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Bioinformatics Advance Access originally published online on September 23, 2009
Bioinformatics 2009 25(23):3197-3198; doi:10.1093/bioinformatics/btp553
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SimCT: a generic tool to visualize ontology-based relationships for biological objects

Carl Herrmann 1,2,*, Sèverine Bérard 3 and Laurent Tichit 2,4

1 TAGC–U928 Inserm, 2 Faculté des Sciences, Université de la Méditerranée, Campus de Luminy Case 928, Marseille, 3 Université Montpellier 2, UMR AMAP, and UMR LIRMM – CNRS, 34000 Montpellier and 4 IML – UMR 6206 CNRS, Marseille, France

* To whom correspondence should be addressed.


  Abstract

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.

Availability: http://tagc.univ-mrs.fr/SimCT

Contact: carl.herrmann{at}univmed.fr

Supplementary information: Supplementary data are available at Bioinformatics online

Associate Editor: Alfonso Valencia

Received on June 5, 2009; revised on August 27, 2009; accepted on September 15, 2009

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