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Studying biological organisms at the systems level is a complex task. Computational approaches require structured representations of existing biological knowledge. This necessity has prompted the development of formal representations of specific areas of knowledge, resulting in ontologies such as Gene Ontology and BioPAX. However, only part of this formalized knowledge is exploited for the interpretation of experimental data. Specifically, it is common to use the association between entities and annotations, like genes and functions, while the structure of the annotation is not considered beyond some common features as inheritance. This is partly due to a lack of tools and methods that bridge resources related to ontologies to the ones related to data analysis. Here we present a platform that merges a semantic web toolkit with a widely adopted modular tool for systems biology investigation. We demonstrate how in this environment it is possible to query ontologies not only as a list of annotations but as a knowledge base from which new information can be derived. We also show how this knowledge can be integrated with biological data.