PubMed search with keyword optimization, result parsing, and metadata extraction
SKILL.md
Searching Scientific Literature
Overview
Search PubMed for scientific literature using optimized queries. Extract metadata and prepare papers for relevance evaluation.
Core principle: Cast a wide enough net to find relevant papers, but use targeted keywords to keep results manageable.
When to Use
Use this skill when:
Starting a new research question
User asks "find papers about..."
Need initial paper set for evaluation
Searching for specific methods, compounds, diseases, techniques
Search Strategy
1. Parse User Query
Extract:
Keywords: Main concepts (e.g., "BTK inhibitor", "selectivity", "kinase")
Data types: What user needs (IC50 values, methods, structures, results)
Constraints: Date ranges, specific journals, author names
Synonyms: Alternative terms (e.g., "Bruton's tyrosine kinase" = "BTK")
2. Construct PubMed Query
Boolean operators:
AND - narrow results (must have both terms)
OR - broaden results (either term)
NOT - exclude terms
Example queries:
"BTK inhibitor"[Title/Abstract] AND selectivity[Title/Abstract]
("kinase inhibitor" OR "protein kinase") AND (selectivity OR "off-target")
"ibrutinib"[Title/Abstract] AND ("IC50" OR "inhibitory concentration")
Too narrow: Only 5 results → Use OR, remove constraints
Too broad: 5000 results → Add AND terms, use field tags
Missing abstracts: Use efetch instead of esummary for full abstract text
DOI not found: Many older papers lack DOI - use PMID as fallback
Rate limiting: Add 500ms delays (single agent) or longer (parallel subagents sharing rate limit)
Next Steps
After completing search:
Announce: "Found N papers matching query"
Begin evaluation using skills/research/evaluating-paper-relevance
