SuperCharged-Claude-Code-Upgrade/biorxiv-search/skill.md

name, description, keywords, license

name	description	keywords	license
biorxiv-search	Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.	biorxiv biology-preprints molecular-biology genetics life-sciences semantic-search	MIT

bioRxiv Search

Search the complete bioRxiv database of biological sciences preprints 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: Access to all bioRxiv preprints in biological sciences

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:

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

Then use the full path for all commands:

$BIORXIV_SCRIPT "CRISPR gene editing" 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 bioRxiv, 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.

Example Flow:

User: Search bioRxiv for CRISPR advances
→ Response: {"success": false, "setup_required": true, ...}
→ Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
→ User: "val_abc123..."
→ Claude runs: scripts/search setup val_abc123...
→ Response: {"success": true, "type": "setup", ...}
→ Claude retries: scripts/search "CRISPR advances" 10
→ Success!

When to Use This Skill

• Finding biology research not yet published in journals
• Cross-disciplinary life sciences research
• Rapid access to unpublished experimental data
• Disease mechanism research
• Evolutionary and developmental biology studies
• Ecological research and conservation biology

Output Format

{
  "success": true,
  "type": "biorxiv_search",
  "query": "CRISPR gene editing",
  "result_count": 10,
  "results": [
    {
      "title": "Article Title",
      "url": "https://biorxiv.org/content/...",
      "content": "Full article text with figures...",
      "source": "biorxiv",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}

Processing Results

With jq

# Get article titles
scripts/search "query" 10 | jq -r '.results[].title'

# Get URLs
scripts/search "query" 10 | jq -r '.results[].url'

# Extract full content
scripts/search "query" 10 | jq -r '.results[].content'

Common Use Cases

Molecular Biology

# Find recent molecular biology papers
scripts/search "protein-protein interaction networks" 50

Neuroscience

# Search for neuroscience research
scripts/search "optogenetics in behavior studies" 20

Genomics

# Find genomics papers
scripts/search "single cell RNA sequencing analysis" 15

Developmental Biology

# Search for developmental biology papers
scripts/search "embryonic stem cell differentiation" 25

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 bioRxiv 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-biorxiv"],
    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-biorxiv"],
  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.