The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection

PLoS One. 2017 Feb 16;12(2):e0171746. doi: 10.1371/journal.pone.0171746. eCollection 2017.

Abstract

Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were investigated and indexed in 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. The virus life-cycle is classically described by schematic pictures. Using this ontology, it can be represented by a combination of successive terms: "entry", "latency", "transcription", "replication" and "exit". Each of these parts is broken down into discrete steps. For example Zika virus "entry" is broken down in successive steps: "Attachment", "Apoptotic mimicry", "Viral endocytosis/ macropinocytosis", "Fusion with host endosomal membrane", "Viral factory". 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.

MeSH terms

  • Databases, Genetic
  • Eukaryotic Cells / virology*
  • Terminology as Topic*
  • Virus Diseases / virology*
  • Virus Physiological Phenomena*
  • Virus Replication
  • Viruses / genetics
  • Viruses / pathogenicity

Grants and funding

The Swiss-Prot group is part of the SIB Swiss Institute of Bioinformatics and of the UniProt Consortium. Swiss-Prot group activities are supported by the Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI, the National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI) and National Institute of General Medical Sciences (NIGMS) grant U41HG007822 and the Swiss National Science Foundation (SNSF) grant IZLSZ3_148802.