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

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 lifecycle 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.