{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:06:31Z","timestamp":1773270391873,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The Ontologizer is a Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer implements the standard approach to statistical analysis based on the one-sided Fisher's exact test, the novel parent\u2013child method, as well as topology-based algorithms. A number of multiple-testing correction procedures are provided. The Ontologizer allows users to visualize data as a graph including all significantly overrepresented GO terms and to explore the data by linking GO terms to all genes\/proteins annotated to the term and by linking individual terms to child terms.<\/jats:p>\n               <jats:p>Availability: The Ontologizer application is available under the terms of the GNU GPL. It can be started as a WebStart application from the project homepage, where source code is also provided: http:\/\/compbio.charite.de\/ontologizer<\/jats:p>\n               <jats:p>Requirements: Ontologizer requires a Java SE 5.0 compliant Java runtime engine and GraphViz for the optional graph visualization tool.<\/jats:p>\n               <jats:p>Contact: \u00a0sebastian.bauer@charite.de; peter.robinson@charite.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn250","type":"journal-article","created":{"date-parts":[[2008,5,30]],"date-time":"2008-05-30T00:33:45Z","timestamp":1212107625000},"page":"1650-1651","source":"Crossref","is-referenced-by-count":433,"title":["Ontologizer 2.0\u2014a multifunctional tool for GO term enrichment analysis and data exploration"],"prefix":"10.1093","volume":"24","author":[{"given":"Sebastian","family":"Bauer","sequence":"first","affiliation":[{"name":"1 Institute of Medical Genetics, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and 2Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"Steffen","family":"Grossmann","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Genetics, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and 2Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Genetics, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and 2Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"Peter N.","family":"Robinson","sequence":"additional","affiliation":[{"name":"1 Institute of Medical Genetics, Charit\u00e9 Universit\u00e4tsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and 2Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2008,5,29]]},"reference":[{"key":"2023020210480323000_B1","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020210480323000_B2","unstructured":"Eclipse Foundation\n          Eclipse\n          2007\n          Available at http:\/\/www.eclipse.org(last accessed date December 15, 2007)."},{"key":"2023020210480323000_B3","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/btl567","article-title":"Using GOstats to test gene lists for GO term association","volume":"23","author":"Falcon","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020210480323000_B4","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1002\/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N","article-title":"An open graph visualization system and its applications to software engineering","volume":"30","author":"Gansner","year":"1999","journal-title":"Software Pract. 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