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The most widely used structured vocabulary in molecular biology and biomedicine is the Gene Ontology (GO). Although employed in many different data analysis tasks, its main application is in the functional annotation of gene products and the subsequent functional enrichment analysis of large gene\/protein datasets derived from omics experiments. This key position in modern biology means the GO is subject to continuous scrutiny and improvement, not only by its developers but by the community in general. GO\u2019s vocabulary, structure, and gene annotations have been evaluated from multiple points of view, revealing important insights into how we organize our biological knowledge, the associated problems, and strategies for overcoming them. These evaluations range from technical analyses of its ontological architecture to assessments of its effectiveness in supporting biological research. This process ensures that this essential resource is updated and adapted to the new challenges posed by modern biology. In this review, we summarize some key evaluations that the GO has undergone over time.<\/jats:p>","DOI":"10.1093\/database\/baaf058","type":"journal-article","created":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:25:49Z","timestamp":1758810349000},"source":"Crossref","is-referenced-by-count":12,"title":["A review on Gene Ontology evaluations"],"prefix":"10.1093","volume":"2025","author":[{"given":"Borja","family":"Pitarch","sequence":"first","affiliation":[{"name":"Computational Systems Biology, National Center for Biotechnology (CNB-CSIC) , 28049 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00f3nica","family":"Chagoyen","sequence":"additional","affiliation":[{"name":"Computational Systems Biology, National Center for Biotechnology (CNB-CSIC) , 28049 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan A G","family":"Ranea","sequence":"additional","affiliation":[{"name":"University of M\u00e1laga Department of Molecular Biology and Biochemistry, , 29071 M\u00e1laga ,","place":["Spain"]},{"name":"CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]},{"name":"Institute of Biomedical Research in Malaga and Platform of Nanomedicine (IBIMA Platform BIONAND) , 29071 Malaga ,","place":["Spain"]},{"name":"Spanish National Bioinformatics Institute (INB\/ELIXIR-ES) , 08034 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2646-6226","authenticated-orcid":false,"given":"Florencio","family":"Pazos","sequence":"additional","affiliation":[{"name":"Computational Systems Biology, National Center for Biotechnology (CNB-CSIC) , 28049 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,9,24]]},"reference":[{"key":"2025092510254095600_bib1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0169-023X(99)00022-1","article-title":"Toward principles for the representation of hierarchical knowledge in formal ontologies","volume":"31","author":"Jones","year":"1999","journal-title":"Data Knowl Eng"},{"key":"2025092510254095600_bib2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-4939-3743-1_1","article-title":"Primer on ontologies","volume":"1446","author":"Hastings","year":"2017","journal-title":"Methods Mol Biol"},{"key":"2025092510254095600_bib3","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1093\/bib\/bbv011","article-title":"The role of ontologies in biological and biomedical research: a functional perspective","volume":"16","author":"Hoehndorf","year":"2015","journal-title":"Brief Bioinform"},{"key":"2025092510254095600_bib4","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.bbe.2014.06.002","article-title":"Biomedical ontologies\u2014a review","volume":"35","author":"Konopka","year":"2015","journal-title":"Biocybernet Biomed Eng"},{"key":"2025092510254095600_bib5","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1093\/bib\/1.4.398","article-title":"Ontology-based knowledge representation for bioinformatics","volume":"1","author":"Stevens","year":"2000","journal-title":"Brief Bioinform"},{"key":"2025092510254095600_bib6","doi-asserted-by":"publisher","first-page":"W541","DOI":"10.1093\/nar\/gkr469","article-title":"BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications","volume":"39","author":"Whetzel","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2025092510254095600_bib7","doi-asserted-by":"crossref","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The Gene Ontology knowledgebase in 2023","volume":"224","author":"The Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"2025092510254095600_bib8","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/978-1-4939-3743-1_2","article-title":"The Gene Ontology and the meaning of biological function","volume-title":"The Gene Ontology Handbook","author":"Thomas","year":"2017"},{"key":"2025092510254095600_bib9","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1016\/S0959-440X(98)80074-2","article-title":"Systems for categorizing functions of gene products","volume":"8","author":"Riley","year":"1998","journal-title":"Curr Opin Struct Biol"},{"key":"2025092510254095600_bib10","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. 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