Další formáty:
BibTeX
LaTeX
RIS
@inproceedings{1193175,
author = {Klement, Matej and Děd, Tadeáš and Šafránek, David and Červený, Jan and Mueller, Stefan and Steuer, Ralf},
address = {Amsterdam},
booktitle = {Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14)},
doi = {http://dx.doi.org/10.1016/j.entcs.2014.06.013},
keywords = {biological models; model annotation; systems biology; cyanobacteria},
howpublished = {elektronická verze "online"},
language = {eng},
location = {Amsterdam},
pages = {31-44},
publisher = {Elsevier},
title = {Biochemical Space: A Framework for Systemic Annotation of Biological Models},
url = {http://www.sciencedirect.com/science/article/pii/S1571066114000590},
year = {2014}
}
TY - JOUR
ID - 1193175
AU - Klement, Matej - Děd, Tadeáš - Šafránek, David - Červený, Jan - Mueller, Stefan - Steuer, Ralf
PY - 2014
TI - Biochemical Space: A Framework for Systemic Annotation of Biological Models
PB - Elsevier
CY - Amsterdam
KW - biological models
KW - model annotation
KW - systems biology
KW - cyanobacteria
UR - http://www.sciencedirect.com/science/article/pii/S1571066114000590
N2 - 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.
ER -
KLEMENT, Matej, Tadeáš DĚD, David ŠAFRÁNEK, Jan ČERVENÝ, Stefan MUELLER a Ralf STEUER. Biochemical Space: A Framework for Systemic Annotation of Biological Models. Online. In \textit{Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14)}. Amsterdam: Elsevier, 2014, s.~31-44. ISSN~1571-0661. Dostupné z: https://dx.doi.org/10.1016/j.entcs.2014.06.013.
|
