biorxiv-search

name biorxiv-search description Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu. keywords ["biorxiv","biology-preprints","molecular-biology","genetics","life-sciences","semantic-search"] license 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 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: $BIORXIV_SCRIPT "CRISPR gene editing" 15 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Skill Finding biology research not yet published in journals Cross-disciplinary life sciences research Rapid access to unpublished experimental data Disease mechanism research Evolutionary and developmental biology studies Ecological research and conservation biology Output Format {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.