The Data-Driven Ontology Toolkit (DDOT) facilitates the inference, analysis, and visualization of biological hierarchies using a data structure called an ontology.
If you use DDOT for your research, please cite
Yu MK, Ma J, Ono K, Zheng F, Fong S, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies . Cell Systems. 2019 Mar 27;8(3):267-273.