rare-disease-skills-index

id	rare_disease_skills_index
name	Rare Disease Skills Index
description	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.
tags	["rare_disease","ontology","orphanet","omim","hpo","clinical_report"]

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

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

---

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

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.

---

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.