Figure 1.
This figure describes the relationship between ViralZone vocabulary, UniProtKB keywords and GO terms.
It also explains the process of curation of UniProtKB sequences using the new ontology.
Table 1.
List of the 65 host-virus interaction processes.
Figure 2.
Host virus interactions in ViralZone A) Main entry page (http://viralzone.expasy.org/all_by_species/886.html).
All global processes are listed and some links allow browsing down in the controlled vocabulary hierarchy. B) Inhibition of host RLR pathway by virus ViralZone. An illustration describes the RLR antiviral signaling pathway. Known viral proteins inhibiting this pathway are indicated in red circles. A side menu allows reaching description pages for each part of the pathway. (C) “Inhibition of host RIG-I by virus” page describes the host process targeted by viruses, and displays viral proteins inhibiting this activity coded by Lyssavirus, Arenavirus, Influenzavirus A and Pneumovirus. The text describes this host-virus interaction at a molecular level, and a table displays known viruses and their method used to evade RIG-I antiviral defense. To the left, links to the corresponding UniProtKB keyword and GO term allow users to visit these resources and access to all annotated proteins related to the corresponding ontology term (Figure 4). The field “virus” contains the list of viruses attacking this process, a publication source, and a link to ViralZone virus fact sheet for each virus. Most pages give direct access to reviewed UniProtKB entries annotated with corresponding keyword within “protein by strain” and “protein by name” tabs. An illustration describes the RLR antiviral signaling pathway, and identified viral proteins interfering with RIG-I are indicated in red circles.
Figure 3.
ViralZone fact sheet for Influenza virus A (http://viralzone.expasy.org/all_by_species/6.html) contains information about virion, molecular biology and cross references to different sequence databases.
A tab “Host-virus interactions” gives access to essential interactions occurring during Influenza A infection. In turn, these interactions are linked to the controlled vocabulary pages where more information concerning the particular interaction of interest is available. From there, users can visit UniProtKB or QuickGO pages related to the keyword or corresponding GO term.
Figure 4.
Relationship between ViralZone, UniProtKB and QuickGO databases.
Because most host virus-interactions vocabulary or ontology share the same concept, users can browse in the three databases and have easy access to different formats about the same process. Links are indicated by large arrows.
Figure 5.
This picture is an example of ontology parent-child relationship.
This tree consists of terms used to annotate viral gene products that inhibit the different host components involved in the pattern recognition receptor pathway. Term hierarchy come from ViralZone controlled vocabulary. If equivalence exists, UniProtKB keyword or GO term accession numbers are indicated.