biomedical-search

Biomedical Search

Search across all major biomedical databases (PubMed, bioRxiv, medRxiv, ClinicalTrials.gov, FDA drug labels) 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 content from literature, trials, and drug labels
Image Links: Includes figures and images when available
Comprehensive Coverage: Search across PubMed, bioRxiv, medRxiv, clinical trials, and drug labels simultaneously
Unified Results: Get results from all biomedical sources in a single query

Requirements

Node.js 18+ (uses built-in fetch)
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:

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:

API Key Setup Flow

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

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"
Once the user provides the key, run:
```
scripts/search setup <api-key>
```
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.