UFO-Cytoscape

Motivation: Biomedical ontologies have been growing quickly and proven to be useful in many biomedical applications. The use of this data is mainly based on semantic similarity calculation between ontology terms and between annotated biomedical entities. Many semantic similarity measures have been proposed for such calculation.
Results: A number of tools have been developed on different platforms for ontology visualization and semantic similarity calculation. However, these tools have implemented a small number of the semantic similarity measures for only one type of biomedical ontology. Note that, the measures can be applied to all types of biomedical ontologies. In addition, each measure is dominant in different biomedical applications. In this study, we developed a Cytoscape app, named UFO, which unifies most of the proposed semantic similarity calculation and visualization for all types of biomedical ontology.