UFO

A tool for unifying biomedical ontology-based semantic similarity calculation and visualization

Motivation: Biomedical ontologies have been growing quickly in different domains as well as in coverage. This kind of data has been proven to be useful in many biomedical problems. The use of this data is mainly based on semantic similarity calculation between ontology terms and annotated biomedical entities such as gene, disease and human phenotype. Many semantic similarity measures have been proposed for such calculation.

Results: To facilitate the use of biomedical ontologies and the semantic similarity measures, a number of tools, which visualize ontology and calculate semantic similarity, have been introduced. These tools run on different platforms, but implement a similar set of semantic similarity measures. The limitation of these tools is that they implemented just a small number of the measures for only one kind of biomedical ontology. Note that, these measures can be applied to any kind of biomedical ontologies. In addition, each measure is dominant in different problems. In this study, we developed a Cytoscape app, named UFO, which unifies most of the proposed semantic similarity calculation and visualization for any biomedical ontology.

Citation:

  1. Le, D.-H., UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PLOS ONE, 2020. 15(7): p. e0235670.

  2. Nguyen, Q.-H. and D.-H. Le, Similarity Calculation, Enrichment Analysis, and Ontology Visualization of Biomedical Ontologies using UFO. Current Protocols, 2021. 1(4): p. e115.