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Viruses 2017, 9(6), 126; doi:10.3390/v9060126

Bacterial Virus Ontology; Coordinating across Databases

1
Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland
2
University Libre de Bruxelles, Génétique et Physiologie Bactérienne (LGPB), 12 rue des Professeurs Jeener et Brachet, 6041 Charleroi, Belgium
3
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)
View Full-Text   |   Download PDF [3994 KB, uploaded 23 May 2017]   |  

Abstract

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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MDPI and ACS Style

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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