| name | ncbi-pubmed-search |
| description | Use this skill to search PubMed through NCBI E-utilities when you need official Entrez-backed literature discovery and summary metadata. Do not use it when you need full text or network-free execution. |
Purpose
Run a PubMed search through NCBI E-utilities and optionally fetch summary metadata for the returned PMIDs.
When to use
- You need a canonical PubMed search path.
- You want lightweight official metadata for biomedical literature triage.
When not to use
- Full text is required.
- A Europe PMC workflow already covers the task better.
Inputs
- Search term
- Optional
--retmax, --email, and --out
Outputs
- Combined JSON payload with
search and summary sections
Requirements
- Python 3.13+
- Network access to
eutils.ncbi.nlm.nih.gov
Procedure
- Run
python3 skills/scientific-knowledge/ncbi-pubmed-search/scripts/search_pubmed.py --term "single-cell RNA-seq" --retmax 3 --out skills/scientific-knowledge/ncbi-pubmed-search/assets/pubmed_single_cell.json.
- Inspect
search.esearchresult.idlist.
- Review
summary.result for titles, journals, and dates.
Validation
- Command exits successfully.
- Search returns at least one PMID for a common query.
- Summary payload includes the returned UID keys.
Failure modes and fixes
- Empty results: broaden the term or use a synonym.
- Courtesy warnings: supply
--email for traceable requests.
Safety and limits
- Metadata discovery only.
- Respect NCBI usage guidance and avoid unnecessary high-rate polling.
Examples
python3 .../search_pubmed.py --term "spatial transcriptomics benchmark" --retmax 2
Provenance
Related skills
europepmc-method-triagecrossref-metadata-search
