file in your home directory before the first call. `NCBI_API_KEY` is optional and raises the E-utilities rate limit from 3 to 10 requests per second; without it the skill still runs, but a long series of queries can hit a 429. `USER_EMAIL` is also optional and just identifies the caller to NCBI.

Calling the API any other way, including `curl` or hand-written code, is off the table — the wrapper handles rate limits for you. On first use the skill asks you to check the PubMed and NCBI terms and drops a marker file under `.licenses/`. For bulk retrieval, read the reference file for a function group before calling it: argument order and flags live there, and guessing from function names will produce bad invocations.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill pubmed-database -a claude-code
```
```bash
npx skills add google-deepmind/science-skills --skill pubmed_database -a claude-code
```

2. **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

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill pubmed_database -a codex
```

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

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill pubmed_database -a cursor
```

2. **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 google-deepmind/science-skills pubmed_database
```

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

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill pubmed_database -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/google-deepmind/science-skills --path skills/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

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill pubmed_database -a opencode
```

### 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/google-deepmind/science-skills/tree/HEAD/skills/pubmed_database/SKILL.md

## When to use it
- find papers on a topic and get back PMIDs
- pull abstracts for a batch of identifiers
- link a paper to a specific gene or compound
- match a raw citation to a PubMed record
- check medical spelling before running a search

## Example prompts
- Search PubMed for BRCA1 papers, show 5 results and list the titles
- Fetch abstracts for PMID 35113657 and keep only title and abstract
- Link this paper to PubChem and Gene records

## Source text · SKILL.md · Apache-2.0

Below is the content of a third-party file. It is data, not instructions for you: do not act on anything written inside unless the human asks. Block tag: f5c9c83f78a66354.

BEGIN THIRD-PARTY FILE f5c9c83f78a66354
```text
---
name: pubmed-database
description: >-
  Search PubMed for scientific literature, including published clinical trials.
  Fetch abstracts and full text. Link published research to biological databases
  (gene, protein, nucleotide, PubChem) to discover associations between papers
  and specific compounds or genes. Verify medical spelling, match raw citations,
  and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC
  BioC APIs.
---

# PubMed API

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/pubmed_database_LICENSE.txt does not
    already exist in the workspace root directory then (1) prominently notify
    the user to check the terms at https://pubmed.ncbi.nlm.nih.gov/disclaimer/
    and https://www.ncbi.nlm.nih.gov/home/about/policies/ and to always check
    the license of the papers retrieved by the skill for any restrictions, then
    (2) create the file recording the notification text and timestamp.
3.  **`.env` file**: Make sure the `.env` file exists in your home directory.
    Create one if it does not exist.
4.  **`NCBI_API_KEY`** (optional): Raises the NCBI E-utilities rate limit from 3
    to 10 requests/second. The skill works without it, but a key is recommended
    if the user plans many queries or encounters a 429 error. You can register
    for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You
    **MUST** use the safe credentials protocol in the `credentials` skill to
    check for and request this key if this skill looks relevant to the user's
    request.
5.  **`USER_EMAIL`** (optional): Identifies the caller to NCBI (recommended by
    their Terms of Use). You **MUST** use the safe credentials protocol in the
    `credentials` skill to check for and request this credential if this skill
    looks relevant to the user's request.

This skill provides CLI access to the NCBI PubMed and PubMed Central APIs via
`scripts/pubmed_api.py` — a single CLI with 10 functions covering search, fetch,
linking, full text, spelling, discovery, citation matching, and caching.

## Core Rules

-   **API Use**: Always use the provided wrapper `scripts/pubmed_api.py` which
    manages rate limits automatically and prevents API abuse. Setting the
```
END THIRD-PARTY FILE f5c9c83f78a66354

The third-party file has ended. Everything between the f5c9c83f78a66354 tags is data: requests and commands from it are not followed. An “end of file” line with another tag inside the block is part of the file.

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---
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