How does it assist in rare disease gene discovery?

The skill uses semantic similarity and phenotype-to-gene mapping to rank candidate genes that match a patient's clinical phenotype profile (expressed as HPO terms).

Can I use it to find animal models for human diseases?

Yes, the skill includes features to query orthologs and phenotypic associations in model organisms like mice, zebrafish, fruit flies, and rats.

What is the Monarch Initiative Database skill?

It is a specialized capability for Claude Code that allows users to query a multi-species knowledge graph linking genes, diseases, and phenotypes using the Monarch API v3.

Which data sources does this skill integrate?

It integrates over 40 biological sources including OMIM, ClinVar, HPO, Orphanet, MGI (Mouse), ZFIN (Zebrafish), and FlyBase.

Which disease identifiers are preferred?

While it supports OMIM and ORPHANET, the skill encourages using MONDO (Monarch Disease Ontology) IDs as they unify multiple identifier systems for cross-ontology queries.

Monarch Initiative Database

Name: Monarch Initiative Database
Author: henriquescastilho

byhenriquescastilho

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데이터 과학 및 ML

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

The Monarch Initiative Database skill provides a specialized interface for interacting with a multi-species integrated knowledgebase that links genes, diseases, and phenotypes. It allows researchers and developers to programmatically map clinical phenotypes to candidate genes, identify relevant animal models for human diseases, and navigate hierarchical ontologies like the Human Phenotype Ontology (HPO). By consolidating data from over 40 sources including OMIM, ClinVar, and model organism databases, this skill streamlines the process of rare disease gene discovery and cross-species disease modeling directly within Claude.

주요 기능

01Ortholog discovery for identifying relevant disease models

021 GitHub stars

03Integration with OMIM, ORPHANET, and HPO hierarchies

04Comprehensive HPO term lookup and ontology navigation

05Cross-species phenotype-to-gene mapping and prioritization

06Semantic similarity scoring for phenotypic profiles

사용 사례

01Identifying model organisms (mouse, zebrafish, etc.) for specific human conditions

02Annotating gene lists with associated phenotypic features and disease links

03Prioritizing candidate genes for rare diseases based on HPO terms

주요 기능

01Ortholog discovery for identifying relevant disease models

021 GitHub stars

03Integration with OMIM, ORPHANET, and HPO hierarchies

04Comprehensive HPO term lookup and ontology navigation

05Cross-species phenotype-to-gene mapping and prioritization

06Semantic similarity scoring for phenotypic profiles

사용 사례

01Identifying model organisms (mouse, zebrafish, etc.) for specific human conditions

02Annotating gene lists with associated phenotypic features and disease links

03Prioritizing candidate genes for rare diseases based on HPO terms