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 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.

Fig 1. Example of ontology parent-child relationship.

This tree consists of terms used to annotate the entry step of viral genomes. ViralZone pages (VZ), UniProtKB keyword (KW) or GO term accession numbers (GO:) are indicated. The hierarchy indicated is shared by GO and KW.

Fig 2. Entry pathways of eukaryotic viruses.

This picture represents all the ViralZone controlled vocabularies concerning the virus entry pathway. The representation of viral entry is chronological. The virus genome begins on the top of the picture and will follow alternative pathways until reaching transcription/replication processes.

Fig 3. Viral specific transcription, replication and translation processes.

This table lists all specific viral processes involved in transcription, replication or translation processes. The processes with orange backgrounds are also naturally used by eukaryotic cells, the others are specifically viral. All the processes are classified by the Baltimore classification (top row) which describes the nature of viral genome in the virion.

Fig 4. Exit pathways of eukaryotic viruses.

This picture represents all the ViralZone controlled vocabularies concerning the virus exit pathway. The representation is chronological: The virus genome begins at the bottom of the picture at transcription/replication processes and will follow alternative pathways until exiting the host cell at the top of picture.