Sysdiag CNRS Bio-Rad UMR 3145, Cap delta/Parc euromédecine, 1682 rue de la Valsière CS 61003, 34184 Montpellier Cedex 4, France.
Bioinformatics. 2010 Jun 15;26(12):1542-7. doi: 10.1093/bioinformatics/btq169. Epub 2010 May 6.
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.
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.
www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/.
Supplementary data are available at Bioinformatics online.
在现有的数据库中，生物过程是从分子和细胞的角度来描述的，但这些描述是用文本注释来表示的，这使得它们难以进行计算处理。因此，需要对生物过程进行形式化描述。
我们提出了一种形式化方法，该方法使用 BioPsi 概念来对生物过程进行建模，从分子细节到网络。这种基于基本操作块的计算方法使我们能够计算生物功能（例如过程比较、映射结构-功能关系等）。我们用两个例子来说明它的应用：蛋白酶的功能比较和糖酵解网络的功能描述。这种计算方法与详细的生物学知识兼容，并可应用于不同类型的模拟系统。
www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/。
补充数据可在 Bioinformatics 在线获得。
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