# Pubmed Database

Search PubMed for scientific literature, including published clinical trials.

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Data and ML
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill pubmed-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill pubmed-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill pubmed-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill pubmed-database -g -a gemini-cli -y`

## 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/pubmed_database/SKILL.md