MCPInstall

literature-search

Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries 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 literature-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 literature-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.

Literature Search

Search across all major scientific literature databases (PubMed, arXiv, bioRxiv, medRxiv) 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 article content, not just abstracts
  • Image Links: Includes figures and images from papers
  • Comprehensive Coverage: Search across PubMed, arXiv, bioRxiv, and medRxiv simultaneously
  • Unified Results: Get results from all 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:

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

Then use the full path for all commands:

$LITERATURE_SCRIPT "CRISPR gene editing advances" 15

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 scientific literature, 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

  • Comprehensive literature reviews across all domains
  • Finding all relevant research on a topic
  • Cross-domain scientific discovery
  • Combining biomedical, physics, and preprint literature
  • Emerging research across disciplines

Output Format

{
  "success": true,
  "type": "literature_search",
  "query": "CRISPR gene editing advances",
  "result_count": 15,
  "results": [
    {
      "title": "Article Title",
      "url": "https://...",
      "content": "Full article text with figures...",
      "source": "pubmed|arxiv|biorxiv|medrxiv",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}

Processing Results

With jq

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

Common Use Cases

Comprehensive Literature Review

# Search across all sources for thorough review
scripts/search "mechanisms of cellular senescence" 100

Cross-Disciplinary Research

# Find papers spanning multiple fields
scripts/search "quantum computing applications in drug discovery" 50

Recent Developments

# Get latest preprints and publications
scripts/search "foundation models for protein folding" 30

Medical Research

# Search biomedical literature comprehensively
scripts/search "immunotherapy checkpoint inhibitors resistance" 40

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 Literature 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-arxiv", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv"],
    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-arxiv", "valyu/valyu-biorxiv", "valyu/valyu-medrxiv"],
  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 literature-search skill do?

Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search.

How do I install literature-search?

Run npx skills add https://github.com/yorkeccak/scientific-skills --skill literature-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/literature-search/ (personal) or .claude/skills/literature-search/ (project).

Which AI agents can use literature-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 literature-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 literature-search?

It is published by yorkeccak in yorkeccak/scientific-skills. It has 601 recorded installs.

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