Publication details

Biochemical Space: A Framework for Systemic Annotation of Biological Models

Authors

KLEMENT Matej DĚD Tadeáš ŠAFRÁNEK David ČERVENÝ Jan MUELLER Stefan STEUER Ralf

Year of publication 2014
Type Article in Proceedings
Conference Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14)
MU Faculty or unit

Faculty of Informatics

Citation
Web Elsevier URL
Doi http://dx.doi.org/10.1016/j.entcs.2014.06.013
Field Informatics
Keywords biological models; model annotation; systems biology; cyanobacteria
Description 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 well-structured 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.
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