The AtgO web application provides a novel and intuitive visualization system for exploring AtgO ontology. In this system, ontology is factored hierarchically and explored with semantic zooming in the style of Google Maps. This system includes:

• Hierarchical layout of the complete ontology according to its most informative parent-child term relations, enabling the entire ontology to be explored as a multi-scale geographic map.
• Semantic zooming, providing details on demand so the user sees different amounts of detail in a view by zooming in and out.

Navigation

Terms are nodes. Each node in the ontology represents a functional group of genes or a term. Some of the terms are manually labeled.

Term relations are edges. Each edge in the ontology represents a parent-child relation between terms.

Browsing

Browse the AtgO ontology using the mouse. Click-and-drag to pan. Use the mouse wheel (two-finger scroll) to zoom in or out of selected regions of the ontology. Click on an ontology term to select it. When a term is selected, the relations to ancestral terms are highlighted and a term summary view is presented with information about the selected term (see below). Double-click on the page background to reset the current selection and re-zoom the ontology to fit the page.

Basic navigation buttons

Use the navigation buttons (lower left) to zoom-in and out of the ontology, fit the ontology layout to screen.

Zoom -in

Zoom -out

Fit to Screen

Searching for terms or genes. Search the AtgO ontologies either by keyword or by gene. Results are displayed below the search box. Click on a search result to select and highlight a gene or term in the displayed ontology. Use the refresh button to clear search results and the search box. Queries are case insensitive.

Clicking on a term in the ontology opens a summary information panel for the selected term. This information panel includes the term name, ID and term similarity score. Also, this panel includes legend for interaction types.

List of genes assigned to the term

Raw interactions

The genes annotated to the AtgO term and the interactions between them are also displayed in the form of a dynamic network which allows zooming and interactive inspection of gene names and interactions. Click genes in the interaction view to find them in the main tree. Interaction types are color coded and the legend for them is available in the summary panel. If the term has too many assigned interactions, top 500 interactions (based on interaction strength) will be displayed.