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Search journals, retrieve full text via OAI-PMH, batch harvest for RAG pipelines. No API key required.\nversion: 1.0.0\nauthor: Ania\nmetadata:\n  clawdbot:\n    emoji: \"📚\"\n    requires:\n      bins: [\"node\"]\n---\n\n# PMC Harvest\n\nFetch full-text articles from PubMed Central using official NCBI APIs.\n\n## Features\n\n- **E-utilities search** — Find articles by journal, year, query\n- **OAI-PMH full text** — Retrieve complete article XML (open access only)\n- **Batch harvesting** — Process multiple journals at once\n- **Abstract fetch** — Lightweight retrieval for review queues\n- **No API key required** — Uses public NCBI APIs (rate-limited)\n\n## Usage\n\n```bash\n# Search a journal\nnode {baseDir}/scripts/pmc-harvest.js --search \"J Stroke[journal]\" --year 2025\n\n# Fetch full text for a specific article\nnode {baseDir}/scripts/pmc-harvest.js --fetch PMC12345678\n\n# Batch harvest from multiple journals\nnode {baseDir}/scripts/pmc-harvest.js --harvest journals.json --year 2025\n\n# Test with known journals\nnode {baseDir}/scripts/pmc-harvest.js --test\n```\n\n## Options\n\n| Flag | Description |\n|------|-------------|\n| `--search <query>` | PMC search query (use journal[name] format) |\n| `--year <year>` | Filter by publication year |\n| `--max <n>` | Max results (default: 100) |\n| `--fetch <pmcid>` | Fetch full text for specific PMCID |\n| `--harvest <file>` | Batch harvest from JSON journal list |\n| `--test` | Run test with sample journals |\n\n## Programmatic API\n\n```javascript\nconst pmc = require('{baseDir}/lib/api.js');\n\n// Search\nconst { count, pmcids } = await pmc.searchJournal('\"J Stroke\"[journal]', { year: 2025 });\n\n// Get summaries\nconst summaries = await pmc.getSummaries(pmcids);\n\n// Fetch full text\nconst { available, xml, reason } = await pmc.fetchFullText('PMC12345678');\n\n// Parse JATS XML\nconst { title, abstract, body } = pmc.parseJATS(xml);\n\n// Fetch abstract only (lightweight)\nconst { title, abstract } = await pmc.fetchAbstract('PMC12345678');\n```\n\n## Journal Query Examples\n\n```javascript\nconst queries = {\n  'Stroke': '\"Stroke\"[journal]',\n  'Journal of Stroke': '\"J Stroke\"[journal]',\n  'Stroke & Vascular Neurology': '\"Stroke Vasc Neurol\"[journal]',\n  'European Stroke Journal': '\"Eur Stroke J\"[journal]',\n  'BMC Neurology': '\"BMC Neurol\"[journal]'\n};\n```\n\n## Limitations\n\n- **OAI-PMH only returns open-access articles** — restricted content unavailable\n- **Rate limits** — ~3 requests/second without API key\n- **Peak hours** — NCBI recommends avoiding 5AM-9PM ET for large batches\n\n## API Reference\n\nThis skill wraps NCBI's official APIs:\n\n- **E-utilities**: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils`\n  - `esearch.fcgi` — Search PMC\n  - `esummary.fcgi` — Get article metadata\n- **OAI-PMH**: `https://pmc.ncbi.nlm.nih.gov/api/oai/v1/mh`\n  - `GetRecord` — Fetch full text XML\n\nFull docs: https://www.ncbi.nlm.nih.gov/books/NBK25501/\n","readmeExcerpt":"--- 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 journ","codeSnippets":[],"executableExamples":[{"language":"bash","snippet":"# Search a journal\nnode {baseDir}/scripts/pmc-harvest.js --search \"J Stroke[journal]\" --year 2025\n\n# Fetch full text for a specific article\nnode {baseDir}/scripts/pmc-harvest.js --fetch PMC12345678\n\n# Batch harvest from multiple journals\nnode {baseDir}/scripts/pmc-harvest.js --harvest journals.json --year 2025\n\n# Test with known journals\nnode {baseDir}/scripts/pmc-harvest.js --test"},{"language":"javascript","snippet":"const pmc = require('{baseDir}/lib/api.js');\n\n// Search\nconst { count, pmcids } = await pmc.searchJournal('\"J Stroke\"[journal]', { year: 2025 });\n\n// Get summaries\nconst summaries = await pmc.getSummaries(pmcids);\n\n// Fetch full text\nconst { available, xml, reason } = await pmc.fetchFullText('PMC12345678');\n\n// Parse JATS XML\nconst { title, abstract, body } = pmc.parseJATS(xml);\n\n// Fetch abstract only (lightweight)\nconst { title, abstract } = await pmc.fetchAbstract('PMC12345678');"},{"language":"javascript","snippet":"const queries = {\n  'Stroke': '\"Stroke\"[journal]',\n  'Journal of Stroke': '\"J Stroke\"[journal]',\n  'Stroke & Vascular Neurology': '\"Stroke Vasc Neurol\"[journal]',\n  'European Stroke Journal': '\"Eur Stroke J\"[journal]',\n  'BMC Neurology': '\"BMC Neurol\"[journal]'\n};"}],"parameters":{},"dependencies":[],"permissions":[],"extractedFiles":[],"languages":["typescript"],"docsSourceLabel":"CLAWHUB","editorialOverview":"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. --- 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. 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