monarch-database

To find candidate genes for a rare disease using HPO terms, you query the Monarch Initiative knowledge graph for phenotype-to-gene mapping. Inputting patient phenotypes like HP:0001250 retrieves a ranked list of potential causative genes and their known disease associations.

Yes, you can retrieve disease-gene associations using OMIM, ORPHANET, or MONDO IDs. The Skill queries the Monarch knowledge graph to return specific genes linked to those diseases, facilitating rare disease gene discovery and cross-species disease modeling.

Cross-species disease modeling in the Monarch Initiative knowledge graph identifies orthologous genes in model organisms like mouse or zebrafish for human diseases. It integrates model organism databases to help researchers study genetic disorders across species.

To get definitions and hierarchy information for Human Phenotype Ontology terms, you perform an HPO term lookup within the Monarch knowledge graph. This integrates HPO data to provide names, definitions, and hierarchical relationships for clinical phenotypes.

Yes, querying the knowledge graph requires the requests and pandas Python dependencies. These libraries handle the API calls to the Monarch Initiative and structure the returned multi-species disease-gene-phenotype association data for analysis.

Beyond HPO, rare disease gene discovery integrates OMIM, ORPHANET, ClinVar, and model organism databases. This multi-species knowledge graph maps phenotypes to genes and provides comprehensive cross-species disease associations for clinical research.