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Biochemical Space: A Framework for Systemic Annotation of Biological Models
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SYSNO ASEP 0438527 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Ostatní články Title Biochemical Space: A Framework for Systemic Annotation of Biological Models Author(s) Klement, M. (CZ)
Děd, T. (CZ)
Šafránek, D. (CZ)
Červený, Jan (UEK-B) RID, ORCID, SAI
Müller, Stefan (UEK-B)
Steuer, Ralf (UEK-B)Source Title Electronic Notes in Theoretical Computer Science. - : Elsevier - ISSN 1571-0661
Roč. 306, JUL (2014), s. 31-44Number of pages 13 s. Language eng - English Country NL - Netherlands Keywords biological models ; model annotation ; systems biology ; cyanobacteria Subject RIV EH - Ecology, Behaviour R&D Projects EE2.3.20.0256 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Institutional support RVO:67179843 - RVO:67179843 DOI 10.1016/j.entcs.2014.06.013 Annotation 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. Workplace Global Change Research Institute Contact Nikola Šviková, svikova.n@czechglobe.cz, Tel.: 511 192 268 Year of Publishing 2015
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