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

Chantal Hulo,Edouard De Castro,Jane Lomax,Andrea H Auchincloss,Rebecca Foulger,Ioannis Xenarios,Patrick Masson,Sylvain Poux,Lydie Bougueleret,Philippe Le Mercier,Gualtiero Alvisi

doi:10.1371/journal.pone.0171746

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.

Highlights

What could be more alien than a virus? These parasitic entities evolve at the periphery of cellular organisms, and have developed unique methods to replicate and disseminate their genetic material
This work describes the creation of a virus life-cycle vocabulary in ViralZone, UniProtKB and Gene Ontology
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

Summary

Introduction

These parasitic entities evolve at the periphery of cellular organisms, and have developed unique methods to replicate and disseminate their genetic material Many of these unique molecular processes may find their root in ancient biochemistry, down to the RNA world [1]. Natural selection has privileged dsDNA cellular organisms, while keeping complete viral genomic diversity This is advantageous to viruses, because their host cells have difficulty setting up antiviral defenses against that much diverse invading genetic material. This amazing viral diversity calls for various replication strategies: each kind of virus family has their own way of entering, replicating and exiting the host cell

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Conclusion