create-tooluniverse-skill

Files (2)

• REFERENCE.md
• SKILL.md

SKILL.md (first lines)

# Create ToolUniverse Skill

Systematic workflow for creating production-ready ToolUniverse skills that integrate multiple scientific tools, follow implementation-agnostic standards, and achieve 100% test coverage.

## Core Principles (Critical)

**CRITICAL - Read devtu-optimize-skills**: This skill builds on principles from `devtu-optimize-skills`. Invoke that skill first or review its 10 pillars:

1. **TEST FIRST** - Never write documentation without testing tools
2. **Verify tool contracts** - Don't trust function names
3. **Handle SOAP tools** - Add `operation` parameter where needed
4. **Implementation-agnostic docs** - Separate SKILL.md from code
5. **Foundation first** - Use comprehensive aggregators
6. **Disambiguate carefully** - Resolve IDs properly
7. **Implement fallbacks** - Primary → Fallback → Default
8. **Grade evidence** - T1-T4 tiers on claims
9. **Require quantified completeness** - Numeric minimums
10. **Synthesize** - Models and hypotheses, not just lists

## When to Use This Skill

Use this skill when:
- Creating new ToolUniverse skills for specific domains
- Building research workflows using scientific tools
- Developing analysis capabilities (e.g., metabolomics, single-cell, cancer genomics)
- Integrating multiple databases into coherent pipelines
- Following up on "create [domain] skill" requests

## Overview: 7-Phase Workflow

```
Phase 1: Domain Analysis →
Phase 2: Tool Discovery & Testing →
Phase 3: Tool Creation (if needed) →
Phase 4: Implementation →
Phase 5: Documentation →
Phase 6: Testing & Validation →
Phase 7: Packaging
```

**Time per skill**: ~1.5-2 hours (tested and documented)

---

## Phase 1: Domain Analysis

**Objective**: Understand the scientific domain and identify required capabilities

**Duration**: 15 minutes

### 1.1 Understand Use Cases

Gather concrete examples of how the skill will be used:
- "What analyses should this skill perform?"
- "Can you give examples of typical queries?"
- "What outputs do users expect?"

**Example queries to clarify**:
- For metabolomics: "Identify metabolites in a sample" vs "Find pathways for metabolites" vs "Compare metabolite profiles"
- For cancer genomics: "Interpret mutations" vs "Find therapies" vs "Match clinical trials"

### 1.2 Identify Required Data Types

List what the skill needs to work with:
- **Input types**: Gene lists, protein IDs, compound names, disease names, etc.
- **Output types**: Reports, tables, visualizations, data files
- **Intermediate data**: ID mappings, enrichment results, annotations

### 1.3 Define Analysis Phases

Break the workflow into logical phases:

**Example - Metabolomics Skill**:
1. Phase 1: Metabolite identification (name → IDs)
2. Phase 2: Metabolite annotation (properties, pathways)
3. Phase 3: Pathway enrichment (statistical analysis)
4. Phase 4: Comparative analysis (samples/conditions)

**Example - Cancer Genomics Skill**:
1. Phase 1: Mutation validation (check databases)
2. Phase 2: Clinical significance (actionability)
3. Phase 3: Therapy matching (FDA approvals)
4. Phase 4: Trial matching (clinical trials)

### 1.4 Review Related Skills

Check existing ToolUniverse skills for relevant patterns:
- Read similar skills in `skills/` directory
- Note tool usage patterns
- Identify reusable approaches

**Useful related skills**:
- `tooluniverse-systems-biology` - Multi-database integration
- `tooluniverse-target-research` - Comprehensive profiling
- `tooluniverse-drug-research` - Pharmaceutical workflows

---

## Phase 2: Tool Discovery & Testing

**Objective**: Find and verify tools needed for each analysis phase

**Duration**: 30-45 minutes

**CRITICAL**: Following test-driven development from devtu-optimize-skills

### 2.1 Search Available Tools

**Tool locations**: `/src/tooluniverse/data/*.json` (186 tool files)

**Search strategies**:
1. **Keyword search**: `grep -r "keyword" src/tooluniverse/data/*.json`
2. **Tool listing**: List all tools from specific database
3. **Function search**: Search by domain (metabolomics, genomics, etc.)

**Example searches**:
```bash
# Find metabolomics tools
grep -l "metabol" src/tooluniverse/data/*.json

From Zaoqu-Liu/ScienceClaw, MIT.

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