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Pmc Harvest

Fetch articles from PubMed Central using NCBI APIs.

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Downloads: 2,418 downloads
Version: 1.0.0

Overview

Fetch articles from PubMed Central using NCBI APIs.

✨Key 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)

Complete Documentation

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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

bash

# 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

javascript

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

javascript

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/

Installation

Terminal bash


openclaw install pmc-harvest

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💻Code Examples

node {baseDir}/scripts/pmc-harvest.js --test

node-basedirscriptspmc-harvestjs---test.txt

## 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

example.sh

# 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

example.js

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');

example.js

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]'
};