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:

$BIOMEDICAL_SCRIPT "CAR-T cell therapy" 20

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

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.