Ncbi pubmed search

Skill ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/ncbi-pubmed-search

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.From its SKILL.md

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill ncbi-pubmed-search

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.9 KB, 405 tokens by cl100k_base, as published. Nobody here has run it

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

NCBI E-utilities guide: https://www.ncbi.nlm.nih.gov/books/NBK25501/
NCBI developer API landing page: https://www.ncbi.nlm.nih.gov/home/develop/api/

Related skills

europepmc-method-triage
crossref-metadata-search

What ships with it: 7 files

18.8 KB alongside SKILL.md, 1 of them executable