Agent skill · research science · google-deepmind
pubmed-database
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.
Why this skill is useful
Adds a CLI tool with multiple functions for interacting with the PubMed API, enabling advanced search and data processing capabilities that the AI cannot generate on its own.
What it needs
Requires jq, uv installed locally. Requires ncbi account access. About 4k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
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/pubmeddatabaseLICENSE.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. NCBIAPIKEY (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. USEREMAIL (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/pubmedapi.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/pubmedapi.py which manages rate limits automatically and prevents API abuse. Setting the NCBIAPIKEY environment variable raises the rate limit from 3 to 10 requests/second. Querying the API any other way (e.g. via curl, wget, or hand-written code) is strictly forbidden. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/pubmed_database