Search Pubmed

Search biomedical literature on PubMed via NCBI E-Utilities. Use this skill whenever the user needs to search for scientific papers, biomedical articles, life science research, or any PubMed-indexed content. Triggers: 'search literature', 'find papers', 'PubMed', 'NCBI', 'PMID', 'biomedical', 'scientific articles', 'life science', 'organism research', 'gene/disease/drug papers'. Also use for any mention of searching literature about bacteria, plants, animals, diseases, genes, proteins, drugs, or clinical/biological topics — even if the user doesn't explicitly say 'PubMed'.

PubMed Literature Search

Search PubMed (and other NCBI databases) via the E-Utilities API, using a bundled Python script that wraps Biopython's Bio.Entrez.

Quick start

bash

python scripts/search_pubmed.py "<query>" [--max N] [--db DB] [--pmid ID] [--full]

The script lives at scripts/search_pubmed.py relative to this skill directory. Run it from the workspace root, using the skill's install path to locate the script.

If the skill is installed at .claude/skills/search-pubmed/, invoke it as:

bash

python .claude/skills/search-pubmed/scripts/search_pubmed.py "cancer AND immunotherapy"

Common patterns

Keyword search (default)

bash

python .claude/skills/search-pubmed/scripts/search_pubmed.py "Sinorhizobium fredii biofilm"

Control result count

bash

python .claude/skills/search-pubmed/scripts/search_pubmed.py "CRISPR" --max 20

Boolean logic (AND / OR / NOT)

bash

python .claude/skills/search-pubmed/scripts/search_pubmed.py "hopanoid AND rhizobium"
python .claude/skills/search-pubmed/scripts/search_pubmed.py "mouse OR rat"

Field-qualified search

bash

python .claude/skills/search-pubmed/scripts/search_pubmed.py "hopanoid[Title/Abstract]"
python .claude/skills/search-pubmed/scripts/search_pubmed.py "Smith J[Author] AND 2024[Date - Publication]"

PMID lookup

bash

# Fast — title / author / journal / DOI only (1 request)
python .claude/skills/search-pubmed/scripts/search_pubmed.py --pmid 41185614

# With abstract (2 requests)
python .claude/skills/search-pubmed/scripts/search_pubmed.py --pmid 41185614 --full

# Multiple PMIDs
python .claude/skills/search-pubmed/scripts/search_pubmed.py --pmid 41185614,42332334 --full

Other NCBI databases

bash

python .claude/skills/search-pubmed/scripts/search_pubmed.py "TP53" --db nucleotide
python .claude/skills/search-pubmed/scripts/search_pubmed.py "cancer" --db pmc

Parameters

Parameter	Description	Default
query	Search keywords (Entrez syntax supported)	Required (or use --pmid)
--max N	Maximum results to return	10
--db NAME	Target NCBI database	pubmed
--email ADDR	NCBI contact email (optional, avoids warning)	—
--api-key KEY	NCBI API Key (optional, raises rate limit)	—
--pmid ID	Lookup by PMID directly, skip search	—
--full	Include abstract text (with --pmid)	off

Output format

Each result includes:

• PMID — PubMed ID (clickable link: https://pubmed.ncbi.nlm.nih.gov/PMID)
• Title — article title
• Author — first author | last author
• Source — journal abbreviation
• Date — publication date
• DOI — digital object identifier (when available)

Rate limits

Condition	Limit
No API key	3 requests/sec
With API key (--api-key)	10 requests/sec

A typical search uses 2 requests (search + summaries). PMID lookup uses 1 (or 2 with --full). Staying within the rate limit is generally not a concern for interactive use.

Search tips

1. Start broad, then narrow. Use AND to add terms, not to restrict fields.
2. Try synonyms and alternative classifications. Example: Sinorhizobium fredii is also classified as Ensifer fredii — search both with "Sinorhizobium fredii" OR "Ensifer fredii".
3. Zero results is information. A null result may indicate a genuine research gap — tell the user this explicitly.
4. Use [Title/Abstract] qualifier for precision when a broad search returns too many off-topic hits.
5. When cross-searching two topics (e.g., organism X + pathway Y), if the AND query returns 0, run them separately to show the user the landscape — how many papers exist on each side of the gap.
6. A PubMed gap doesn't mean a total gap. When you identify a research gap in PubMed, suggest the user cross-check gene/protein databases (NCBI Gene, UniProt, KEGG) for genomic evidence — genes may be annotated but unstudied in the literature.

Dependencies

• Python 3.6+
• biopython package: pip install biopython

Bundled resources

• scripts/search_pubmed.py — the search executable
• references/entrez-help.md — NCBI Entrez query syntax reference