{"id":16705,"date":"2020-05-21T07:56:12","date_gmt":"2020-05-21T07:56:12","guid":{"rendered":"http:\/\/cio.edu.umh.es\/?p=16705"},"modified":"2021-07-22T09:50:09","modified_gmt":"2021-07-22T07:50:09","slug":"evaluation-of-ontology-structural-metrics-based-on-public-repository-data-briefings-in-bioinformatics-212-2020-473-485","status":"publish","type":"post","link":"https:\/\/cio.umh.es\/en\/2020\/05\/21\/evaluation-of-ontology-structural-metrics-based-on-public-repository-data-briefings-in-bioinformatics-212-2020-473-485\/","title":{"rendered":"Evaluation of ontology structural metrics based on public repository data, Briefings in Bioinformatics, 21(2), 2020, 473\u2013485"},"content":{"rendered":"<p>[:es]<strong>Manuel Franco <\/strong>(<em>University of Murcia<\/em>), <strong>Juana Mar\u00eda Vivo\u00a0<\/strong>(<em>University of Murcia<\/em>), <strong>Manuel Quesada-Mart\u00ednez<\/strong> (<em>Miguel Hern\u00e1ndez University<\/em>),\u00a0<strong>Astrid Duque-Ramos\u00a0<\/strong>(<em>University of Antioquia)<\/em>\u00a0and <strong>Jesualdo<\/strong> <strong>Tom\u00e1s Fern\u00e1ndez-Breis\u00a0<\/strong>(<em>University of Murcia<\/em>).<br \/>\n<strong>Abstract:\u00a0<\/strong>The development and application of biological ontologies have increased significantly in recent years. These ontologies can\u00a0be retrieved from different repositories, which do not provide much information about quality aspects of the ontologies. In\u00a0the past years, some ontology structural metrics have been proposed, but their validity as measurement instrument has not\u00a0been sufficiently studied to date. In this work, we evaluate a set of reproducible and objective ontology structural metrics.\u00a0Given the lack of standard methods for this purpose, we have applied an evaluation method based on the stability and\u00a0goodness of the classifications of ontologies produced by each metric on an ontology corpus. The evaluation has been done\u00a0using ontology repositories as corpora. More concretely, we have used 119 ontologies from the OBO Foundry repository and\u00a078 ontologies from AgroPortal. First, we study the correlations between the metrics. Second, we study whether the clusters\u00a0for a given metric are stable and have a good structure. The results show that the existing correlations are not biasing the\u00a0evaluation, there are no metrics generating unstable clusterings and all the metrics evaluated provide at least reasonable\u00a0clustering structure. Furthermore, our work permits to review and suggest the most reliable ontology structural metrics in\u00a0terms of stability and goodness of their classifications.<br \/>\n<strong>Keywords:\u00a0<\/strong>biological ontologies; quantitative metrics; metrics comparison; data analysis.[:]<\/p>","protected":false},"excerpt":{"rendered":"<p>[:es]Manuel Franco (University of Murcia), Juana Mar\u00eda Vivo\u00a0(University of Murcia), Manuel Quesada-Mart\u00ednez (Miguel Hern\u00e1ndez University),\u00a0Astrid Duque-Ramos\u00a0(University of Antioquia)\u00a0and Jesualdo Tom\u00e1s Fern\u00e1ndez-Breis\u00a0(University of Murcia).<br \/>\nAbstract:\u00a0The development and application of biological ontologies have increased significantly in recent years. These ontologies can\u00a0be retrieved from different repositories, which do not provide much information about quality aspects of the ontologies. In\u00a0the [&#8230;]<\/p>","protected":false},"author":6202,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_links_to":"","_links_to_target":""},"categories":[369888],"tags":[],"_links":{"self":[{"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/posts\/16705"}],"collection":[{"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/users\/6202"}],"replies":[{"embeddable":true,"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/comments?post=16705"}],"version-history":[{"count":0,"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/posts\/16705\/revisions"}],"wp:attachment":[{"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/media?parent=16705"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/categories?post=16705"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/cio.umh.es\/en\/wp-json\/wp\/v2\/tags?post=16705"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}