Počet záznamů: 1

Biochemical Space: A Framework for Systemic Annotation of Biological Models

SYSNO ASEP	0438527
Druh ASEP	J - Článek v odborném periodiku
Zařazení RIV	J - Článek v odborném periodiku
Poddruh J	Ostatní články
Název	Biochemical Space: A Framework for Systemic Annotation of Biological Models
Tvůrce(i)	Klement, M. (CZ) Děd, T. (CZ) Šafránek, D. (CZ) Červený, Jan (UEK-B)_{RID, ORCID, SAI} Müller, Stefan (UEK-B) Steuer, Ralf (UEK-B)
Zdroj.dok.	Electronic Notes in Theoretical Computer Science. - : Elsevier - ISSN 1571-0661 Roč. 306, JUL (2014), s. 31-44
Poč.str.	13 s.
Jazyk dok.	eng - angličtina
Země vyd.	NL - Nizozemsko
Klíč. slova	biological models ; model annotation ; systems biology ; cyanobacteria
Vědní obor RIV	EH - Ekologie - společenstva
CEP	EE2.3.20.0256 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
Institucionální podpora	RVO:67179843 - RVO:67179843
DOI	10.1016/j.entcs.2014.06.013
Anotace	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.
Pracoviště	Ústav výzkumu globální změny
Kontakt	Nikola Šviková, svikova.n@czechglobe.cz, Tel.: 511 192 268
Rok sběru	2015

Počet záznamů: 1