ICBO_2018_29: Graph Summary of Ontology-based Annotations

TitleICBO_2018_29: Graph Summary of Ontology-based Annotations
Publication TypeConference Paper
Year of Publication2018
AuthorsLee, R, Chan, J, Grove, C, Sternberg, P
Conference NameInternational Conference on Biomedical Ontology (ICBO 2018)
Date Published08/06/2018
PublisherInternational Conference on Biological Ontology
KeywordsDAG, GO, Ontology, phenotype, summary graph
Abstract

It is desirable to learn about gene function in ever more detail and to communicate the information using the vocabularies of ontologies. However, rich annotations can exacerbate the challenge of intuitive comprehension of that complex knowledge by a human. We developed a graph-based tool called SObA (Summary of Ontology-based Annotations) to simplify and summarize complex annotations while allowing users to drill down into details easily by following the graph paths.In contrast to fixed-category summaries, such as ribbons or slims, for SObA, ontology graphs are trimmed dynamically, strictly dictated by available annotations. By following a set of simple rules, any node and path in the graph that is redundant or less informative is removed. Furthermore, visual cues to important nodes are provided by node color and size, which are determined by the type and amount of annotations. The SObA graph was implemented using the Cytoscape Javascript library, making it easy for users to traverse the graph at multiple levels of detail.SObA can be applied on any annotations that use DAG (directed acyclic graph) ontologies. We have implemented it on C. elegans phenotype annotations and on Gene Ontology annotations of many species. We are exploring the feasibility of applying SObA to summarize annotations of post-composed ontologies such as the mammalian phenotype ontology.

URLhttp://icbo2018.cgrb.oregonstate.edu/