G Fuellen

BACKGROUND Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces of knowledge available in a formal (and thus computable) manner. RESULTS We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. CONCLUSIONS We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions.

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin.