Data Sources
Ontologies
Biomedical ontologies for standardized terminology.
OptimusKG integrates four major biomedical ontologies to provide standardized terminology and hierarchical relationships.
Gene Ontology (GO)
Gene Ontology provides structured vocabulary for gene product attributes across three domains:
- Biological Process - Biological objectives accomplished by ordered assemblies of molecular functions
- Cellular Component - Locations relative to cellular structures where gene products perform functions
- Molecular Function - Elemental activities of gene products at the molecular level
Human Phenotype Ontology (HP)
HPO provides standardized vocabulary for phenotypic abnormalities encountered in human disease.
MONDO
MONDO provides a unified disease ontology that harmonizes disease definitions across multiple sources.
UBERON
UBERON is a cross-species anatomical structural ontology covering anatomical entities.
Dataset Type
Ontologies are loaded using the OWLDataset which parses OWL files via owlready2. The bioontology provider downloads ontology files from BioPortal.
Source Files
optimuskg/pipelines/bronze/nodes/ontology/