# Rare Disease Skills Index

> Skills for rare disease case support: ontology-first normalization/retrieval and the clinical genetics consult report format contract (structure + theme). Load the relevant skill file when performing the matching task.

- Skill: `gabrielmoreira/rare-disease-skills-index` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add gabrielmoreira/rare-disease-skills-index`
- Raw SKILL.md: https://api.skillmd.com/api/skills/gabrielmoreira/rare-disease-skills-index/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Docs & Writing
- Author: gabrielmoreira (https://skillmd.com/u/gabrielmoreira)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/gabrielmoreira/rare-disease-skills-index

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# Agent Skills for Rare Disease Case Support

Curated playbooks for the rare disease MDT workflow. Each agent loads the skill
file that matches its current task — do not inline these contracts into prompts.

## Ontology-First Workflow

Deterministic normalization against the local Orphanet/OMIM/HPO layer before any
online evidence retrieval. Disease alias normalization, phenotype alignment,
xref resolution, and the SQLite query scripts live here.

**Skill file**: [rd_ontology_first.md](./rd_ontology_first.md)

**When to use**:
- Normalizing free-text phenotype or disease aliases (researcher, `ontology` mode)
- Resolving ORPHA/OMIM/MONDO/HPO cross-IDs before retrieval (researcher, `ontology` mode)
- Any candidate-name standardization step

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## Clinical Report Format

The authoritative format contract for the final clinical genetics consult report:
cover page, 4-level numbering, 9 sections, sign-off block, machine-readable JSON,
and the standalone HTML theme (embedded CSS, weasyprint PDF path).

**Skill file**: [clinical_report_format.md](./clinical_report_format.md)

**When to use**:
- Producing the final report (leader, after audit)
- Any time a deliverable must follow the signed-report structure and theme

**IMPORTANT**: This file is the single source of truth for report layout and
styling. The leader must follow it exactly rather than improvising structure
or CSS.

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## Guardrails (apply across all rare disease skills)

- Ontology normalization comes before retrieval, never after.
- Do not fabricate xref IDs, PMIDs, DOIs, or database annotations.
- Do not present online evidence as ontology truth.
- The report is decision-support, never a definitive diagnosis.