# Pubmed Database > Make sure to use this skill whenever the user asks about biomedical or life sciences literature, medical research, clinical trials, systematic reviews, meta-analyses, drug studies, or any topic that might be in PubMed or MEDLINE — even if they don't mention PubMed explicitly. Also invoke for questions about specific PMIDs, DOIs, journal articles, abstracts, or citation lookups. Trigger phrases include: pubmed, medline, ncbi, biomedical research, medical literature, clinical trial, systematic review, meta-analysis, randomized controlled trial, RCT, MeSH terms, PMID, biomedical journal, life sciences paper, find article by author, find study on, search medical literature, evidence-based medicine, drug efficacy study, cancer research papers, diabetes research, cardiovascular study, neurology research, infectious disease literature, genomics paper, CRISPR study, COVID-19 research, vaccine efficacy study, find papers on, what does the literature say about, research on treatment of, studies on, cite this paper, loo - Skill: `marchelleintrinsical938/pubmed-database` (Agent Skill, multi-file: 18 files) - Install (CLI): `npx skillmds@latest add marchelleintrinsical938/pubmed-database` - Raw SKILL.md: https://api.skillmd.com/api/skills/marchelleintrinsical938/pubmed-database/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Research & Search - Author: Marchelleintrinsical938 (https://skillmd.com/u/marchelleintrinsical938) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/marchelleintrinsical938/pubmed-database --- # 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 ```bash bun run skills/pubmed-database/cli/src/cli.ts search --query "" [flags] ``` Key flags: - `--query ` — **required**; full PubMed query syntax supported (Boolean, MeSH, field tags, date ranges, wildcards) - `--max ` — number of results (default 20) - `--start ` — offset for pagination (default 0) - `--sort ` — `relevance` (default), `pub_date`, `first_author` - `--limit ` — client-side cap - `--format json|table|plain` Returns `{ meta: { total, returnedCount, retstart }, results: [{ pmid, title, authors, source, pubDate, doi }] }`. ### Fetch abstracts by PMID ```bash bun run skills/pubmed-database/cli/src/cli.ts fetch --ids [--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 ```bash bun run skills/pubmed-database/cli/src/cli.ts detail [--format json|plain] ``` Returns complete bibliographic record including volume, issue, pages, DOI, PMC ID, publication types, citation count. ### Find PMID from partial citation ```bash bun run skills/pubmed-database/cli/src/cli.ts cite-match \ [--journal ] [--year ] [--volume ] [--page

] [--author ] ``` Returns `{ results: [{ citation, pmid, found }], rawResponse }`. --- ## How to use effectively **Natural workflow: `search` → `fetch` or `detail`.** 1. Use `search` to find relevant PMIDs for a topic. 2. Call `fetch --ids ` to read the full abstract. 3. Call `detail ` 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? ```bash 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 ```bash bun run skills/pubmed-database/cli/src/cli.ts fetch --ids 38123456 ``` ### Full bibliographic record for a PMID ```bash bun run skills/pubmed-database/cli/src/cli.ts detail 20536893 --format plain ``` ### Find the PMID for a known journal article ```bash 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 ```bash 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 ```bash 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`.