Biochemical Space: A Framework for Systemic Annotation of Biological Models

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67179843%3A_____%2F14%3A00438527" target="_blank" >RIV/67179843:_____/14:00438527 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1016/j.entcs.2014.06.013" target="_blank" >http://dx.doi.org/10.1016/j.entcs.2014.06.013</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.entcs.2014.06.013" target="_blank" >10.1016/j.entcs.2014.06.013</a>

Result language
angličtina
Original language name
Biochemical Space: A Framework for Systemic Annotation of Biological Models
Original language 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 softwaretools 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
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
EH - Ecology - communities
OECD FORD branch
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Project
<a href="/en/project/EE2.3.20.0256" target="_blank" >EE2.3.20.0256: Local team and international consortium for computational modelling of a cyanobacterial cell</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2014
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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