pmc-harvest
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.
Best use case
pmc-harvest is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
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.
Teams using pmc-harvest should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/pmc-harvest/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How pmc-harvest Compares
| Feature / Agent | pmc-harvest | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
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.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
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SKILL.md Source
# 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 <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
```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/Related Skills
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