tooluniverse-rare-disease-diagnosis

Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant interpretation, and structure-based variant analysis. Use for diagnostic odyssey assistance, phenotype-to-disease ranking, and genetic-counseling differential generation.

Quality

96%

Does it follow best practices?

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Critical

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Quality

Content

92%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is lean, highly actionable, and sequences an 8-phase workflow with validation and fallbacks. The main weakness is progressive disclosure: three of the four referenced files are missing from the bundle.

Suggestions

Create the referenced DIAGNOSTIC_WORKFLOW.md, REPORT_TEMPLATE.md, and CHECKLIST.md (or remove the broken links) so the 'Reference Files' navigation resolves.

Move the per-phase detail (scoring tiers, frequency classes, ACMG codes) into DIAGNOSTIC_WORKFLOW.md to keep SKILL.md a true overview, reducing inline bulk.

Verify the scripts/clinical_patterns.py interface is documented inline with a one-line usage example so Claude can invoke it without reading the full 36 KB file.

Dimension	Reasoning	Score
Conciseness	Dense, table-driven, and reference-rich with no padding about concepts Claude already knows; each line carries domain-specific signal (tool params, scoring tiers, frequency thresholds).	5 / 5
Actionability	Provides concrete, copy-paste-ready tool invocations with exact parameters — e.g. `Orphanet_search_diseases(operation="search_diseases", query=keyword)`, `FAVOR_annotate_variant("chr-pos-ref-alt")` — plus explicit scoring rules and ACMG criteria.	5 / 5
Workflow Clarity	Clear 8-phase sequence (Phase 0–7) with validation checkpoints (evidence grading T1–T4, ClinGen inclusion/exclusion rules) and feedback loops (the Fallback Chains table for error recovery).	5 / 5
Progressive Disclosure	The 'Reference Files' section signals one-level-deep references clearly, but DIAGNOSTIC_WORKFLOW.md, REPORT_TEMPLATE.md, and CHECKLIST.md do not exist in the bundle — navigation would break — and substantial phase detail is inlined rather than split into those files.	3 / 5
	Total	18 / 20 Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong description: it names concrete capabilities, gives an explicit 'Use for...' trigger clause with natural terms, and carves out a distinct niche. It is concise without being vague.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — "HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant interpretation, and structure-based variant analysis" — giving comprehensive coverage of the domain.	5 / 5
Completeness	Explicitly answers both what (the four analysis actions) and when ("Use for diagnostic odyssey assistance, phenotype-to-disease ranking, and genetic-counseling differential generation") with concrete trigger phrases.	5 / 5
Trigger Term Quality	Natural trigger phrases clinicians and genetic counselors actually say are present — "rare disease differential diagnosis", "patient phenotype", "diagnostic odyssey", "phenotype-to-disease ranking", "genetic-counseling differential".	5 / 5
Distinctiveness Conflict Risk	Occupies a clear niche — rare-disease diagnosis via HPO/Orphanet/OMIM — with distinct triggers that are unlikely to fire for unrelated skills.	5 / 5
	Total	20 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
relative_links	Relative link issues: 3 missing	Warning

	Total	15 / 16 Passed

Repository: mims-harvard/ToolUniverse
Path: plugins/tooluniverse/skills/tooluniverse-rare-disease-diagnosis/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

Discovery Implementation Validation

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