Program for Bioinformatics , Boston University , Boston , Massachusetts 02215 , United States.
Department of Biochemistry , Boston University , Boston , Massachusetts 02215 , United States.
J Proteome Res. 2019 Sep 6;18(9):3532-3537. doi: 10.1021/acs.jproteome.9b00367. Epub 2019 Jul 30.
Glycoinformatics is a critical resource for the study of glycobiology, and glycobiology is a necessary component for understanding the complex interface between intra- and extracellular spaces. Despite this, there is limited software available to scientists studying these topics, requiring each to create fundamental data structures and representations anew for each of their applications. This leads to poor uptake of standardization and loss of focus on the real problems. We present glypy, a library written in Python for reading, writing, manipulating, and transforming glycans at several levels of precision. In addition to understanding several common formats for textual representation of glycans, the library also provides application programming interfaces (APIs) for major community databases, including GlyTouCan and UnicarbKB. The library is freely available under the Apache 2 common license with source code available at https://github.com/mobiusklein/ and documentation at https://glypy.readthedocs.io/ .
糖组学是糖生物学研究的关键资源，而糖生物学是理解细胞内外空间复杂界面的必要组成部分。尽管如此，研究这些课题的科学家可用的软件有限，这使得每个科学家都需要为他们的每个应用程序重新创建基本的数据结构和表示。这导致标准化程度低，并且无法专注于真正的问题。我们提出了 glypy，这是一个用 Python 编写的库，用于在几个精度级别上读取、写入、操作和转换聚糖。除了理解聚糖的几种常见文本表示格式外，该库还为主要的社区数据库（包括 GlyTouCan 和 UnicarbKB）提供应用程序编程接口 (API)。该库在 Apache 2 通用许可证下免费提供，源代码可在 https://github.com/mobiusklein/ 获得，文档可在 https://glypy.readthedocs.io/ 获得。
