Abstract
Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the 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. Classically, the viral life-cycle is described by schematic pictures. Using this ontology, it can be represented by a combination of successive events: entry, latency, transcription/replication, host–virus interactions and virus release. Each of these parts is broken down into discrete steps. For example enterobacteria phage lambda entry is broken down in: viral attachment to host adhesion receptor, viral attachment to host entry receptor, viral genome ejection and viral genome circularization. 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
Bacterial viruses, are the most abundant biological entity on earth
This work describes the creation of a vocabulary of bacterial virus molecular biology in ViralZone, UniProtKB, and Gene Ontology
An exhaustive study was performed of the Bacteriophage textbook [18], published reviews, and existing ontologies in Gene Ontology (GO) [15] and ACLAME (A CLAssification of Mobile genetic Elements) [19]
Summary
Bacterial viruses, are the most abundant biological entity on earth. Since their discovery and the advent of molecular biology, much has been learned about their infectious cycle. Bacterial viruses have proven to be potent molecular tools because they grow quickly ex vivo, their genetic material is small and manageable, and they are mostly harmless to humans. These factors contributed to put bacterial viruses at the forefront of molecular biology and promise a brilliant future for phage biotechnologies [2]. An important current challenge is to monitor antibiotic resistant bacterial strains, and we know that phage therapy
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