tooluniverse-rare-disease-genomics

Rare disease genomics — disease identification (Orphanet), causative gene discovery, gene-disease validity (GenCC), variant interpretation (ClinVar), and translational research (ClinicalTrials.gov, drug repurposing for orphans). Use for rare-disease-gene curation, novel-gene-discovery analysis, and rare-disease drug-development support.

Quality

90%

Does it follow best practices?

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Adds up to 20 points to the overall score

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Securityby

Low

Low-risk findings worth noting

Quality

Content

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

A highly actionable, well-sequenced research workflow with explicit checkpoints and error-recovery fallbacks. The main improvement opportunity is splitting the per-tool API reference detail into a reference file to reduce SKILL.md length.

Suggestions

Move the per-tool parameter reference (Phases 0–8 tool blocks) into a references/TOOLS.md file, keeping SKILL.md as a strategy-and-workflow overview that points to it.

Trim regulatory/definitional asides (e.g., the EU/US "Below 1 in 2,000" rare-disease threshold and prevalence-tier definitions) since Claude already knows them.

Add a short "Quick start" example near the top so the most common single-query case is answerable before the full phase-by-phase walkthrough.

Dimension	Reasoning	Score
Conciseness	Largely token-efficient — tool names, required parameters, association-type distinctions, and review-star thresholds each earn their place — with only minor explanatory padding (e.g., prevalence regulatory thresholds) that could be trimmed.	4 / 5
Actionability	Every tool is documented with required parameters, aliases, exact executable example calls (e.g., Orphanet_search_diseases(name="Marfan syndrome")), allele-frequency thresholds, and explicit parameter-name corrections covering the common cases.	5 / 5
Workflow Clarity	Phases 0–9 are explicitly sequenced with a numbered variant-prioritization checklist, validation checkpoints ("Check BEFORE ClinVar", "always check for subtypes"), fallback error-recovery loops, and a closing completeness checklist.	5 / 5
Progressive Disclosure	Well-organized section structure with a top-level workflow overview and no nested references, but no bundle files exist and a fair amount of API-reference-style detail is inlined rather than split into a separate reference file.	4 / 5
	Total	18 / 20 Passed

Description

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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, specific description that clearly states both capabilities and use triggers with minimal conflict risk. Minor room to soften technical terms toward more natural user phrasing.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions across the domain — "disease identification (Orphanet)", "causative gene discovery", "gene-disease validity (GenCC)", "variant interpretation (ClinVar)", and "translational research (ClinicalTrials.gov, drug repurposing for orphans)" — giving comprehensive coverage.	5 / 5
Completeness	Explicitly answers both what (the five named capabilities) and when ("Use for rare-disease-gene curation, novel-gene-discovery analysis, and rare-disease drug-development support") with concrete trigger phrases.	5 / 5
Trigger Term Quality	Includes natural phrases users would say ("rare disease", "orphan", "HPO", "phenotype", "rare-disease-gene curation") but leans slightly technical and is missing a few common synonym variations, sitting just below comprehensive coverage.	4 / 5
Distinctiveness Conflict Risk	Occupies a clear niche (rare disease genomics) and the body's "NOT for" list explicitly separates it from common-disease, cancer, GWAS, pharmacogenomics, and differential-diagnosis skills, minimizing conflict risk.	5 / 5
	Total	19 / 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
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

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

Reviewed: 1 day ago

Table of Contents

Discovery Implementation Validation

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