GDADataset

class mowl.datasets.builtin.GDADataset(url=None)

Bases: RemoteDataset

Abstract class for gene-disease association datasets.

This dataset represents the gene-disease association in a particular species. This dataset is built using phenotypic annotations of genes and diseases. For genes annotations we used the Mouse/Human Orthology with Phenotype Annotations document. Disease annotations were obtained from the HPO annotations for rare disease document. These annotations were added to the Unified Phenotype Ontology (uPheno) to build the training ontology. Futhermore, gene-disease associations were obtained from the Associations of Mouse Genes with DO Diseases file, from which associations for human and mouse were extracted (to build separate datasets) and each of them were randomly split 80:10:10, added to the training ontology and created the validation and testing ontologies, respectively.

Attributes Summary

evaluation_classes

List of classes used for evaluation.

Methods Summary

get_evaluation_property()

Attributes Documentation

evaluation_classes

List of classes used for evaluation. Depending on the dataset, this method could return a single OWLClasses object (as in PPIYeastDataset) or a tuple of OWLClasses objects (as in GDAHumanDataset). If not overriden, this method returns the classes in the testing ontology obtained from the OWLAPI method getClassesInSignature() as a OWLClasses object.

Methods Documentation

get_evaluation_property()