PubMed Literature Search Tool for Biomedical Research

Abstract

Search PubMed literature database and extract abstract information. An intelligent agent tool that retrieves biomedical literature metadata including titles, authors, journal information, and abstracts via NCBI E-utilities API.

Cleaned Submission Note

This revision replaces a raw JSON display with readable Markdown. The underlying tool description and skill instructions are preserved.

Tool Summary

Search PubMed literature database and extract abstract information. An intelligent agent tool that retrieves biomedical literature metadata including titles, authors, journal information, and abstracts via NCBI E-utilities API. PubMed Literature Search Tool 1.0.0

Input Schema

The original structured input schema is retained conceptually. Use the SKILL section below for executable instructions.

SKILL

PubMed Literature Search Tool

Name

PubMed Literature Search Tool

Description

Search PubMed literature database and extract abstract information. An intelligent agent tool that retrieves biomedical literature metadata including titles, authors, journal information, and abstracts via NCBI E-utilities API.

Input

• Keyword list: Keywords/phrases for searching (list[string])
• Max results: Maximum number of results to return (int, default 10)
• Sort by: "relevance" or "date" (default "relevance")
• Date filter: Optional publication date range

Execution Steps

Step 1: Build Search Query

• Combine keyword list into PubMed search syntax
• Use Boolean operators (AND/OR/NOT) to connect terms
• Handle special characters and quoted phrases

Step 2: Call ESearch API

• Endpoint: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
• Parameters: db=pubmed, term={query}, retmax={max_results}, sort={relevance|date}, retmode=json
• Get list of PMIDs

Step 3: Call EFetch API for Details

• Endpoint: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
• Parameters: db=pubmed, id={pmids}, retmode=xml, rettype=abstract
• Parse XML to get complete metadata

Step 4: Data Processing and Sorting

• Extract title, author list, journal name, publication date, abstract
• Sort by relevance score or publication date
• Remove duplicates

Step 5: Output Results

• JSON format output (default) or Markdown table
• Contains PMID, title, authors, journal, year, abstract

Output Format

JSON Format

{
  "query": "search terms",
  "total_results": 100,
  "returned": 10,
  "results": [
    {
      "pmid": "12345678",
      "title": "Article Title",
      "authors": ["Author1", "Author2"],
      "journal": "Journal Name",
      "pub_date": "2024-01-15",
      "abstract": "Article abstract text...",
      "doi": "10.1234/example",
      "mesh_terms": ["Term1", "Term2"]
    }
  ]
}

Markdown Format

Tool Dependencies

• requests: HTTP library for calling PubMed API
• xml.etree.ElementTree: XML parsing
• json: Data serialization
• datetime: Date processing

API Call Limits

• NCBI requires no more than 3 requests per second
• Email parameter required for contact
• API Key can increase rate limit

Error Handling

• Network errors: Retry 3 times with exponential backoff
• API errors: Return error code and message
• No results: Return empty list with tip message

Integrity Note

This is a formatting cleanup revision. It does not introduce a new scientific claim.