Inputs Outputs Method

GMI Outbreak Detector Evaluator

The Global Microbial Identifier pathogen tracking initiative (GMI) develops a global resource of sequence data for identification and diagnostics of pathogenic organisms and infectious diseases. A worldwide network of shared genomic information for bacterial, viral, and parasitic microorganisms can be used widely, from establishing a global disease outbreak detection system to personalised medicine.


GMI Outbreak Detector Evaluator is an OpenEBench Benchmarking Workflow that evaluates the prediction of outbreaks based in phylogenetic information. When new predictions are submitted to the server using this workflow, several metrics, such as precision/recall or Robinson-Foulds distance are computed. This allows to benchmark the predicted outbreak against the rest of the participants currently engaged in GMI, allowing the user to visualize the results in 2D-plot or HeatMap format, and apply several classification methods in order to transform the results to table format.