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yorkeccak/scientific-skills/pubmed-search

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version: "1.0.1" 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:

bash

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:

bash

$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:

``bash 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

bash

scripts/search "your natural language query" [maxResults]

Examples

bash

# 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

bash

scripts/search setup <api-key>

Output Format

json

{
  "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

bash

# 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

bash

# Find all papers on a topic
scripts/search "mechanisms of aging in humans" 50

Drug Discovery

bash

# Search for drug targets
scripts/search "novel targets for Alzheimer's disease treatment" 20

Clinical Research

bash

# Find clinical trial results
scripts/search "phase 3 trials for rheumatoid arthritis biologics" 15

Gene Function

bash

# Research gene function
scripts/search "role of TP53 in cancer development" 25

Error Handling

All commands return JSON with success field:

json

{
  "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

python

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

typescript

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.

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