ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-variant-interpretationgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-variant-interpretation)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-variant-interpretation"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-variant-interpretation/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-variant-interpretation"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-variant-interpretation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Excessive Agency · line 31 Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00143 | $0.06494 |
| Opus 5.5 | $0.00057 | $0.02598 |
| Sonnet 5.5 | $0.00029 | $0.01299 |
| Haiku 4.5 | $0.00014 | $0.00649 |
Grade A, and why
tooluniverse-variant-interpretation scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 380 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Clinical Variant Interpreter
Systematic variant interpretation using ToolUniverse - from raw variant calls to ACMG-classified clinical recommendations with structural impact analysis.
Triggers
Use this skill when users:
- Ask about variant interpretation, classification, or pathogenicity
- Have VCF data needing clinical annotation
- Need ACMG classification for variants
- Want structural impact analysis for missense variants
Key Principles
- ACMG-Guided - Follow ACMG/AMP 2015 guidelines with explicit evidence codes
- Structural Evidence - Use AlphaFold2 for novel structural impact analysis
- Population Context - gnomAD frequencies with ancestry-specific data
- Actionable Output - Clear recommendations, not just classifications
- English-first queries - Always use English terms in tool calls; respond in user's language
LOOK UP, DON'T GUESS
When asked about a variant's significance, query ClinVar/gnomAD/CIViC FIRST. Never classify a variant without checking databases. When you're not sure about a fact, your first instinct should be to SEARCH for it using tools, not to reason harder from memory.
Workflow Overview
Phase 1: VARIANT IDENTITY → Normalize HGVS, map gene/transcript/consequence, resolve ClinGen CA ID
Phase 2: CLINICAL DATABASES → ClinVar, gnomAD, OMIM, ClinGen, COSMIC, SpliceAI
Phase 2.5: REGULATORY CONTEXT → ChIPAtlas/ENCODE annotation + DL variant-effect (AlphaGenome/Enformer/Borzoi/ChromBPNet/Evo2) (non-coding only)
Phase 3: COMPUTATIONAL PREDICTIONS → CADD, AlphaMissense, EVE, SIFT/PolyPhen
Phase 4: STRUCTURAL ANALYSIS → PDB/AlphaFold2, domains, functional sites (VUS/novel)
Phase 4.5: EXPRESSION CONTEXT → CELLxGENE, GTEx tissue expression
Phase 5: LITERATURE EVIDENCE → PubMed, EuropePMC, BioRxiv, MedRxiv
Phase 6: ACMG CLASSIFICATION → Evidence codes, classification, recommendations
Phase 1: Variant Identity
Tools: MyVariant_query_variants, EnsemblVar_get_variant_consequences, NCBIGene_search, VariantValidator_gene2transcripts, VariantValidator_validate_variant, Tark_get_mane_transcripts, Tark_get_transcript, ClinGenAllele_lookup_hgvs, ClinGenAllele_get_allele
What ships with it
5 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 10d ago Changed · +2 lines 8e0bf88af7fe
- 1mo ago Changed 94b2d37a1b88
- 1mo ago Changed · +1 lines 524bbf340c8c
- 1mo ago First seen · 377 lines · 143 tokens per session scan A 1fe218575329
tooluniverse-variant-interpretation is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 143 tokens to every session and 6,494 once invoked, about $0.0006 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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