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tooluniverse-model-organism-genetics

Maps human genes to model organism orthologs and synthesizes cross-species phenotype data.

1.7k|254|Updated Mar 3, 2025
Search Tags:#bioinformatics#comparative genomics#gene function#cross-species#phenotype analysis#ortholog mapping#model organisms
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-model-organism-genetics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-model-organism-genetics
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-model-organism-genetics
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-model-organism-genetics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, scipy, statsmodels, matplotlib.

What problem does it solve?

Researchers studying a human gene or disease often need to know which model organism best captures its biology, but ortholog mapping and phenotype data are scattered across MGI, FlyBase, WormBase, ZFIN, SGD, RGD, and other databases. This Skill unifies those lookups into one cross-species pipeline that maps human genes to orthologs, retrieves phenotype and expression data per species, and assesses functional conservation.

Core Features & Use Cases

  • Ortholog Mapping: Resolves human genes via MyGene/Ensembl, then finds orthologs across mouse, fly, worm, zebrafish, frog, rat, and yeast using Ensembl Compara, PANTHER, and Monarch, with paralog-contamination checks.
  • Per-Species Phenotype Retrieval: Pulls knockout, RNAi, morpholino, and mutant phenotypes plus expression data from MGI, FlyBase, WormBase, ZFIN, Xenbase, RGD, and SGD.
  • Cross-Species Synthesis: Builds a phenotype matrix, identifies the core ancestral function, grades conservation, and recommends the best animal model for a human disease.
  • Use Case: Given a human gene implicated in cardiomyopathy, map its orthologs, compare knockout phenotypes in mouse and zebrafish, confirm pathway conservation via STRING/Reactome, and receive a recommendation on which organism to use for follow-up experiments.

Quick Start

Ask the agent to map the human gene FOXP2 to its model organism orthologs and recommend the best animal model for studying it.

Frequently Asked Questions about tooluniverse-model-organism-genetics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find model organism orthologs of a human gene?▼

Resolve the human gene to its Ensembl ID with MyGene, then call EnsemblCompara_get_orthologues with the target species such as mouse, zebrafish, or drosophila_melanogaster. If that returns nothing, fall back to PANTHER, NCBI Datasets, or Monarch gene homolog associations.

Which model organism is best for studying a human disease gene?▼

It depends on the biology: mouse for mammalian physiology and CNS disease, fly for rapid genetic screens, worm for cell lineage and RNAi, zebrafish for development and imaging, yeast for cell cycle and DNA repair. The pipeline compares cross-species phenotypes to recommend the best fit.

How do I distinguish true orthologs from paralogs?▼

Check the homology type: 1:1 mappings indicate likely true orthologs, while 1:many or many:many mappings suggest paralog expansion. Also verify synteny and whether conserved protein domains, not just raw sequence identity, support functional equivalence.

Why does Ensembl Compara return an error for fruit fly orthologs?▼

The target_species parameter must be drosophila_melanogaster, not fruitfly, which returns HTTP 400. Accepted values include mouse, zebrafish, caenorhabditis_elegans, saccharomyces_cerevisiae, and xenopus_tropicalis.

What does it mean when no ortholog is found for a human gene?▼

A negative tool result does not prove absence of an ortholog, since sequence divergence can hide functional conservation. Try manual text searches such as FlyMine for fly or WormBase gene records before concluding the gene is human-specific.

When should I not use this cross-species genetics pipeline?▼

Do not use it for human variant interpretation, drug target validation, or human disease characterization, which are covered by other ToolUniverse skills. It is designed for ortholog mapping, model organism phenotypes, and conservation assessment.

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