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Statements

Subject Item
n2:RIV%2F67179843%3A_____%2F14%3A00438527%21RIV15-AV0-67179843
rdf:type
n17:Vysledek skos:Concept
dcterms: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 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. 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.
dcterms:title
Biochemical Space: A Framework for Systemic Annotation of Biological Models Biochemical Space: A Framework for Systemic Annotation of Biological Models
skos:prefLabel
Biochemical Space: A Framework for Systemic Annotation of Biological Models Biochemical Space: A Framework for Systemic Annotation of Biological Models
skos:notation
RIV/67179843:_____/14:00438527!RIV15-AV0-67179843
n3:aktivita
n9:P n9:I
n3:aktivity
I, P(EE2.3.20.0256)
n3:cisloPeriodika
JUL
n3:dodaniDat
n15:2015
n3:domaciTvurceVysledku
n4:4419715 Steuer, Ralf Müller, Stefan
n3:druhVysledku
n10:J
n3:duvernostUdaju
n12:S
n3:entitaPredkladatele
n5:predkladatel
n3:idSjednocenehoVysledku
5301
n3:idVysledku
RIV/67179843:_____/14:00438527
n3:jazykVysledku
n18:eng
n3:klicovaSlova
biological models; model annotation; systems biology; cyanobacteria
n3:klicoveSlovo
n7:systems%20biology n7:cyanobacteria n7:model%20annotation n7:biological%20models
n3:kodStatuVydavatele
NL - Nizozemsko
n3:kontrolniKodProRIV
[104267B01516]
n3:nazevZdroje
Electronic Notes in Theoretical Computer Science
n3:obor
n16:EH
n3:pocetDomacichTvurcuVysledku
3
n3:pocetTvurcuVysledku
6
n3:projekt
n13:EE2.3.20.0256
n3:rokUplatneniVysledku
n15:2014
n3:svazekPeriodika
306
n3:tvurceVysledku
Steuer, Ralf Klement, M. Červený, Jan Šafránek, D. Děd, T. Müller, Stefan
s:issn
1571-0661
s:numberOfPages
13
n14:doi
10.1016/j.entcs.2014.06.013