# Co Scientist Monarch Ontology

> Monarch ontology skill. Monarch Initiative queries for disease-gene associations, phenotype ontology navigation, cross-species phenotype comparison, and knowledge graph exploration. Use when working with monarch initiative queries for disease-gene associations, phenotype ontology navigation, cross-species phenotype comparison.

- Skill: `nahisaho/co-scientist-monarch-ontology` (Agent Skill)
- Install (CLI): `npx skillmds@latest add nahisaho/co-scientist-monarch-ontology`
- Raw SKILL.md: https://api.skillmd.com/api/skills/nahisaho/co-scientist-monarch-ontology/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: nahisaho (https://skillmd.com/u/nahisaho)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/nahisaho/co-scientist-monarch-ontology

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# Monarch ontology

Monarch ontology skill. Monarch Initiative queries for disease-gene associations, phenotype ontology navigation, cross-species phenotype comparison, and knowledge graph exploration.

## Use This Skill When

- Monarch Initiative queries for disease-gene associations.
- Phenotype ontology navigation.
- Cross-species phenotype comparison.
- Knowledge graph exploration.

## Required Inputs

- Research objective, decision target, or hypothesis.
- Available data, source constraints, and domain assumptions.
- Required outputs, success metrics, and deadline or reproducibility constraints.

## Workflow

1. Confirm scope, assumptions, and the exact artifact set to save.
2. Apply the narrowest domain method that answers the request with defensible evidence.
3. Save code, tables, figures, and intermediate outputs to files instead of chat-only output.
4. State limitations, uncertainty, and any validation or sensitivity checks performed.
5. Append skill selection, handoff I/O, and file writes to `logs/process-log.jsonl`.

## Deliverables

- `report.md`: concise method, results, interpretation, and file inventory in the user's language.
- `results/`: structured outputs, metrics, model artifacts, or extracted findings.
- `figures/`: English-only charts, diagrams, or panels when visual output is needed.
- `data/`: processed or derived datasets when transformation occurs.

## Available Tools (MCP)

> External tools available via [ToolUniverse](https://github.com/mims-harvard/ToolUniverse) MCP server.
> Falls back to Python `requests` + public REST APIs when MCP is unavailable.

| Source | Tool | Description |
|--------|------|-------------|
| Monarch Initiative | `Monarch_search` | Monarch Initiative API |
| Monarch Initiative | `Monarch_get_associations` | Monarch Initiative API |

## Quality Gates

- [ ] The selected method matches the scientific question and stated assumptions.
- [ ] Outputs are reproducible, saved to files, and traceable from inputs to conclusions.
- [ ] Missing data, uncertainty, bias, and hard limits are made explicit.
- [ ] `report.md` and `logs/process-log.jsonl` reference the generated artifacts.
- [ ] No essential result remains chat-only.

If any gate fails: identify the specific failing check, fix the issue, and re-validate before proceeding.

## Gotchas

- Database API versions change frequently. Pin the API version or record access date for reproducibility
- Gene/protein identifiers differ across databases. Map to a canonical namespace before cross-database queries
- Enrichment analysis p-values require multiple testing correction. Report adjusted p-values, not raw

## Validation Loop

1. Execute analysis and generate outputs
2. Check:
   - Method selection matches the research question and stated assumptions
   - All outputs are saved to files (no chat-only results)
   - Limitations and uncertainty are explicitly stated
   - `logs/process-log.jsonl` is updated with execution trace
3. If any check fails:
   - Identify the failing gate
   - Fix the specific issue
   - Re-run validation
4. Proceed only after all gates pass