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The development of computable phenotype algorithms to solve these tasks is a challenging problem, caused by various reasons. Firstly, the term \u2018phenotype\u2019 has no generally agreed definition and its meaning depends on context. Secondly, the phenotypes are most commonly specified as non-computable descriptive documents. Recent attempts have shown that ontologies are a suitable way to handle phenotypes and that they can support clinical research and decision making.<\/jats:p>\n                <jats:p>The SMITH Consortium is dedicated to rapidly establish an integrative medical informatics framework to provide physicians with the best available data and knowledge and enable innovative use of healthcare data for research and treatment optimisation. In the context of a methodological use case \u2018phenotype pipeline\u2019 (PheP), a technology to automatically generate phenotype classifications and annotations based on electronic health records (EHR) is developed. A large series of phenotype algorithms will be implemented. This implies that for each algorithm a classification scheme and its input variables have to be defined. Furthermore, a phenotype engine is required to evaluate and execute developed algorithms.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this article, we present a Core Ontology of Phenotypes (COP) and the software Phenotype Manager (PhenoMan), which implements a novel ontology-based method to model, classify and compute phenotypes from already available data. Our solution includes an enhanced iterative reasoning process combining classification tasks with mathematical calculations at runtime. The ontology as well as the reasoning method were successfully evaluated with selected phenotypes including SOFA score, socio-economic status, body surface area and WHO BMI classification based on available medical data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We developed a novel ontology-based method to model phenotypes of living beings with the aim of automated phenotype reasoning based on available data. This new approach can be used in clinical context, e.g., for supporting the diagnostic process, evaluating risk factors, and recruiting appropriate participants for clinical and epidemiological studies.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13326-020-00230-0","type":"journal-article","created":{"date-parts":[[2020,12,21]],"date-time":"2020-12-21T12:02:58Z","timestamp":1608552178000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Ontological representation, classification and data-driven computing of phenotypes"],"prefix":"10.1186","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9558-5352","authenticated-orcid":false,"given":"Alexandr","family":"Uciteli","sequence":"first","affiliation":[]},{"given":"Christoph","family":"Beger","sequence":"additional","affiliation":[]},{"given":"Toralf","family":"Kirsten","sequence":"additional","affiliation":[]},{"given":"Frank A.","family":"Meineke","sequence":"additional","affiliation":[]},{"given":"Heinrich","family":"Herre","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,12,21]]},"reference":[{"key":"230_CR1","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1006\/jtbi.1996.0335","volume":"186","author":"M Mahner","year":"1997","unstructured":"Mahner M, Kary M. 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This article has been updated to correct this.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.More details about LIFE Adult participants, their invitation and consenting as well as examinations, interviews, questionnaires and taken specimen can be found in [].","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"15"}}