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In the case of prostate cancer (PCa), 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 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. In this study, we constructed an updated PCa ontology (PCAO2) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology. The PCAO2 with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCAO2 contains 633 concepts organized under three biomedical viewpoints, namely, epidemiology, diagnosis and treatment. These concepts are enriched by the addition of definition, synonym, relationship and reference. For the precision diagnosis and treatment, the PCa-associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa. PCAO2 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 PCAO2 is freely available at https:\/\/bioportal.bioontology.org\/ontologies\/PCAO, http:\/\/pcaontology.net\/ and http:\/\/pcaontology.net\/mobile\/.<\/jats:p>","DOI":"10.1093\/bib\/bbae136","type":"journal-article","created":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T10:11:47Z","timestamp":1711966307000},"source":"Crossref","is-referenced-by-count":10,"title":["PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data"],"prefix":"10.1093","volume":"25","author":[{"given":"Chunjiang","family":"Yu","sequence":"first","affiliation":[{"name":"Department of Urology and Institutes for Systems Genetics , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"},{"name":"Sichuan University , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"},{"name":"School of Artificial Intelligence, Suzhou Industrial Park Institute of Services Outsourcing , Suzhou, 215123 , China"},{"name":"Center for Systems Biology, Soochow University , Suzhou, 215006 , China"}]},{"given":"Hui","family":"Zong","sequence":"additional","affiliation":[{"name":"Department of Urology and Institutes for Systems Genetics , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"},{"name":"Sichuan University , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"}]},{"given":"Yalan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Urology and Institutes for Systems Genetics , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"},{"name":"Sichuan University , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"},{"name":"Center for Systems Biology, Soochow University , Suzhou, 215006 , China"},{"name":"Department of Medical Informatics , School of Medicine, , Nantong, 226001 , China"},{"name":"Nantong University , School of Medicine, , Nantong, 226001 , China"}]},{"given":"Yibin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Soochow University , Suzhou, 215011 , China"}]},{"given":"Xingyun","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Urology and Institutes for Systems Genetics , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"},{"name":"Sichuan University , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , Chengdu, 610041 , China"}]},{"given":"Yuxin","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Urology, The First Affiliated Hospital of Soochow University , Suzhou, 215000 , 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