Informace o publikaci

Biochemical Space: A Framework for Systemic Annotation of Biological Models

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

Rok publikování 2014
Druh Článek ve sborníku
Konference Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14)
Fakulta / Pracoviště MU

Fakulta informatiky

Citace
www Elsevier URL
Doi http://dx.doi.org/10.1016/j.entcs.2014.06.013
Obor Informatika
Klíčová slova biological models; model annotation; systems biology; cyanobacteria
Popis 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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