Research Department, The Noguchi Institute, 1-9-7 Kaga, Itabashi, Tokyo 173-0003, Japan.
Institute for Glycomics, Griffith University at Gold Coast, Southport, QLD 4215, Australia.
Glycobiology. 2021 Aug 7;31(7):741-750. doi: 10.1093/glycob/cwab013.
Recent years have seen great advances in the development of glycoproteomics protocols and methods resulting in a sustainable increase in the reporting proteins, their attached glycans and glycosylation sites. However, only very few of these reports find their way into databases or data repositories. One of the major reasons is the absence of digital standard to represent glycoproteins and the challenging annotations with glycans. Depending on the experimental method, such a standard must be able to represent glycans as complete structures or as compositions, store not just single glycans but also represent glycoforms on a specific glycosylation side, deal with partially missing site information if no site mapping was performed, and store abundances or ratios of glycans within a glycoform of a specific site. To support the above, we have developed the GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoproteomics data. GlycoCoO can be used to represent glycoproteomics data in triplestores and can serve as a basis for data exchange formats. The ontology, database providers and supporting documentation are available online (https://github.com/glycoinfo/GlycoCoO).
近年来，糖蛋白质组学协议和方法的发展取得了重大进展，导致报告的蛋白质、其连接的聚糖和糖基化位点数量持续增加。然而，只有极少数这些报告能够进入数据库或数据存储库。其中一个主要原因是缺乏表示糖蛋白的数字标准以及糖基化的挑战性注释。根据实验方法，这样的标准必须能够表示完整的聚糖结构或组成，不仅存储单个聚糖，还能代表特定糖基化位点的糖型，在没有进行位点映射时处理部分缺失的位点信息，并在特定位点的糖型内存储聚糖的丰度或比例。为了支持上述内容，我们开发了糖缀合物本体 (GlycoConjugate Ontology, GlycoCoO) 作为描述和表示糖蛋白质组学数据的标准语义框架。GlycoCoO 可用于在三元存储中表示糖蛋白质组学数据，并可作为数据交换格式的基础。本体、数据库提供程序和支持文档可在线获取 (https://github.com/glycoinfo/GlycoCoO)。
