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BytesAgain β€Ί Skills β€Ί PMC Harvest
πŸ¦€ ClawHub

PMC Harvest

by @angusthefuzz

Fetch and retrieve full-text or abstracts of open-access articles from PubMed Central by journal, year, or PMCID using NCBI's public APIs without an API key.

Versionv1.0.0
Downloads1,318
Stars⭐ 3
#clawhub
TERMINAL
clawhub install pmc-harvest

πŸ“– About This Skill

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: "πŸ“š" requires: bins: ["node"]

PMC Harvest

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

Features

  • E-utilities search β€” Find articles by journal, year, query
  • OAI-PMH full text β€” Retrieve complete article XML (open access only)
  • Batch harvesting β€” Process multiple journals at once
  • Abstract fetch β€” Lightweight retrieval for review queues
  • No API key required β€” 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 | PMC search query (use journal[name] format) | | --year | Filter by publication year | | --max | Max results (default: 100) | | --fetch | Fetch full text for specific PMCID | | --harvest | 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 β€” restricted content unavailable
  • Rate limits β€” ~3 requests/second without API key
  • Peak hours β€” 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 β€” Search PMC - esummary.fcgi β€” Get article metadata
  • OAI-PMH: https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh
    • - GetRecord β€” Fetch full text XML

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

    πŸ’‘ Examples

    # 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

    βš™οΈ Configuration

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