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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.

SUBMITTER: Hulo C 

PROVIDER: S-EPMC5313201 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Hulo Chantal C   Masson Patrick P   de Castro Edouard E   Auchincloss Andrea H AH   Foulger Rebecca R   Poux Sylvain S   Lomax Jane J   Bougueleret Lydie L   Xenarios Ioannis I   Le Mercier Philippe P  

PloS one 20170216 2


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  ...[more]

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