pubmed-database - Search PubMed literature and link to biological databases
Search PubMed literature, fetch abstracts and PMC full text, link papers to biological data, match citations, and cache results for bulk processing.
Tags
Updated: 2026-09-19Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Search PubMed for literature PMIDs
- Count query matches across NCBI databases
- Fetch metadata and abstracts for PMIDs
- Retrieve open-access full text from PMC
- Resolve NCBI UIDs into metadata
- Find linked biological database records
- List available ELink linknames for records
- Upload PMIDs to NCBI History Server
- Verify spelling of biomedical terms
- Match raw citations to PMIDs
Inputs
- PubMed search queries
- PMIDs or NCBI UIDs
- Raw bibliographic citations
- Biomedical search terms
- Optional NCBI API key
- Optional user email address
Outputs
- JSON files with literature metadata and abstracts
- PMC full-text articles
- NCBI History Server session handles
- License notification file
Requirements
- uv package manager
- Python execution environment
- Dotenv configuration file in home directory
- Access to NCBI E-utilities and PMC BioC APIs