Skills pmc-harvest

Name: pmc-harvest
Author: openclaw

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.

install

source · Clone the upstream repo

git clone https://github.com/openclaw/skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/openclaw/skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/angusthefuzz/pmc-harvest" ~/.claude/skills/openclaw-skills-pmc-harvest && rm -rf "$T"

OpenClaw · Install into ~/.openclaw/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/openclaw/skills "$T" && mkdir -p ~/.openclaw/skills && cp -r "$T/skills/angusthefuzz/pmc-harvest" ~/.openclaw/skills/openclaw-skills-pmc-harvest && rm -rf "$T"

manifest: skills/angusthefuzz/pmc-harvest/SKILL.md

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/