pubmed-search

name pubmed-search description Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, integrate into your AI projects. keywords ["pubmed","biomedical-literature","medical-research","semantic-search","natural-language-queries","full-text-search","research-integration"] license MIT PubMed Search Search the complete PubMed database of biomedical literature 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 of PubMed's biomedical literature Requirements Node.js 18+ (uses built-in fetch) Valyu API key from https://platform.valyu.ai ($10 free credits) CRITICAL: Script Path Resolution The scripts/search commands in this documentation are relative to this skill's installation directory. Before running any command, locate the script using: PUBMED_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/pubmed-search/*/scripts/*" - type f 2>/dev/null | head -1) Then use the full path for all commands: $PUBMED_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 PubMed, 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 PubMed for CAR-T cell therapy 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 "CAR-T cell therapy advances" 10 → Success! Usage Basic Search scripts/search "your natural language query" [maxResults] Examples # Search for recent COVID-19 research scripts/search "COVID-19 vaccine efficacy studies" 15 # Find papers on a specific gene scripts/search "BRCA1 mutations and breast cancer risk" 20 # Search for treatment approaches scripts/search "immunotherapy for melanoma clinical trials" 10 # Drug mechanism research scripts/search "mechanism of action of metformin in type 2 diabetes" 12 Setup Command scripts/search setup <api-key> Output Format { "success" : true , "type" : "pubmed_search" , "query" : "CRISPR gene editing" , "result_count" : 10 , "results" : [ { "title" : "Article Title" , "url" : "https://pubmed.ncbi.nlm.nih.gov/..." , "content" : "Full article text with figures..." , "source" : "pubmed" , "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 Literature Review # Find all papers on a topic scripts/search "mechanisms of aging in humans" 50 Drug Discovery # Search for drug targets scripts/search "novel targets for Alzheimer's disease treatment" 20 Clinical Research # Find clinical trial results scripts/search "phase 3 trials for rheumatoid arthritis biologics" 15 Gene Function # Research gene function scripts/search "role of TP53 in cancer development" 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 PubMed 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= "immunotherapy for melanoma" , included_sources=[ "valyu/valyu-pubmed" ], 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 : "immunotherapy for melanoma" , includedSources : [ "valyu/valyu-pubmed" ], 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.