Ontologies are being used in bioinformatics and systems biology, among others, for
communication between people and organizations, as the basis for interoperability between
systems, and as query models and indexes to repositories of information. In this chapter we
give a background of the area and provide a state of the art overview. We present different
possible definitions of ontology, examples of bio-ontologies and their use, formalisms that
can be used to represent ontologies as well as tools that support the different stages in the …

Computer simulation is now becoming a central scientific paradigm of systems biology and a
basic tool for the theoretical study and understanding of the complex mechanisms of living
systems. The increase in the number and complexity of these models leads to the need for
their collaborative development, reuse of models, their verification, and the description of
computational experiments and their results. Ontological modeling is used to develop
formats for knowledge-oriented mathematical modeling of biological systems. In this sense …