User Guide/SObA

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Summary of Ontology-based Annotations (SObA)

What is a SObA graph?

SObA is an abridged version of the ontology graph, trimmed based on annotations and hierarchical relationships.

Starting with the full ontology graph, we trim 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). (E), scaling node sizes based on the relative number of annotations that each node carries to indicate possible relative importance.

SObA graph is drawn with Cytoscape. The graph may be manipulated in the following ways.

1. zoom and move nodes around.