yorkeccak/scientific-skills/chembl-search

ChEMBL Search

Search the complete ChEMBL database of bioactive molecules, drug targets, and binding data 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 compound and target information
• Image Links: Includes molecular structures and data visualizations
• Comprehensive Coverage: Access to all ChEMBL bioactive molecule data for drug discovery

Requirements

1. Node.js 18+ (uses built-in fetch)
2. 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:

CHEMBL_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/chembl-search/*/scripts/*" -type f 2>/dev/null | head -1)

Then use the full path for all commands:

$CHEMBL_SCRIPT "kinase inhibitors" 15

API Key Setup Flow

When you run a search and receive "setup_required": true, follow this flow:

1. Ask the user for their API key:

"To search ChEMBL, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"

1. Once the user provides the key, run:

``bash scripts/search setup <api-key> ``

1. Retry the original search.

When to Use This Skill

• Finding bioactive compounds for drug discovery
• Target-based compound searching
• Compound property optimization
• Assay data and biological activity research
• Structure-activity relationship studies
• Lead compound identification

Output Format

{
  "success": true,
  "type": "chembl_search",
  "query": "kinase inhibitors",
  "result_count": 10,
  "results": [
    {
      "title": "Compound/Assay Title",
      "url": "https://chembl.org/...",
      "content": "Compound data, targets, assay results...",
      "source": "chembl",
      "relevance_score": 0.95,
      "images": ["https://example.com/structure.png"]
    }
  ],
  "cost": 0.025
}

Processing Results

With jq

# Get compound 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

Drug Discovery

# Find lead compounds
scripts/search "JAK2 selective inhibitors for myelofibrosis" 50

Target Validation

# Search for target information
scripts/search "protein kinase B binding assays" 20

SAR Analysis

# Find structure-activity relationships
scripts/search "benzimidazole derivatives anticancer activity" 15

Mechanism Research

# Search for mechanism data
scripts/search "allosteric modulators of NMDA receptors" 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 ChEMBL 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-chembl"],
    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-chembl"],
  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.