User Guide/SObA

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Summary of Ontology-based Annotations (SObA)

What is a SObA graph?

SObA provides an abridged, summary view of a full ontology graph, trimmed based on annotations and hierarchical relationships.

For inference reasoning, we follow that defined by GO Relations where "is a", "part of", and "regulates" are included in inference.

Starting with the full ontology graph, we edit the graph by:

(A) removing all nodes (and their edges) that do not carry any (direct or inferred) annotations; 
(B) removing all nodes that do not have direct (as opposed to inferred) annotations unless they are the lowest common ancestral nodes of two or more descending nodes (lowest common ancestor, LCA); 
(C) applying transitive reduction by removing all paths between a pair of nodes unless they are the longest paths;
(D) reducing hierarchy depth to focus on broader aspects of ontology (top slicing as a user option).
(E) scaling node sizes based on the relative number of annotations that each node carries to indicate possible relative importance.

The graph may be manipulated in the following ways:

1. zoom and move nodes around.
2. Select a node or edge for specific information.
3. "Save Image" turns the graph into a high resolution PNG file.
4. Node size scaling may be removed by ticking "Uniform".
5. Displayed graph depth may be set at will (Maximum Depth).
6. Graph display may be faceted by evidence types or ontology aspects (GO only).

Types of SObA graph

1. Single gene: SObA single gene graph presents the ontology annotations of a single gene.
2. Pair of genes: SObA paired genes combines and compares ontology annotations of a pair of genes.
3. List of terms: A list of ontology terms (of the same type) and their associated statistical (correct-P or Q) value are used as input to make a SObA graph.