Dataset Information

Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.

ABSTRACT:

Motivation

In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes.

Results

We present a formalism that uses the BioPsi concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure-function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation.

Availability

www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Peres S

PROVIDER: S-EPMC2881354 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature

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Publications

Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.

Pérès Sabine S Felicori Liza L Rialle Stéphanie S Jobard Elodie E Molina Franck F

Bioinformatics (Oxford, England) 20100506 12

<h4>Motivation</h4>In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes.<h4>Results</h4>We present a formalism that uses the BioPsi concepts to model biological processes from molecular details to networks. This computational approach, based o ...[more]

PMID: 20448138

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Dataset Information

Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.

Motivation

Results

Availability

Supplementary information

Publications

Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.

Similar Datasets

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