A taxonomy for bioinformatics tools: exploiting semantics, parallelism, and services for analyzing omics data

The overwhelming availability of omics data poses new challenges to bioinformatics applications, such as the efficient storage, preprocessing, and analysis of experimental data; the building of reproducible "in silico" experiments; the an- notation of omics data with terms extracted from ontologies; and the integration of omics and clinical data. We present BioTax, a taxonomy for bioinformatics tools, and its web- based system that users can access either to query the tax- onomy and retrieve metadata about bioinformatics tools, or to submit and classify new bioinformatics tools according to the taxonomy itself. BioTax is implemented by using the OWL Web Ontology Language and currently it classiffies 14 bioinformatics tools. BioTax can help both decision makers as well as application designers in choosing bioinfor- matics tools during the development of complex biomedical applications and in better understanding their strengths and weaknesses in the various stages of the bioinformatics analysis pipeline.