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literature-search

Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search.

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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:

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:

$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:

    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

{
  "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

# 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

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

Cross-Disciplinary Research

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

Recent Developments

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

Medical Research

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

Error Handling

All commands return JSON with success field:

{
  "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

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

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

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.

Repository
wu-yc/LabClaw
Path

skills/literature/literature-search/SKILL.md

Commit

df37802

Last updated
First committed

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