Beust Cécile, Becker Emmanuelle, Théret Nathalie, Dameron Olivier
Univ Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France.
Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, F-35000, France.
Comput Struct Biotechnol J. 2024 Nov 4;23:3999-4010. doi: 10.1016/j.csbj.2024.10.045. eCollection 2024 Dec.
In systems biology, the study of biological pathways plays a central role in understanding the complexity of biological systems. The massification of pathway data made available by numerous online databases in recent years has given rise to an important need for standardization of this data. The BioPAX format (Biological Pathway Exchange) emerged in 2010 as a solution for standardizing and exchanging pathway data across databases. BioPAX is a Semantic Web format associated to an ontology. It is highly expressive, allowing to finely describe biological pathways at the molecular and cellular levels, but the associated intrinsic complexity may be an obstacle to its widespread adoption. Here, we report on the use of the BioPAX format in 2024. We compare how the different pathway databases use BioPAX to standardize their data and point out possible avenues for improvement to make full use of its potential. We also report on the various tools and software that have been developed to work with BioPAX data. Finally, we present a new concept of abstraction on BioPAX graphs that would allow to specifically target areas in a BioPAX graph needed for a specific analysis, thus differentiating the format suited for representation and the abstraction suited for contextual analysis.
在系统生物学中，生物途径的研究在理解生物系统的复杂性方面起着核心作用。近年来，众多在线数据库提供的途径数据大量增加，引发了对该数据进行标准化的重要需求。BioPAX格式（生物途径交换）于2010年出现，作为跨数据库标准化和交换途径数据的解决方案。BioPAX是一种与本体相关联的语义网格式。它具有高度的表达能力，能够在分子和细胞水平上精细描述生物途径，但相关的内在复杂性可能成为其广泛采用的障碍。在此，我们报告2024年BioPAX格式的使用情况。我们比较了不同途径数据库如何使用BioPAX来标准化其数据，并指出充分利用其潜力的可能改进途径。我们还报告了为处理BioPAX数据而开发的各种工具和软件。最后，我们提出了一种关于BioPAX图的抽象新概念，该概念将允许专门针对特定分析所需的BioPAX图中的区域，从而区分适合表示的格式和适合上下文分析的抽象。
