title: 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.
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Chantal
authors.initials: C
authors.lastname: Hulo
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Masson
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Edouard
authors.initials: E
authors.lastname: de Castro
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Andrea H
authors.initials: AH
authors.lastname: Auchincloss
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Foulger
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Poux
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: Jane
authors.initials: J
authors.lastname: Lomax
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Lydie
authors.initials: L
authors.lastname: Bougueleret
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Philippe
authors.identifier: http://orcid.org/0000-0001-8528-090X
authors.initials: P
authors.lastname: Le Mercier
mesh_terms: D030541:Databases, Genetic; D005057:Eukaryotic Cells / Q000821:virology*; D009626:Terminology as Topic; D014777:Virus Diseases / Q000821:virology*; D018406:Virus Physiological Phenomena; D014779:Virus Replication; D014780:Viruses / Q000235:genetics / Q000472:pathogenicity