db-monarch

To find candidate genes for rare diseases, you can input a list of Human Phenotype Ontology (HPO) terms describing patient symptoms. The Skill queries the Monarch Initiative knowledge graph and returns a ranked list of potential causative genes based on known disease-gene-phenotype associations.

Yes, you can search for model organisms relevant to human diseases across species. The Skill queries the Monarch knowledge graph to integrate model organism databases, enabling cross-species disease modeling for genes and phenotypes associated with mice, zebrafish, and other organisms.

You can retrieve definitions and hierarchies for Human Phenotype Ontology terms using the Skill's HPO term lookup and navigation features. It queries the Monarch API v3 to return specific HPO term definitions, structural hierarchies, and related phenotype data.

Yes, the Skill integrates data from OMIM, ORPHANET, ClinVar, and model organism databases for phenotype-to-gene mapping. It queries the Monarch Initiative knowledge graph to consolidate these sources for rare disease gene discovery and phenotypic similarity assessment.

The best way to compare phenotypic similarity between different diseases is to query the Monarch knowledge graph using the Skill's disease comparison features. It analyzes shared HPO terms and gene associations to assess phenotypic overlap across the integrated disease data.

Yes, you need the Python requests and pandas libraries installed. The Skill utilizes a Python client that depends on requests to interact with the Monarch API v3 for data retrieval, and pandas to structure and analyze the returned disease-gene-phenotype association datasets.