MCPInstall

biomedical-search

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

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Install

Works with every agent the skills CLI supports.

npx skills add https://github.com/yorkeccak/scientific-skills --skill biomedical-search
  1. 01

    Install

    Run the command in your project. The CLI asks which agents to install for.

  2. 02

    Describe the task

    Ask your agent for something this skill covers. It loads biomedical-search automatically when relevant.

  3. 03

    Review the result

    The agent follows the SKILL.md steps, scripts and references bundled with the skill.

SKILL.md

The instructions your agent reads when the skill is triggered.

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:

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.

FAQ

What does the biomedical-search skill do?

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

How do I install biomedical-search?

Run npx skills add https://github.com/yorkeccak/scientific-skills --skill biomedical-search in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/biomedical-search/ (personal) or .claude/skills/biomedical-search/ (project).

Which AI agents can use biomedical-search?

Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.

Is biomedical-search safe to install?

No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.

Who maintains biomedical-search?

It is published by yorkeccak in yorkeccak/scientific-skills. It has 732 recorded installs.

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