monarch-database

You can find candidate genes by querying the Monarch Initiative knowledge graph to identify diseases sharing your patient's HPO phenotype terms, then retrieving the causal genes associated with those matched diseases.

To query disease-gene-phenotype associations, you use Python requests to access the Monarch Initiative REST API, leveraging pandas to retrieve, filter, and structure the resulting entity metadata and association data.

Yes, you can retrieve causal genes for a specific disease by querying the Monarch Initiative knowledge graph with its MONDO ID to fetch directly mapped gene-disease associations.

Cross-species orthology is supported by the Monarch Initiative API, allowing you to analyze gene-phenotype links across different model organisms for comparative rare disease research.

You need pandas for data retrieval and manipulation to build disease-phenotype networks, while matplotlib can be used to visually plot the mapped HPO terms and their disease associations.

The Monarch Initiative API has limitations based on available knowledge graph data coverage and cross-references; querying may yield incomplete associations for poorly characterized rare diseases or unmapped model organisms.