pi-pubmed

A Pi package for searching PubMed and fetching biomedical literature articles directly from your coding agent.

Features

• Search PubMed — Find articles using full PubMed query syntax (boolean operators, field tags, MeSH terms, date ranges)
• Fetch article details — Retrieve titles, authors, journals, publication dates, DOIs, and full abstracts
• Zero dependencies — Uses the NCBI E-utilities REST API directly
• Configurable — Optional API key support for higher rate limits

Installation

pi install npm:pi-pubmed

Or install from a local path:

pi install /path/to/pi-pubmed

Tools

pubmed_search

Search PubMed for articles matching a query.

| Parameter | Type | Required | Description | |----------------|----------|----------|------------------------------------------------------------------------------------| | query | string | ✅ | PubMed search query (supports boolean operators, field tags, MeSH terms) | | max_results | number | ❌ | Max results to return (1–100, default 10) | | sort_by | string | ❌ | Sort: relevance, pub_date, Author, JournalName | | date_range | string | ❌ | Date range as YYYY:YYYY or YYYY/MM:YYYY/MM |

pubmed_fetch

Fetch detailed article information for specific PubMed IDs.

| Parameter | Type | Required | Description | |-------------------|------------|----------|-------------------------------------------------| | pmids | string[] | ✅ | List of PubMed IDs to fetch | | include_abstract| boolean | ❌ | Include full abstract (default true) |

Usage Examples

Once installed, just ask Pi naturally:

Search PubMed for recent articles about CRISPR gene therapy

Find review articles about machine learning in drug discovery from the last 5 years

Fetch the abstract for PMID 38312345

Configuration (Optional)

Set environment variables for enhanced access:

| Variable | Description | |---------------|----------------------------------------------------| | NCBI_API_KEY| NCBI API key — increases rate limit to 10 req/s | | NCBI_EMAIL | Your email — helps NCBI contact you if needed |

Get a free API key at: https://www.ncbi.nlm.nih.gov/account/settings/

Package Structure

pi-pubmed/
├── package.json          # Package manifest with Pi configuration
├── extensions/
│   └── pubmed.ts         # Extension with pubmed_search & pubmed_fetch tools
├── skills/
│   └── pubmed/
│       └── SKILL.md      # Skill instructions for the agent
└── README.md

License

MIT