Søger i PubMed/MEDLINE efter biomedicinsk litteratur, kliniske forsøg og systematiske reviews.
@mikkelkrogsholm
Community-bidragyder
mikkelkrogsholm/skills
Open source repository
Nedenstående er skillens egen dokumentation, hentet fra kildekoderepoet. Ophavsret tilhører forfatteren.
Search and retrieve biomedical literature from the NCBI PubMed database via the E-utilities REST API. Access 35+ million citations from MEDLINE, life sciences journals, and online books. No authentication required.
Invoke this skill when the user wants to:
bun run skills/pubmed-database/cli/src/cli.ts search --query "<query>" [flags]
Key flags:
--query <q> — required; full PubMed query syntax supported (Boolean, MeSH, field tags, date ranges, wildcards)--max <n> — number of results (default 20)--start <n> — offset for pagination (default 0)--sort <order> — relevance (default), pub_date, first_author--limit <n> — client-side cap--format json|table|plainReturns { meta: { total, returnedCount, retstart }, results: [{ pmid, title, authors, source, pubDate, doi }] }.
bun run skills/pubmed-database/cli/src/cli.ts fetch --ids <pmids> [--format text|medline]
--ids — comma-separated PMIDs (required)--format text (default) — abstract text; medline — MEDLINE tagged formatReturns plain text (not JSON).
bun run skills/pubmed-database/cli/src/cli.ts detail <pmid> [--format json|plain]
Returns complete bibliographic record including volume, issue, pages, DOI, PMC ID, publication types, citation count.
bun run skills/pubmed-database/cli/src/cli.ts cite-match \
[--journal <j>] [--year <y>] [--volume <v>] [--page <p>] [--author <a>]
Returns { results: [{ citation, pmid, found }], rawResponse }.
Natural workflow: search → fetch or detail.
search to find relevant PMIDs for a topic.fetch --ids <pmid> to read the full abstract.detail <pmid> for complete bibliographic metadata (journal, volume, DOI, PMC ID, citation count).Use PubMed query syntax in --query for precise results:
diabetes mellitus, type 2[mh]AND systematic review[pt]AND 2020:2024[dp]AND insulin resistance[tiab]AND free full text[sb]Pagination: Use --start to page through results. --max is the page size (how many PMIDs ESearch retrieves).
Unknown PMID for a paper? Use cite-match with whatever citation details you have — journal, year, volume, page.
bun run skills/pubmed-database/cli/src/cli.ts search \
--query "GLP-1[tiab] AND obesity[mh] AND randomized controlled trial[pt] AND 2022:2024[dp]" \
--max 5 --sort pub_date --format table
bun run skills/pubmed-database/cli/src/cli.ts fetch --ids 38123456
bun run skills/pubmed-database/cli/src/cli.ts detail 20536893 --format plain
bun run skills/pubmed-database/cli/src/cli.ts cite-match \
--journal "N Engl J Med" --year 2021 --volume 385 --page 1487
bun run skills/pubmed-database/cli/src/cli.ts search \
--query "(long covid[tiab] OR post-acute covid[tiab]) AND systematic review[pt]" \
--max 5 --format table
bun run skills/pubmed-database/cli/src/cli.ts search \
--query "Fauci AS[au] AND 2020:2024[dp]" --max 5
| Format | Best for |
|---|---|
json |
Default — data processing, reading fields programmatically |
table |
Quick human-readable overviews |
plain |
Single-record views (detail) |
Extended documentation is in references/:
references/api_reference.md — full E-utilities API docsreferences/search_syntax.md — PubMed query syntax, field tags, Boolean operatorsreferences/common_queries.md — example queries for diseases, study types, populationsAll errors are written to stderr as { "error": "...", "code": "..." } with exit code 1.