Bacterial Virus Ontology; Coordinating across Databases.

Journal: Viruses
Published Date:

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.

Authors

  • Chantal Hulo
    Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Chantal.Hulo@sib.swiss.
  • Patrick Masson
    Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Patrick.Masson@sib.swiss.
  • Ariane Toussaint
    University Libre de Bruxelles, Génétique et Physiologie Bactérienne (LGPB), 12 rue des Professeurs Jeener et Brachet, 6041 Charleroi, Belgium. ariane.toussaint@ulb.ac.be.
  • David Osumi-Sutherland
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
  • Edouard de Castro
    Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. edouard.decastro@sib.swiss.
  • Andrea H Auchincloss
    Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Andrea.Auchincloss@sib.swiss.
  • Sylvain Poux
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Lydie Bougueleret
    Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
  • Ioannis Xenarios
    Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland.
  • Philippe Le Mercier
    Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. philippe.lemercier@sib.swiss.