Rare Disease Genomics (ToolUniverse Claude Skill)

A ToolUniverse agent skill that works a rare disease from name disambiguation through phenotype mapping, causative-gene discovery, variant interpretation, and translational leads including trials and drug repurposing.


Type	Claude Skill (one of ToolUniverse’s pre-built agent skills)
Supplier	Zitnik Lab, Harvard Medical School
Availability	GA — part of the ToolUniverse skills collection (`skills/tooluniverse-rare-disease-genomics/`)
Pricing	Free / OSS (Apache-2.0); wraps public APIs (Orphanet, GenCC, ClinVar, OLS, HMDB, ClinicalTrials.gov, Europe PMC)
Capabilities	Read-only — drives ToolUniverse tool calls; no data writes
Verified	works · 2026-07-20
Security	cleared · 2026-07-20 — provenance matches Zitnik Lab, Apache-2.0, skill dir confirmed, no OSV advisories

How to install

This skill calls ToolUniverse tools, so the ToolUniverse MCP server must be installed first (see the ToolUniverse page). Simplest registration:

claude mcp add --transport stdio tooluniverse -- uvx tooluniverse

Then add the skills:

Claude Code — install the whole skill collection (the skill resolves as tooluniverse-rare-disease-genomics):
```
npx skills add mims-harvard/ToolUniverse
```
Manual / other agents — copy just this skill directory into your skills folder:
```
git clone https://github.com/mims-harvard/ToolUniverse
cp -r ToolUniverse/skills/tooluniverse-rare-disease-genomics ~/.claude/skills/
```
(replace ~/.claude/skills/ with your agent’s skills directory if you are not using Claude Code/Desktop.)

The skill sets disable-model-invocation: true upstream, so invoke it explicitly (e.g. ask Claude to “use the rare-disease-genomics skill”) rather than relying on automatic dispatch.

What it does

Runs a nine-phase (plus disambiguation) rare-disease workflow:

Disambiguation — resolve disease names to ORPHA codes.
Disease characterization — official definitions and classifications (Orphanet).
Phenotype mapping — HPO phenotypes with frequency labels.
Causative gene discovery — genes with association types.
Gene-disease validity — confidence via GenCC submitter consensus.
Pathogenic variant lookup — ClinVar with review-status context.
Epidemiology — prevalence and incidence.
Clinical trials — recruiting and completed studies.
Literature — supporting publications (Europe PMC).
Report — synthesized findings with evidence grading.

Primary use cases: rare-disease gene/variant triage, phenotype-driven diagnosis support, and translational-lead discovery (trials, repurposing candidates).

Notes

It is a reasoning layer over ToolUniverse; without the MCP server registered, the tool calls fail. Distinct from the Rare Disease Diagnosis skill — this one is genomics-anchored (Orphanet→gene→variant), with translational repurposing leads. ToolUniverse ships ~68 such skills; other workflows are catalogued separately.

Sources

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