PubMed Search

Search PubMed (30M+ articles) for abstracts, with auto full-text retrieval for PMC OA articles. Covers both open-access and non-open-access literature. No API key required.

Search the full PubMed database (30M+ articles) — abstracts for all records, full text for PMC open-access articles.

What PMC Harvest misses: PubMed indexes ~30M biomedical articles; only ~4M (13%) are in PMC with full text. This skill retrieves abstracts for the remaining 26M non-OA articles, making it suitable for comprehensive literature review.

Core Workflow

text

Search PubMed (db=pubmed) → get PMIDs
    → esummary: metadata for all (title, authors, journal, PMID, DOI)
    → efetch: structured abstract XML for any PMID
    → idconv: check if PMID maps to PMCID
        → if PMCID exists → OAI-PMH full text (PMC open access)
        → if no PMCID → abstract only (non-OA)

Features

• PubMed-wide search — db=pubmed, covers all 30M+ indexed articles
• Abstract for every article — efetch with rettype=abstract&retmode=xml
• Auto full-text fallback — if PMID maps to PMCID, retrieves full text via OAI-PMH
• Batch processing — search journals, keywords, MeSH terms
• No API key required — public NCBI E-utilities (3 req/s rate limit)

Usage

bash

# Search PubMed by keyword
node {baseDir}/scripts/pubmed-search.js search --query "myasthenia gravis thymus" --max 20

# Search with year filter
node {baseDir}/scripts/pubmed-search.js search --query "IFN alpha thymic epithelial" --year 2023 --max 30

# Search by journal
node {baseDir}/scripts/pubmed-search.js search --query "\"J Neuroimmunol\"[journal] AND MG" --max 20

# Get abstract for specific PMID
node {baseDir}/scripts/pubmed-search.js abstract --pmid 30311866

# Get abstract + try full text
node {baseDir}/scripts/pubmed-search.js fetch --pmid 30311866

# Test with sample query
node {baseDir}/scripts/pubmed-search.js test

Options

Flag	Description
search	Search PubMed for articles
--query <text>	PubMed search query (supports full PubMed syntax)
--year <year>	Filter by publication year
--max <n>	Max results (default: 50)
--offset <n>	Pagination offset (default: 0)
abstract	Get structured abstract for a PMID
--pmid <id>	PubMed ID (PMID)
fetch	Full fetch: abstract + auto full-text if OA
test	Run test with sample query

Programmatic API

javascript

const pubmed = require('{baseDir}/lib/api.js');

// Search PubMed
const { count, pmids } = await pubmed.searchPubMed('myasthenia gravis', { year: 2025, retmax: 50 });

// Get metadata summaries
const summaries = await pubmed.getSummaries(pmids);

// Get structured abstract
const { title, abstract, authors, journal, doi } = await pubmed.fetchAbstract('30311866');

// Fetch full text (auto maps PMID→PMCID, tries OAI-PMH)
const { available, xml, abstract, reason } = await pubmed.fetchArticle('30311866');

// Check if PMID has PMC full text
const { hasPMC, pmcid } = await pubmed.checkPMC('30311866');

// Batch search multiple journals
const articles = await pubmed.harvestJournals([{ name: 'Neurology', query: '"Neurology"[journal]' }], { year: 2025 });

Journal Query Examples

javascript

const queries = {
  'Neurology': '"Neurology"[journal]',
  'J Neuroimmunol': '"J Neuroimmunol"[journal]',
  'Muscle Nerve': '"Muscle Nerve"[journal]',
  'J Neurol Sci': '"J Neurol Sci"[journal]',
  'Autoimmun Rev': '"Autoimmun Rev"[journal]',
  'Front Immunol': '"Front Immunol"[journal]',
  'Nat Rev Neurol': '"Nat Rev Neurol"[journal]',
};

PubMed Search Syntax

Full PubMed query syntax is supported:

• "keyword phrase"[tiab] — title/abstract search
• "journal name"[journal] — journal filter
• YYYY[dp] or YYYY[pdat] — date filter (dp returns exact matches, pdat returns that year forward)
• AND, OR, NOT — boolean operators
• gene[mesh] — MeSH term
• smith j[author] — author filter
• english[lang] — language filter
• review[ptyp] — publication type

Limitations

• Non-OA articles: abstract + metadata only, no full text
• Rate limit: ~3 requests/second without API key (built-in 400ms delay between requests)
• Peak hours: NCBI recommends avoiding 5AM-9PM ET for large batches
• Abstract quality: structured abstracts from PubMed XML; older pre-1975 articles may have limited metadata

API Reference

• E-utilities: https://eutils.ncbi.nlm.nih.gov/entrez/eutils
  • esearch.fcgi?db=pubmed — Search PubMed (30M+ records)
  • esummary.fcgi?db=pubmed — Article metadata (JSON)
  • efetch.fcgi?db=pubmed&rettype=abstract&retmode=xml — Structured abstract
• ID Converter: https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/ — PMID ↔ PMCID mapping
• OAI-PMH: https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh/GetRecord — Full text XML (OA only)

Full docs: https://www.ncbi.nlm.nih.gov/books/NBK25501/