Biochemical Space: A Framework for Systemic Annotation of
Biological Models

D 2014

Biochemical Space: A Framework for Systemic Annotation of Biological Models

KLEMENT, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Jan ČERVENÝ; Stefan MUELLER et al.

Základní údaje

Originální název

Biochemical Space: A Framework for Systemic Annotation of Biological Models

Autoři

KLEMENT, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Jan ČERVENÝ; Stefan MUELLER a Ralf STEUER

Vydání

Amsterdam, Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14), od s. 31-44, 14 s. 2014

Nakladatel

Elsevier

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Odkazy

Elsevier URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/14:00076022

Organizační jednotka

Fakulta informatiky

ISSN

Klíčová slova anglicky

biological models; model annotation; systems biology; cyanobacteria

Změněno: 27. 4. 2015 03:58, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

EE2.3.20.0256, projekt VaV

Název: Vytvoření výzkumného týmu a mezinárodního konzorcia pro počítačový model buňky sinice

Citovat

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 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://doi.org/10.1016/j.entcs.2014.06.013.

@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 = {https://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  - CONF
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://doi.org/10.1016/j.entcs.2014.06.013.

Přehled o publikaci