What data sources does the Monarch Database skill integrate?

It integrates data from over 40 specialized sources, including OMIM, ORPHANET, Human Phenotype Ontology (HPO), ClinVar, and model organism databases like MGI, ZFIN, and FlyBase.

Can I use this for clinical gene prioritization?

Yes, the skill includes workflows to rank candidate genes by their phenotype overlap with a patient's HPO terms, making it ideal for rare disease research.

Why should I use MONDO IDs instead of OMIM?

MONDO (Monarch Disease Ontology) IDs are preferred because they unify multiple coding systems like OMIM, ORPHANET, and MESH into a single, cohesive hierarchy for better cross-species querying.

Does this skill support animal model research?

Absolutely. It can identify cross-species orthologs and retrieve phenotype data from model organisms to help find experimental models for human diseases.

Monarch Disease & Gene Database

Name: Monarch Disease & Gene Database
Author: Yezez9

byYezez9

0•

Ciencia de Datos y ML

Queries the Monarch Initiative knowledge graph to explore complex disease-gene-phenotype associations across multiple species.

The Monarch Database skill provides a powerful interface for interacting with the Monarch Initiative, a multi-species integrated knowledgebase. It allows researchers and developers to map phenotypes across species, identify candidate genes for rare diseases, and navigate the Human Phenotype Ontology (HPO) hierarchy. By integrating data from over 40 sources like OMIM, ClinVar, and various model organism databases, this skill enables advanced bioinformatic workflows including semantic similarity scoring, ortholog mapping, and evidence-based disease modeling directly within your development environment.

Características Principales

010 GitHub stars

02Direct integration with Monarch API v3 for real-time biological data

03Phenotype-to-gene mapping using semantic similarity scoring

04Comprehensive HPO term lookup and ontology hierarchy navigation

05Cross-species ortholog discovery for animal disease modeling

06Unified disease querying via MONDO, OMIM, and ORPHANET identifiers

Casos de Uso

01Automating the annotation of novel genes with known phenotypic associations

02Prioritizing candidate genes for rare disease discovery based on patient HPO profiles

03Identifying relevant model organisms (mouse, zebrafish, fly) for human disease research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent monarch-database

For use in Claude.ai and ChatGPT

Características Principales

010 GitHub stars

02Direct integration with Monarch API v3 for real-time biological data

03Phenotype-to-gene mapping using semantic similarity scoring

04Comprehensive HPO term lookup and ontology hierarchy navigation

05Cross-species ortholog discovery for animal disease modeling

06Unified disease querying via MONDO, OMIM, and ORPHANET identifiers

Casos de Uso

01Automating the annotation of novel genes with known phenotypic associations

02Prioritizing candidate genes for rare disease discovery based on patient HPO profiles

03Identifying relevant model organisms (mouse, zebrafish, fly) for human disease research