Visualization based on the Enzyme Commission nomenclature

We developed a tool for visualizing data related to protein function, based on the nomenclature defined by the International Enzyme Commission. The method represents the 1327 specific reaction types and three additional levels of abstract classifications in the nomenclature as an interactive graph. Each node and link in the graph can have associated with it stored or computed data values of various types, each of which can be assigned to any of a set of visualization methods, including color, size, various chart types and text. Visualizations can then be interactively created for single nodes, groups of nodes or the entire graph. This visualization tool is particularly useful for exploring the distribution of quantitative attributes across protein function classes. As a test of this tool, we developed a visualization of data measuring the effectiveness of sequence similarity for prediction of EC class. Using this tool, it was possible to rapidly scan hundreds of functional classes, and to correlate predictability from sequence with other attributes, facilitating the generation of hypotheses about the causes of predictive failure.