Abstract
Our growing knowledge of viruses reveals how these pathogens manage to evade innate host defenses. A global scheme emerges in which many viruses usurp key cellular defense mechanisms and often inhibit the same components of antiviral signaling. To accurately describe these processes, we have generated a comprehensive dictionary for eukaryotic host-virus interactions. This controlled vocabulary has been detailed in 57 ViralZone resource web pages which contain a global description of all molecular processes. In order to annotate viral gene products with this vocabulary, an ontology has been built in a hierarchy of UniProt Knowledgebase (UniProtKB) keyword terms and corresponding Gene Ontology (GO) terms have been developed in parallel. The results are 65 UniProtKB keywords related to 57 GO terms, which have been used in 14,390 manual annotations; 908,723 automatic annotations and propagated to an estimation of 922,941 GO annotations. ViralZone pages, UniProtKB keywords and GO terms provide complementary tools to users, and the three resources have been linked to each other through host-virus vocabulary.
Highlights
Viruses are genetic entities that infect all kinds of organism
The host-virus vocabulary presented here consists of 57 ViralZone terms, 65 UniProtKB keywords and 57 corresponding Gene Ontology (GO) terms, describing most of known interactions between viruses and their hosts
Our efforts to create eukaryotic host-virus interaction ontology have led to three levels of implementation: global knowledge and facts in ViralZone pages; viral protein annotation in UniProtKB through keywords; and viral gene and protein annotation through GO terms
Summary
Viruses are genetic entities that infect all kinds of organism. Their impact on living beings is huge, affecting human health, agricultural and other economic activity, global ecology, and even evolution. Detailed human- and machine-readable annotation of viral genome sequences – including known geographical sites of isolation, host specificity and interactions, functions and roles of individual viral proteins, and sequence variants – are essential to extract the maximum value from this data deluge, but the majority of available contextual data is published in papers or reviews in textual form that can only be interpreted by humans. Expert curation consists in associating viral sequences with experimental knowledge expressed in the form of human-readable text, ontologies and controlled vocabularies, which are searchable and even amenable to interpretation by machines. This requires human experts with deep knowledge of the underlying biology and a clear understanding of how to express and encode that knowledge in a consistent manner. Curators perform an editorial function, acting to highlight (and where possible resolve) conflicting reports one of the major added values of manual annotation
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