biorxiv-search skill by yorkeccak

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

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:

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:

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 bioRxiv, 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 <api-key>
```
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Rapid access to unpublished experimental data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.

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

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:

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:

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 bioRxiv, 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 <api-key>
```
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.

biorxiv-search

Documentation

Documentation

bioRxiv Search

Why This Skill is Powerful

Requirements

CRITICAL: Script Path Resolution

API Key Setup Flow

Example Flow:

When to Use This Skill

Output Format

Processing Results

With jq

Common Use Cases

Molecular Biology

Neuroscience

Genomics

Developmental Biology

Error Handling

API Endpoint

Architecture

Adding to Your Project

Python Integration

TypeScript Integration

Documentation

biorxiv-search

Documentation

bioRxiv Search

Why This Skill is Powerful

Requirements

CRITICAL: Script Path Resolution

API Key Setup Flow

Example Flow:

When to Use This Skill

Output Format

Processing Results

With jq

Common Use Cases

Molecular Biology

Neuroscience

Genomics

Developmental Biology

Error Handling

API Endpoint

Architecture

Adding to Your Project

Python Integration

TypeScript Integration