{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:55:42Z","timestamp":1761540942953},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2566,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being web-based, it does not require prior installation, and provides an intuitive, easy-to-use service.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/tagc.univ-mrs.fr\/SimCT<\/jats:p>\n               <jats:p>Contact: \u00a0carl.herrmann@univmed.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp553","type":"journal-article","created":{"date-parts":[[2009,9,24]],"date-time":"2009-09-24T01:29:48Z","timestamp":1253755788000},"page":"3197-3198","source":"Crossref","is-referenced-by-count":10,"title":["SimCT: a generic tool to visualize ontology-based relationships for biological objects"],"prefix":"10.1093","volume":"25","author":[{"given":"Carl","family":"Herrmann","sequence":"first","affiliation":[{"name":"1 TAGC\u2013U928 Inserm, 2 Facult\u00e9 des Sciences, Universit\u00e9 de la M\u00e9diterran\u00e9e, Campus de Luminy Case 928, Marseille, 3 Universit\u00e9 Montpellier 2, UMR AMAP, and UMR LIRMM \u2013 CNRS, 34000 Montpellier and 4 IML \u2013 UMR 6206 CNRS, Marseille, France"},{"name":"1 TAGC\u2013U928 Inserm, 2 Facult\u00e9 des Sciences, Universit\u00e9 de la M\u00e9diterran\u00e9e, Campus de Luminy Case 928, Marseille, 3 Universit\u00e9 Montpellier 2, UMR AMAP, and UMR LIRMM \u2013 CNRS, 34000 Montpellier and 4 IML \u2013 UMR 6206 CNRS, Marseille, France"}]},{"given":"S\u00e8verine","family":"B\u00e9rard","sequence":"additional","affiliation":[{"name":"1 TAGC\u2013U928 Inserm, 2 Facult\u00e9 des Sciences, Universit\u00e9 de la M\u00e9diterran\u00e9e, Campus de Luminy Case 928, Marseille, 3 Universit\u00e9 Montpellier 2, UMR AMAP, and UMR LIRMM \u2013 CNRS, 34000 Montpellier and 4 IML \u2013 UMR 6206 CNRS, Marseille, France"}]},{"given":"Laurent","family":"Tichit","sequence":"additional","affiliation":[{"name":"1 TAGC\u2013U928 Inserm, 2 Facult\u00e9 des Sciences, Universit\u00e9 de la M\u00e9diterran\u00e9e, Campus de Luminy Case 928, Marseille, 3 Universit\u00e9 Montpellier 2, UMR AMAP, and UMR LIRMM \u2013 CNRS, 34000 Montpellier and 4 IML \u2013 UMR 6206 CNRS, Marseille, France"},{"name":"1 TAGC\u2013U928 Inserm, 2 Facult\u00e9 des Sciences, Universit\u00e9 de la M\u00e9diterran\u00e9e, Campus de Luminy Case 928, Marseille, 3 Universit\u00e9 Montpellier 2, UMR AMAP, and UMR LIRMM \u2013 CNRS, 34000 Montpellier and 4 IML \u2013 UMR 6206 CNRS, Marseille, France"}]}],"member":"286","published-online":{"date-parts":[[2009,9,23]]},"reference":[{"key":"2023013112191071800_B1","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"GO::TermFinder\u2013open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes","volume":"20","author":"Boyle","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112191071800_B2","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"David: database for annotation, visualization, and integrated discovery","volume":"4","author":"Dennis","year":"2003","journal-title":"Genome Biol."},{"key":"2023013112191071800_B3","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btn068","article-title":"Gotreeplus: an interactive gene ontology browser for proteomics projects","volume":"24","author":"Lee","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112191071800_B4","doi-asserted-by":"crossref","first-page":"e4001","DOI":"10.1371\/journal.pone.0004001","article-title":"Transcriptomebrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the gene expression omnibus database","volume":"3","author":"Lopez","year":"2008","journal-title":"PLoS ONE"},{"key":"2023013112191071800_B5","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","article-title":"Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation","volume":"19","author":"Lord","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013112191071800_B6","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1613\/jair.514","article-title":"Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language","volume":"11","author":"Resnik","year":"1999","journal-title":"J. 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