chembl-search

Original：🇺🇸 English
Translated
2 scripts

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

37installs
Sourceyorkeccak/scientific-skills
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NPX Install

npx skill4agent add yorkeccak/scientific-skills chembl-search

Tags

Translated version includes tags in frontmatter
chembl-searchsemantic-searchdrug-discoverybioactive-moleculesvalyu-api

SKILL.md Content

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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:
bash
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:
bash
$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"
  2. Once the user provides the key, run:
    bash
    scripts/search setup <api-key>
  3. 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

json
{
  "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

bash
# 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

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

Target Validation

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

SAR Analysis

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

Mechanism Research

bash
# Search for mechanism data
scripts/search "allosteric modulators of NMDA receptors" 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 ChEMBL 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="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

typescript
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.