Eur. Phys. J. Plus (2014) 129: 135
https://doi.org/10.1140/epjp/i2014-14135-x

Regular Article

Annotation and retrieval in protein interaction databases

Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy

^* e-mail: cannataro@unicz.it

Received: 13 February 2014
Accepted: 15 May 2014
Published online: 24 June 2014

Abstract

Biological databases have been developed with a special focus on the efficient retrieval of single records or the efficient computation of specialized bioinformatics algorithms against the overall database, such as in sequence alignment. The continuos production of biological knowledge spread on several biological databases and ontologies, such as Gene Ontology, and the availability of efficient techniques to handle such knowledge, such as annotation and semantic similarity measures, enable the development on novel bioinformatics applications that explicitly use and integrate such knowledge. After introducing the annotation process and the main semantic similarity measures, this paper shows how annotations and semantic similarity can be exploited to improve the extraction and analysis of biologically relevant data from protein interaction databases. As case studies, the paper presents two novel software tools, OntoPIN and CytoSeVis, both based on the use of Gene Ontology annotations, for the advanced querying of protein interaction databases and for the enhanced visualization of protein interaction networks.