literature-search

name	literature_search
description	Search PubMed for biomedical research papers by topic, disease, or gene. Use this skill when: (1) User asks to find papers about a topic, (2) User wants recent literature on a disease or gene, (3) User needs citations for research, (4) User asks "papers about X" or "literature on Y".
license	MIT
category	knowledge-retrieval
tags	["pubmed","literature","papers","citations"]

Literature Search

Search PubMed for biomedical research papers.

When to Use

• User asks "find papers about CRISPR"
• User wants recent literature on a disease/gene
• User needs citations or references
• User asks "papers about X" or "literature on Y"

Workflow

Step 1: Parse Query

Extract search terms from user input:

• Topic: "CRISPR base editing"
• Disease: "Alzheimer's disease"
• Gene: "BRCA1 mutations"

Step 2: Search PubMed

from open_rosalind.skills_v2.literature import tools

results = tools.search(query="CRISPR base editing", max_results=5)
# Returns: {hits: [{pmid, title, authors, abstract, date, doi}, ...]}

Step 3: Return Evidence-Grounded Result

return {
    "annotation": {
        "kind": "literature",
        "query": "CRISPR base editing",
        "n_hits": len(results["hits"]),
        "top_pmids": [h["pmid"] for h in results["hits"][:3]]
    },
    "confidence": 0.8,
    "notes": [],
    "pubmed": results  # Full search results (evidence)
}

Expected Outputs

Field	Description
pmid	PubMed ID
title	Paper title
authors	Author list
abstract	Full abstract
date	Publication date
doi	DOI identifier
link	PubMed URL

Design Principles

1. Tool-first: All data from pubmed.search API
2. Evidence-grounded: Return full pubmed object
3. Traceable: API calls logged to trace
4. Fail-safe: Empty results → confidence=0.0, logged to notes

Fallback Strategy

If query returns 0 hits:

1. Remove year filters
2. Try broader terms
3. Log fallback to notes