Furthermore, we find that the labels, synonyms and definitions in ontologies can also provide background knowledge that may be exploited for prediction. ![]() We find that the background knowledge provided by the Gene Ontology and other ontologies significantly improves the performance of ontology-based prediction models through provision of domain-specific background knowledge. We use ontology-based machine learning methods to evaluate the contribution of formal axioms and ontology meta-data to the prediction of protein–protein interactions and gene–disease associations.
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