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Viruses 2017, 9(6), 126;

Bacterial Virus Ontology; Coordinating across Databases

Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland
University Libre de Bruxelles, Génétique et Physiologie Bactérienne (LGPB), 12 rue des Professeurs Jeener et Brachet, 6041 Charleroi, Belgium
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Author to whom correspondence should be addressed.
Academic Editors: Tessa E. F. Quax, Matthias G. Fischer and Laurent Debarbieux
Received: 13 April 2017 / Revised: 16 May 2017 / Accepted: 17 May 2017 / Published: 23 May 2017
(This article belongs to the Special Issue Viruses of Microbes)
Full-Text   |   PDF [3994 KB, uploaded 23 May 2017]   |  


Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted. Classically, the viral life-cycle is described by schematic pictures. Using this ontology, it can be represented by a combination of successive events: entry, latency, transcription/replication, host–virus interactions and virus release. Each of these parts is broken down into discrete steps. For example enterobacteria phage lambda entry is broken down in: viral attachment to host adhesion receptor, viral attachment to host entry receptor, viral genome ejection and viral genome circularization. To demonstrate the utility of a standard ontology for virus biology, this work was completed by annotating virus data in the ViralZone, UniProtKB and Gene Ontology databases. View Full-Text
Keywords: phage; ontology; life-cycle phage; ontology; life-cycle

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Hulo, C.; Masson, P.; Toussaint, A.; Osumi-Sutherland, D.; de Castro, E.; Auchincloss, A.H.; Poux, S.; Bougueleret, L.; Xenarios, I.; Le Mercier, P. Bacterial Virus Ontology; Coordinating across Databases. Viruses 2017, 9, 126.

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