An ontology to structure biological data: the contribution of mathematical models
Abstract
The biology is a research field well known for its huge quantity and diversity of data. Today, these data are still recognized as heterogeneous and fragmented. Despite the fact that several initiatives of biological knowledge representation have been realized, biologists and bioinformaticians do not have a formal representation that, at the level of the entire organism, can help them to organize such a diversity and quantity of data. Recently, in the context of the whole cell modeling approach, the systemic mathematical models have proven to be a powerful tool for understanding the bacterial cell behavior. We advocate that an ontology built on the principles that govern the design of such models, can help to organize the biological data. In this article, we describe the first step in the conception of an ontology dedicated to biological data organization at the level of the entire organism and for molecular scales i.e., the choice of concepts and relations compliant with principles at work in the systemic mathematical models.
