mims-harvard/devtu-auto-discover-apis
skills/devtu-auto-discover-apis/SKILL.md
Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to identify missing tool categories, web searches for APIs, automated tool creation using devtu-create-tool patterns, validation with devtu-fix-tool, and git workflow management. Use when expanding ToolUniverse coverage, adding new API integrations, or systematically discovering scientific resources.
$ install --global
skillsauthnpx skillsauth add mims-harvard/tooluniverse devtu-auto-discover-apisInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- devtu-auto-discover-apis
- description:
- Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to identify missing tool categories, web searches for APIs, automated tool creation using devtu-create-tool patterns, validation with devtu-fix-tool, and git workflow management. Use when expanding ToolUniverse coverage, adding new API integrations, or systematically discovering scientific resources.
Automated Life Science API Discovery & Tool Creation
Discover, create, validate, and integrate life science APIs into ToolUniverse.
Four-Phase Workflow
Gap Analysis → API Discovery → Tool Creation → Validation → Integration
↓ ↓ ↓ ↓ ↓
Coverage Web Search devtu-create devtu-fix Git PR
Human approval gates after: discovery, creation, validation, and before PR.
Phase 1: Discovery & Gap Analysis
1.1 Analyze Current Coverage
Load ToolUniverse, categorize tools by domain (genomics, proteomics, drug discovery, clinical, omics, imaging, literature, pathways, systems biology). Count per category.
1.2 Identify Gap Domains
- Critical Gap: <5 tools in category
- Moderate Gap: 5-15 tools, missing key subcategories
- Emerging Gap: New technologies not represented
Common gaps: single-cell genomics, metabolomics, patient registries, microbial genomics, multi-omics integration, synthetic biology, toxicology.
1.3 Web Search for APIs
For each gap domain, run multiple queries:
"[domain] API REST JSON"— direct API search"[domain] public database"— database discovery"[domain] API 2025 OR 2026"— recent releases"[domain] database" site:nar.oxfordjournals.org— NAR Database Issue
Extract: base URL, endpoints, auth method, parameter schemas, rate limits.
1.4 Score and Prioritize
| Criterion | Max Points | |-----------|------------| | Documentation Quality | 20 | | API Stability | 15 | | Authentication Simplicity | 15 | | Coverage | 15 | | Maintenance | 10 | | Community | 10 | | License | 10 | | Rate Limits | 5 |
High priority (>=70), Medium (50-69), Low (<50).
1.5 Generate Discovery Report
Coverage analysis, prioritized candidates with scores, implementation roadmap.
Phase 2: Tool Creation
For each API, use Skill(skill="devtu-create-tool") or follow these patterns.
Architecture Decision
- Multiple endpoints → multi-operation tool (single class, multiple JSON wrappers)
- Single endpoint → single-operation acceptable
Key Steps
- Design tool class following template — see references/tool-templates.md
- Create JSON config with oneOf return_schema
- Find real test examples (use List endpoint → extract IDs → verify)
- Register in
default_config.py
Critical Requirements
- return_schema MUST have
oneOf(success + error schemas) - test_examples MUST use real IDs (NO placeholders)
- Tool name <= 55 characters
- NEVER raise exceptions in
run()— return error dict - Set timeout on all HTTP requests (30s)
Phase 3: Validation
Full guide: references/validation-guide.md
Quick Validation Checklist
- Schema: oneOf structure, data wrapper, error field
- Placeholders: No TEST/DUMMY/PLACEHOLDER in test_examples
- Loading: 3-step check (class registered, config registered, wrappers generated)
- Integration tests:
python scripts/test_new_tools.py [api_name] -v→ 100% pass
Fix failures with Skill(skill="devtu-fix-tool").
Phase 4: Integration
Use Skill(skill="devtu-github") or:
- Create branch:
feature/add-[api-name]-tools - Stage tool files + default_config.py
- Commit with descriptive message
- Push and create PR with validation results
Processing Patterns
| Pattern | When to Use | |---------|------------| | Batch (multiple APIs → single PR) | Same domain, similar structure | | Iterative (one API at a time) | Complex auth, novel patterns | | Discovery-only (report, no tools) | Planning roadmap | | Validation-only (audit existing) | PR review, quality check |
References
- Tool templates (Python class + JSON config): references/tool-templates.md
- Validation & integration guide: references/validation-guide.md
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