Individual skill
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.
skills/pubmed_database/SKILL.md
Source commit 4de6786171f1479026da5d3a00f110703c8ba35e
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- Not checked yet
- Last checked
- Nov 2, 2026
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- Repository stars (not skill ratings)
- 3,431
- Repository last updated
- Oct 23, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- research Derived category
- data Derived category
- data-databases Derived category
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SKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesSKILL.mdcore · 8,343 bytesreferences/advanced-linking.mddoc · 5,520 bytesreferences/advanced-search.mddoc · 3,660 bytesreferences/bulk-workflows.mddoc · 3,599 bytesreferences/citation-matching.mddoc · 5,344 bytesreferences/citation.bibasset · 1,809 bytesreferences/cross-database-linking.mddoc · 4,025 bytesreferences/fetch-and-resolve.mddoc · 5,606 bytesreferences/search-and-discovery.mddoc · 4,948 bytesreferences/utilities.mddoc · 1,357 bytesscripts/pubmed_api.pyruns · 21,444 bytes
Read excerpt
# 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.