In this paper, we propose a hybrid and exploratory knowledge discovery approach for analyzing metabolomic complex data based on a combination of supervised classifiers, pattern mining and Formal Concept Analysis (FCA). The approach is based on three main operations, preprocessing, classification, and postprocessing. Classifiers are applied to datasets of the form individuals×features and produce sets of ranked features which are further analyzed. Pattern mining and FCA are used to provide a complementary analysis and support for visualization. A practical application of this framework is presented in the context of metabolomic data, where two interrelated problems are considered, discrimination and prediction of class membership. The dataset is characterized by a small set of individuals and a large set of features, in which predictive biomarkers of clinical outcomes should be identified. The problems of combining numerical and symbolic data mining methods, as well as discrimination and prediction, are detailed and discussed. Moreover, it appears that visualization based on FCA can be used both for guiding knowledge discovery and for interpretation by domain analysts.