Ontology- and graph-based similarity assessment in biological networks.

SUMMARY: A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different 'guilt-by-association' analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a 'semantic similarity' space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. AVAILABILITY: http://rosalind.infj.ulst.ac.uk/SimTrek.html CONTACT: francisco.azuaje@crp-sante.lu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.