Agent skill

biomedical-search

Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search.

View SKILL.md on GitHub Repository
Stars 27
Forks 2

Install this agent skill to your Project

npx add-skill https://github.com/yorkeccak/scientific-skills/tree/main/skills/biomedical-search

SKILL.md

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

  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:

bash
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:

bash
$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:

    bash
    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

json
{
  "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

bash
# 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

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

Drug Safety Assessment

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

Treatment Protocol Development

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

Medical Writing

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

Error Handling

All commands return JSON with success field:

json
{
  "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

python
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

typescript
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.

Recommended Agent Skills

Expand your agent's capabilities with these related and highly-rated skills.

yorkeccak/scientific-skills

arxiv-search

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.

27 2
Explore
yorkeccak/scientific-skills

biorxiv-search

Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.

27 2
Explore
yorkeccak/scientific-skills

medrxiv-search

Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search.

27 2
Explore
yorkeccak/scientific-skills

open-targets-search

Search Open Targets drug-disease associations with natural language queries. Target validation powered by Valyu semantic search.

27 2
Explore
yorkeccak/scientific-skills

drugbank-search

Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.

27 2
Explore
yorkeccak/scientific-skills

drug-discovery-search

End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.

27 2
Explore

Didn't find tool you were looking for?

Be as detailed as possible for better results