Data Integration and Semantic Enrichment of Systems Biology Models and Simulations

The rise of Systems Biology approaches, in conjunction with the availability of numerous powerful and user-friendly modeling environments, brought computational models out of the dusty closets of theoreticians to the forefront of research in biology. Those models are becoming larger, more complex and more realistic. As any other type of data in life sciences, models have to be stored, exchanged and re-used. This was made possible by the development of a series of standards, that, when used in conjunction, can cover the whole life-cycle of a model, including the specification of its structure and syntax, the simulations to be run, and the description of its behaviour and resulting numerical output. We will review those standards, well-accepted or still under development, including the Minimal requirements (MIRIAM, MIASE), the description formats (SBML, SED-ML, SBRML) and the associated ontologies (SBO, KiSAO, TEDDY). We will show how their use by the community, through a rich toolkit of complementary software, can permit to leverage on everyone's efforts, to integrate models and simulations with other types of biological knowledge, and eventually lead to the fulfillment of one of Systems Biology's tenets of collaboration between biology, mathematics and computing science.