PCAO: The Ontology for Integration of Prostate Cancer Associated Genotypic, Phenotypic and Lifestyle Data (Preprint)

Abstract

Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer, large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches.

A formal representation of prostate cancer (PCa) -associated knowledge will be essential to the diverse data standardization, data sharing and the future knowledge graph extraction, deep phenotyping and explainable artificial intelligence developing.

We hereby constructed a prostate cancer ontology (PCaO) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology.

The PCaO with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCaO contains 637 concepts organized under three biomedical viewpoints, i.e., epidemiology, diagnosis, and treatment. These concepts are enriched by the addition of definition, synonyms, relationships and references. For the precision diagnosis and treatment, the PCa associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa.

PCaO provides a standardized and systematized semantic framework for studying large amounts of heterogeneous PCa data and knowledge, which can be further, edited and enriched by the scientific community. The current version of the PCaO is available at https://bioportal.bioontology.org/ontologies/PCAO.