Reorganize: Move all skills to skills/ folder
- Created skills/ directory - Moved 272 skills to skills/ subfolder - Kept agents/ at root level - Kept installation scripts and docs at root level Repository structure: - skills/ - All 272 skills from skills.sh - agents/ - Agent definitions - *.sh, *.ps1 - Installation scripts - README.md, etc. - Documentation Co-Authored-By: Claude <noreply@anthropic.com>
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skills/drug-discovery-search/skill.md
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skills/drug-discovery-search/skill.md
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name: drug-discovery-search
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description: End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.
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keywords:
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- drug-discovery
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- drug-development
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- compound-screening
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- target-validation
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- comprehensive-search
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- semantic-search
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license: MIT
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---
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# Drug Discovery Search
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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.
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## Why This Skill is Powerful
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- **No API Parameter Parsing**: Just pass natural language queries directly - no need to construct complex search parameters
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- **Semantic Search**: Understands the meaning of your query, not just keyword matching
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- **Full-Text Access**: Returns complete compound, target, and drug information
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- **Image Links**: Includes molecular structures and data visualizations
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- **Comprehensive Coverage**: Search across ChEMBL, DrugBank, drug labels, and Open Targets simultaneously
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- **Unified Results**: Get results from all drug discovery sources in a single query
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## Requirements
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1. Node.js 18+ (uses built-in fetch)
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2. Valyu API key from https://platform.valyu.ai ($10 free credits)
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## CRITICAL: Script Path Resolution
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The `scripts/search` commands in this documentation are relative to this skill's installation directory.
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Before running any command, locate the script using:
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```bash
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DRUG_DISCOVERY_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/drug-discovery-search/*/scripts/*" -type f 2>/dev/null | head -1)
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```
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Then use the full path for all commands:
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```bash
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$DRUG_DISCOVERY_SCRIPT "JAK2 inhibitors" 20
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```
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## API Key Setup Flow
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When you run a search and receive `"setup_required": true`, follow this flow:
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1. **Ask the user for their API key:**
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"To search drug discovery databases, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
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2. **Once the user provides the key, run:**
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```bash
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scripts/search setup <api-key>
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```
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3. **Retry the original search.**
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## When to Use This Skill
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- End-to-end drug discovery information
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- Target validation through compounds and trials
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- Complete drug development information
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- Compound optimization with target data
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- Safety and efficacy research
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## Output Format
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```json
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{
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"success": true,
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"type": "drug_discovery_search",
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"query": "JAK2 inhibitors",
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"result_count": 20,
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"results": [
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{
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"title": "Compound/Drug/Target Title",
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"url": "https://...",
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"content": "Full data including compounds, targets, mechanisms...",
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"source": "chembl|drugbank|drug-labels|open-targets",
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"relevance_score": 0.95,
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"images": ["https://example.com/structure.png"]
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}
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],
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"cost": 0.035
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}
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```
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## Processing Results
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### With jq
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```bash
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# Get titles
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scripts/search "query" 20 | jq -r '.results[].title'
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# Get URLs
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scripts/search "query" 20 | jq -r '.results[].url'
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# Extract full content
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scripts/search "query" 20 | jq -r '.results[].content'
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# Filter by source
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scripts/search "query" 20 | jq -r '.results[] | select(.source == "chembl") | .title'
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```
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## Common Use Cases
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### Target Identification
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```bash
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# Find validated targets and compounds
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scripts/search "BTK inhibitors for autoimmune diseases" 50
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```
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### Lead Optimization
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```bash
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# Search SAR and compound data
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scripts/search "EGFR inhibitors blood-brain barrier penetration" 40
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```
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### Drug Repurposing
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```bash
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# Find repurposing opportunities
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scripts/search "mTOR inhibitors cancer and aging" 30
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```
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### Safety Assessment
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```bash
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# Gather safety and interaction data
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scripts/search "tyrosine kinase inhibitors cardiac toxicity" 60
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```
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## Error Handling
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All commands return JSON with `success` field:
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```json
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{
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"success": false,
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"error": "Error message"
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}
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```
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Exit codes:
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- `0` - Success
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- `1` - Error (check JSON for details)
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## API Endpoint
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- Base URL: `https://api.valyu.ai/v1`
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- Endpoint: `/search`
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- Authentication: X-API-Key header
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## Architecture
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```
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scripts/
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├── search # Bash wrapper
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└── search.mjs # Node.js CLI
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```
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Direct API calls using Node.js built-in `fetch()`, zero external dependencies.
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## Adding to Your Project
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If you're building an AI project and want to integrate Drug Discovery Search directly into your application, use the Valyu SDK:
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### Python Integration
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```python
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from valyu import Valyu
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client = Valyu(api_key="your-api-key")
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response = client.search(
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query="your search query here",
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included_sources=["valyu/valyu-chembl", "valyu/valyu-drugbank", "valyu/valyu-drug-labels", "valyu/valyu-open-targets"],
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max_results=20
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)
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for result in response["results"]:
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print(f"Title: {result['title']}")
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print(f"URL: {result['url']}")
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print(f"Content: {result['content'][:500]}...")
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```
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### TypeScript Integration
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```typescript
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import { Valyu } from "valyu-js";
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const client = new Valyu("your-api-key");
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const response = await client.search({
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query: "your search query here",
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includedSources: ["valyu/valyu-chembl", "valyu/valyu-drugbank", "valyu/valyu-drug-labels", "valyu/valyu-open-targets"],
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maxResults: 20
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});
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response.results.forEach((result) => {
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console.log(`Title: ${result.title}`);
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console.log(`URL: ${result.url}`);
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console.log(`Content: ${result.content.substring(0, 500)}...`);
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});
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```
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See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
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