Searching Scientific Literature

by brycewang-stanford4.6k

Communication

PubMed search with keyword optimization, result parsing, and metadata extraction

Install

The skill file stays in the publisher's repository.

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill searching-literature -a cursor -y

How do I install Searching Scientific Literature?: Download skills/05-kthorn-research-superpower/research/searching-literature/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does Searching Scientific Literature live?: The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use Searching Scientific Literature?: Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.

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.

Task	Command
Search PubMed	`curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=QUERY&retmax=100&retmode=json"`
Get metadata	`curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=PMID1,PMID2&retmode=json"`
URL encode query	Replace spaces with `+`, special chars with `%XX`
Narrow results	Use AND, add field tags, more specific terms
Broaden results	Use OR, remove field tags, add synonyms