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KNeXT:一个基于NetworkX的拓相关KEGG解析器

Everest Uriel Castaneda^1,2, Erich J Baker³

¹Department of Biology, Baylor University, Waco, TX, United States.

Frontiers in genetics

|February 28, 2024

概括

由于数据结构的限制,从KEGG标记语言 (KGML) 文件中自动创建基因网络是很困难的. KNeXT解析器准确地重建遗传和混合网络,保留拓环境和节点位置,以可靠的路径可视化.

科学领域:

生物信息学是一种生物信息学.
计算生物学计算生物学
系统生物学系统生物学

背景情况:

从基因和基因组 (KEGG) 标记语言 (KGML) 文件中重建基因和混合基因复合网络具有挑战性.
当前的数据结构掩盖了原来的拓环境,导致了不准确的网络表示.
重叠的接入号码和重复的标识符会导致网络社区的人工崩.

研究的目的:

开发一种新的基于Python的解析器,KNeXT,用于从KGML数据中准确地回顾基因和混合网络.
克服现有的解析器在保护生物网络的拓环境方面的局限性.
确保高保真度的拓表示和对原始节点位置的程序访问.

主要方法:

开发了一个基于Python的KEGG NetworkX拓 (KNeXT) 解析器.
通过内置的API来摄取KGML文件以动态创建拓表示.
使用NetworkX框架生成与其他图形框架兼容的分别为tab的文件.
启用了本地文件或单个文件的解析,并将其转换为NCBI或UniProt ID.

主要成果:

KNeXT从KGML地图数据中准确地汇总了基因和混合网络.
解析器保留了原来的拓环境和节点位置 (x-y轴).
生成的以标签区分的文件保留了对路径数据的程序访问权限,并且可以导入其他图形框架.
KNeXT支持对本地文件/文件进行解析和ID转换 (NCBI/UniProt).

结论:

KNeXT提供了一个强大的解决方案,可以准确地重建KEGG路径,克服以前方法的局限性.
该工具确保保留原始网络上下文和拓细节.
在生物信息学研究中,KNeXT提高了途径可视化和分析的可靠性.

关键词:

凯格 (KEGG) 是一个在KGML图表中,KGML图表显示了这是一个KGML解析器.网络X 网络X 网络X Python 是一个 Python 语言.

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