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However, traditional phenotyping methods are often manual, time-intensive, and limited in scope. To address these challenges, this work introduces the TOP Framework, a software suite that leverages a structured approach. It provides tools for the formal definition of phenotypes, their organisation into ontological classes, the creation of phenotype models for disease-specific knowledge representation, and the generation of phenotype queries for automated data retrieval and analysis. A dynamic phenotype algorithm integrates these modules to efficiently identify individuals meeting complex phenotypic criteria. The Model for End-Stage Liver Disease (MELD) score serves as a running example to illustrate the framework\u2019s capabilities. Furthermore, this paper presents a preliminary evaluation of the TOP Framework\u2019s user experience by means of the User Experience Questionnaire (UEQ), assessing its usability and suitability for researchers and clinicians.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The TOP Framework includes a robust implementation of a reasoner model for deriving complex phenotypes and an automated testing module to ensure reliability. The user experience evaluation yielded generally positive results on a scale from \u22123 to 3 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200911), with mean scores and 95% confidence intervals as follows: attractiveness, 1.50 (CI\u2009=\u2009(1.07, 1.93)); pragmatic quality, 1.38 (CI\u2009=\u2009(1.00, 1.77)); and hedonic quality, 1.40 (CI\u2009=\u2009(0.76, 2.03)).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The TOP Framework offers a novel and automated approach to phenotyping, with the potential to enhance the efficiency, scalability, and reproducibility of phenotyping studies. This advancement contributes to a deeper understanding of disease and the progression of precision medicine.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-026-00364-7","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T07:54:46Z","timestamp":1785138886000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Introducing the TOP framework: a novel phenotyping solution for collaborative phenotype algorithm development and application"],"prefix":"10.1186","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1166-0368","authenticated-orcid":false,"given":"Christoph","family":"Beger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2871-0605","authenticated-orcid":false,"given":"Dorothea","family":"Strobach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4349-6726","authenticated-orcid":false,"given":"Ralph","family":"Sch\u00e4fermeier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7196-506X","authenticated-orcid":false,"given":"Franz","family":"Matthies","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7358-3217","authenticated-orcid":false,"given":"Konrad","family":"H\u00f6ffner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9558-5352","authenticated-orcid":false,"given":"Alexandr","family":"Uciteli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,27]]},"reference":[{"key":"364_CR1","unstructured":"Scheuermann RH, Ceusters W, Smith B. 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