Literature Search

Literature Search

Search across all major scientific literature databases (PubMed, arXiv, bioRxiv, medRxiv) simultaneously using natural language queries powered by Valyu's semantic search API.

Why This Skill is Powerful

• No API Parameter Parsing: Just pass natural language queries directly - no need to construct complex search parameters
• Semantic Search: Understands the meaning of your query, not just keyword matching
• Full-Text Access: Returns complete article content, not just abstracts
• Image Links: Includes figures and images from papers
• Comprehensive Coverage: Search across PubMed, arXiv, bioRxiv, and medRxiv simultaneously
• Unified Results: Get results from all sources in a single query

Requirements

1. Node.js 18+ (uses built-in fetch)
2. Valyu API key from https://platform.valyu.ai ($10 free credits)

CRITICAL: Script Path Resolution

The scripts/search commands in this documentation are relative to this skill's installation directory.

Before running any command, locate the script using:

bashCopy code
LITERATURE_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/literature-search/*/scripts/*" -type f 2>/dev/null | head -1)

Then use the full path for all commands:

bashCopy code
$LITERATURE_SCRIPT "CRISPR gene editing advances" 15

API Key Setup Flow

When you run a search and receive "setup_required": true, follow this flow:

1. Ask the user for their API key: "To search scientific literature, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"

2. Once the user provides the key, run:

   bashCopy code
   scripts/search setup <api-key>
   

3. Retry the original search.

When to Use This Skill

• Comprehensive literature reviews across all domains
• Finding all relevant research on a topic
• Cross-domain scientific discovery
• Combining biomedical, physics, and preprint literature
• Emerging research across disciplines

Output Format

jsonCopy code
{
  "success": true,
  "type": "literature_search",
  "query": "CRISPR gene editing advances",
  "result_count": 15,
  "results": [
    {
      "title": "Article Title",
      "url": "https://...",
      "content": "Full article text with figures...",
      "source": "pubmed|arxiv|biorxiv|medrxiv",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}

Processing Results

With jq

bashCopy code
# Get article titles
scripts/search "query" 20 | jq -r '.results[].title'

# Get URLs
scripts/search "query" 20 | jq -r '.results[].url'

# Extract full content
scripts/search "query" 20 | jq -r '.results[].content'

# Filter by source
scripts/search "query" 20 | jq -r '.results[] | select(.source == "arxiv") | .title'

Common Use Cases

Comprehensive Literature Review

bashCopy code
# Search across all sources for thorough review
scripts/search "mechanisms of cellular senescence" 100

Cross-Disciplinary Research

bashCopy code
# Find papers spanning multiple fields
scripts/search "quantum computing applications in drug discovery" 50

Recent Developments

bashCopy code
# Get latest preprints and publications
scripts/search "foundation models for protein folding" 30

Medical Research

bashCopy code
# Search biomedical literature comprehensively
scripts/search "immunotherapy checkpoint inhibitors resistance" 40

Error Handling

All commands return JSON with success field:

jsonCopy code
{
  "success": false,
  "error": "Error message"
}

Exit codes:

• 0 - Success
• 1 - Error (check JSON for details)

API Endpoint

• Base URL: https://api.valyu.ai/v1
• Endpoint: /search
• Authentication: X-API-Key header

Architecture

Copy code
scripts/
├── search          # Bash wrapper
└── search.mjs      # Node.js CLI

Direct API calls using Node.js built-in fetch(), zero external dependencies.

Adding to Your Project

If you're building an AI project and want to integrate Literature Search directly into your application, use the Valyu SDK:

Python Integration

pythonCopy code
from valyu import Valyu

client = Valyu(api_key="your-api-key")

response = client.search(
    query="your search query here",
    included_sources=["valyu/valyu-pubmed", "valyu/valyu-arxiv", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv"],
    max_results=20
)

for result in response["results"]:
    print(f"Title: {result['title']}")
    print(f"URL: {result['url']}")
    print(f"Content: {result['content'][:500]}...")

TypeScript Integration

typescriptCopy code
import { Valyu } from "valyu-js";

const client = new Valyu("your-api-key");

const response = await client.search({
  query: "your search query here",
  includedSources: ["valyu/valyu-pubmed", "valyu/valyu-arxiv", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv"],
  maxResults: 20
});

response.results.forEach((result) => {
  console.log(`Title: ${result.title}`);
  console.log(`URL: ${result.url}`);
  console.log(`Content: ${result.content.substring(0, 500)}...`);
});

See the Valyu docs for full integration examples and SDK reference.