Biochemical Space: A Framework for Systemic Annotation of Biological Models

0438527 - ÚVGZ 2015 RIV NL eng J - Journal Article
Klement, M. - Děd, T. - Šafránek, D. - Červený, Jan - Müller, Stefan - Steuer, Ralf
Biochemical Space: A Framework for Systemic Annotation of Biological Models.
Electronic Notes in Theoretical Computer Science. Roč. 306, JUL (2014), s. 31-44. ISSN 1571-0661
R&D Projects: GA MŠMT(CZ) EE2.3.20.0256
Institutional support: RVO:67179843
Keywords : biological models * model annotation * systems biology * cyanobacteria
Subject RIV: EH - Ecology, Behaviour

In this tool paper, we target the problem of unique annotation of organism-specific computational models presented in a public model database. In particular, we present Biochemical Space, a novel annotation methodology accompanied with a set of software tools that allow to create, manage and maintain the Biochemical Space content. The main idea behind is to create a transparent well-annotated reaction network of chemical entities and elemental reactions onto which the mathematical models are projected. For a given organism, the Biochemical Space represents a unifying platform for understanding of the related biological processes. The contribution of the methodology is three-fold: (i) systemic projection of models to a wellstructured biological knowledge, (ii) simplification of annotation procedure, (iii) targetting several problems such as the presence of lumped model variables, combinatorial explosion in chemical modifications of entities, and hierarchical organisation of locations of individual entities. In these aspects the Biochemical Space goes beyond the features of current standards such as SBML. Application of the framework is demonstrated on a set of annotation data compiled for complex cyanobacteria processes.
Permanent Link: http://hdl.handle.net/11104/0241896