Biomedical Search

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:

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

Then use the full path for all commands:

$BIOMEDICAL_SCRIPT "CAR-T cell therapy" 20

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 biomedical databases, 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

• Complete biomedical information gathering
• Clinical research combined with basic science
• Finding trials, literature, and official drug info together
• Evidence-based medicine research
• Disease understanding from multiple angles

Output Format

{
  "success": true,
  "type": "biomedical_search",
  "query": "CAR-T cell therapy",
  "result_count": 20,
  "results": [
    {
      "title": "Title",
      "url": "https://...",
      "content": "Full content...",
      "source": "pubmed|biorxiv|medrxiv|clinical-trials|drug-labels",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.035
}

Processing Results

With jq

# Get 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 type
scripts/search "query" 20 | jq -r '.results[] | select(.source == "clinical-trials") | .title'

Common Use Cases

Clinical Research Planning

# Gather evidence for clinical study design
scripts/search "phase 2 trials checkpoint inhibitors melanoma" 50

Drug Safety Assessment

# Search literature, labels, and trials for safety data
scripts/search "SGLT2 inhibitors cardiovascular safety" 40

Treatment Protocol Development

# Find current practice and emerging approaches
scripts/search "pembrolizumab dosing regimens NSCLC" 30

Medical Writing

# Comprehensive research for medical communications
scripts/search "JAK inhibitors rheumatoid arthritis efficacy" 60

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 Biomedical 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-biorxiv", "valyu/valyu-medrxiv", "valyu/valyu-clinical-trials", "valyu/valyu-drug-labels"],
    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-biorxiv", "valyu/valyu-medrxiv", "valyu/valyu-clinical-trials", "valyu/valyu-drug-labels"],
  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.