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Schilling et al. BioData Mining 2011, 4:9 /content/4/1/9 BioData Mining RESEARCH Open Access pGQL: A probabilistic graphical query language for gene expression time courses Ruben Schilling1*, Ivan G Costa2 and Alexander Schliep3 * Correspondence: ruben. Abstract schilling@molgen.mpg.de 1Max Planck Institute for Molecular Background: Timeboxes are graphical user interface widgets that were proposed to Genetics, Department of Computational Biology, Ihnestr. 63- specify queries on time course data. As queries can be very easily defined, an 73, 14195 Berlin, Germany exploratory analysis of time course data is greatly facilitated. While timeboxes are Full list of author information is effective, they have no provisions for dealing with noisy data or data with available at the end of the article fluctuations along the time axis, which is very common in many applications. In particular, this is true for the analysis of gene expression time courses, which are mostly derived from noisy microarray measurements at few unevenly sampled time points. From a data mining point of view the robust handling of data through a sound statistical model is of great importance. Results: We propose probabilistic timeboxes, which correspond to a specific class of Hidden Markov Models, that constitutes an established method in data mining. Since HMMs are a particular class of probabilistic graphical models we call o