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
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
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.