SKILL.md

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.

pubmed-search