Agent skill

drug-discovery-search

End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.

View SKILL.md on GitHub Repository
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Install this agent skill to your Project

npx add-skill https://github.com/yorkeccak/scientific-skills/tree/main/skills/drug-discovery-search

SKILL.md

Drug Discovery Search

Search across all major drug discovery databases (ChEMBL, DrugBank, FDA drug labels, Open Targets) simultaneously 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, target, and drug information
  • Image Links: Includes molecular structures and data visualizations
  • Comprehensive Coverage: Search across ChEMBL, DrugBank, drug labels, and Open Targets simultaneously
  • Unified Results: Get results from all drug discovery sources in a single query

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

Then use the full path for all commands:

bash
$DRUG_DISCOVERY_SCRIPT "JAK2 inhibitors" 20

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 drug discovery databases, 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

  • End-to-end drug discovery information
  • Target validation through compounds and trials
  • Complete drug development information
  • Compound optimization with target data
  • Safety and efficacy research

Output Format

json
{
  "success": true,
  "type": "drug_discovery_search",
  "query": "JAK2 inhibitors",
  "result_count": 20,
  "results": [
    {
      "title": "Compound/Drug/Target Title",
      "url": "https://...",
      "content": "Full data including compounds, targets, mechanisms...",
      "source": "chembl|drugbank|drug-labels|open-targets",
      "relevance_score": 0.95,
      "images": ["https://example.com/structure.png"]
    }
  ],
  "cost": 0.035
}

Processing Results

With jq

bash
# Get titles
scripts/search "query" 20 | jq -r '.results[].title'

# Get URLs
scripts/search "query" 20 | jq -r '.results[].url'

# Extract full content
scripts/search "query" 20 | jq -r '.results[].content'

# Filter by source
scripts/search "query" 20 | jq -r '.results[] | select(.source == "chembl") | .title'

Common Use Cases

Target Identification

bash
# Find validated targets and compounds
scripts/search "BTK inhibitors for autoimmune diseases" 50

Lead Optimization

bash
# Search SAR and compound data
scripts/search "EGFR inhibitors blood-brain barrier penetration" 40

Drug Repurposing

bash
# Find repurposing opportunities
scripts/search "mTOR inhibitors cancer and aging" 30

Safety Assessment

bash
# Gather safety and interaction data
scripts/search "tyrosine kinase inhibitors cardiac toxicity" 60

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 Drug Discovery 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", "valyu/valyu-drugbank", "valyu/valyu-drug-labels", "valyu/valyu-open-targets"],
    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", "valyu/valyu-drugbank", "valyu/valyu-drug-labels", "valyu/valyu-open-targets"],
  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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