pmc-harvest

name	pmc-harvest
description	Fetch articles from PubMed Central using NCBI APIs. Search journals, retrieve full text via OAI-PMH, batch harvest for RAG pipelines. No API key required.
version	1.0.0
author	Ania
metadata	{"clawdbot":{"emoji":"📚","requires":{"bins":["node"]}}}

PMC Harvest

Fetch full-text articles from PubMed Central using official NCBI APIs.

Features

• E-utilities search — Find articles by journal, year, query
• OAI-PMH full text — Retrieve complete article XML (open access only)
• Batch harvesting — Process multiple journals at once
• Abstract fetch — Lightweight retrieval for review queues
• No API key required — Uses public NCBI APIs (rate-limited)

Usage

# Search a journal
node {baseDir}/scripts/pmc-harvest.js --search "J Stroke[journal]" --year 2025

# Fetch full text for a specific article
node {baseDir}/scripts/pmc-harvest.js --fetch PMC12345678

# Batch harvest from multiple journals
node {baseDir}/scripts/pmc-harvest.js --harvest journals.json --year 2025

# Test with known journals
node {baseDir}/scripts/pmc-harvest.js --test

Options

Flag	Description
--search <query>	PMC search query (use journal[name] format)
--year <year>	Filter by publication year
--max <n>	Max results (default: 100)
--fetch <pmcid>	Fetch full text for specific PMCID
--harvest <file>	Batch harvest from JSON journal list
--test	Run test with sample journals

Programmatic API

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

// Search
const { count, pmcids } = await pmc.searchJournal('"J Stroke"[journal]', { year: 2025 });

// Get summaries
const summaries = await pmc.getSummaries(pmcids);

// Fetch full text
const { available, xml, reason } = await pmc.fetchFullText('PMC12345678');

// Parse JATS XML
const { title, abstract, body } = pmc.parseJATS(xml);

// Fetch abstract only (lightweight)
const { title, abstract } = await pmc.fetchAbstract('PMC12345678');

Journal Query Examples

const queries = {
  'Stroke': '"Stroke"[journal]',
  'Journal of Stroke': '"J Stroke"[journal]',
  'Stroke & Vascular Neurology': '"Stroke Vasc Neurol"[journal]',
  'European Stroke Journal': '"Eur Stroke J"[journal]',
  'BMC Neurology': '"BMC Neurol"[journal]'
};

Limitations

• OAI-PMH only returns open-access articles — restricted content unavailable
• Rate limits — ~3 requests/second without API key
• Peak hours — NCBI recommends avoiding 5AM-9PM ET for large batches

API Reference

This skill wraps NCBI's official APIs:

• E-utilities: https://eutils.ncbi.nlm.nih.gov/entrez/eutils
  • esearch.fcgi — Search PMC
  • esummary.fcgi — Get article metadata
• OAI-PMH: https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh
  • GetRecord — Fetch full text XML

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