PubMed Skill

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.

When to use this skill

Invoke this skill when the user wants to:

Search PubMed for papers on any biomedical or life sciences topic
Find clinical trials, systematic reviews, meta-analyses, or RCTs on a specific condition or treatment
Retrieve abstracts or full citation details for one or more PMIDs
Look up a specific paper by author, journal, year, volume, and page number
Find papers using MeSH terms, field tags, or advanced Boolean queries
Get the full bibliographic record for a known article (journal, volume, pages, DOI, PMC ID)
Explore what the medical literature says about a drug, disease, or intervention

Commands

Search PubMed for articles

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|plain

Returns { meta: { total, returnedCount, retstart }, results: [{ pmid, title, authors, source, pubDate, doi }] }.

Fetch abstracts by PMID

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 format

Returns plain text (not JSON).

Full record for a single PMID

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.

Find PMID from partial citation

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 }.

How to use effectively

Natural workflow: search → fetch or detail.

Use search to find relevant PMIDs for a topic.
Call fetch --ids <pmid> to read the full abstract.
Call detail <pmid> for complete bibliographic metadata (journal, volume, DOI, PMC ID, citation count).

Use PubMed query syntax in --query for precise results:

MeSH terms: diabetes mellitus, type 2[mh]
Publication type: AND systematic review[pt]
Date range: AND 2020:2024[dp]
Title/abstract: AND insulin resistance[tiab]
Free full text: 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.

Usage examples

What are the latest RCTs on GLP-1 drugs for obesity?

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

Get the abstract for PMID 38123456

bun run skills/pubmed-database/cli/src/cli.ts fetch --ids 38123456

Full bibliographic record for a PMID

bun run skills/pubmed-database/cli/src/cli.ts detail 20536893 --format plain

Find the PMID for a known journal article

bun run skills/pubmed-database/cli/src/cli.ts cite-match \
  --journal "N Engl J Med" --year 2021 --volume 385 --page 1487

Systematic reviews on COVID-19 long-term effects

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

Search by author

bun run skills/pubmed-database/cli/src/cli.ts search \
  --query "Fauci AS[au] AND 2020:2024[dp]" --max 5

Output formats

Format	Best for
`json`	Default — data processing, reading fields programmatically
`table`	Quick human-readable overviews
`plain`	Single-record views (`detail`)

Reference files

Extended documentation is in references/:

references/api_reference.md — full E-utilities API docs
references/search_syntax.md — PubMed query syntax, field tags, Boolean operators
references/common_queries.md — example queries for diseases, study types, populations

All errors are written to stderr as { "error": "...", "code": "..." } with exit code 1.