UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations
UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations
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DOI：
10.1016/j.bbagen.2016.02.016
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发表时间：
2016-08-01
影响因子：
3
通讯作者：
Packer, Nicolle H.
中科院分区：
文献类型：
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作者：
Campbell, Matthew P.;Packer, Nicolle H.
背景：UniCarbKB旨在为哺乳动物糖生物学知识的表示提供一个资源，通过提供一个精心策划的结构和实验数据数据库，由一个web应用程序支持，允许用户轻松查找和查看丰富的注释信息。该数据库包含两个级别的注释(i)从单个纯化糖蛋白释放和表征的低聚糖的全球特异性数据和（ii）与位点特异性聚糖异质性有关的信息。此外，还提供了上下文信息，包括每个条目的结构、书目和分类信息。方法：自2012年推出UniCarbKB以来，我们不断改进数据模型的组织。最近，我们已经扩展了我们的管道，以整理不同人类疾病状态和实验模型中低聚糖的结构和丰度变化，以扩大我们对人类糖的覆盖范围。结果：在本文中，我们以一组已发表的结直肠癌和前列腺癌细胞系为例，展示了UniCarbKB存储和查询相对聚糖丰度数据的能力。此外，我们概述了我们管理大规模糖蛋白组学数据、位点特异性和聚糖组成数据的策略，以及这些信息如何为UniCarbKB增加价值。最后，我们总结了通过整合疾病本体来提高疾病术语的有效表示和聚糖异质性相关变化的努力。结论：UniCarbKB的更新和改进引入了存储和显示哺乳动物糖蛋白糖基化特征的独特功能。从大规模糖蛋白组学中获得的位点特异性糖基化数据的整合和细胞系研究的引入将改善糖蛋白和整个糖蛋白的分析。一般意义：分析技术的不断进步和新的数据类型正在推进与疾病相关的糖组学。越来越有必要确保所有的数据都得到全面的注释。UniCarbKB的建立，其使命是通过捕获广泛的数据和相应的注释，为人类糖生物学提供资源。这篇文章是题为“个性化医疗中的聚糖”特刊的一部分，客座编辑：Gordan Lauc教授。(C) 2016 Elsevier B.V.版权所有
Background: UniCarbKB aims to provide a resource for the representation of mammalian glycobiology knowledge by providing a curated database of structural and experimental data, supported by a web application that allows users to easily find and view richly annotated information. The database comprises two levels of annotation (i) global-specific data of oligosaccharides released and characterised from single purified glycoproteins and (ii) information pertaining to site-specific glycan heterogeneity. Additional, contextual information is provided including structural, bibliographic, and taxonomic information for each entry.Methods: Since the launch of UniCarbKB in 2012, we have continued to improve the organisation of our data model. Recently, we have extended our pipeline to collate structural and abundance changes of oligosaccharides in different human disease states and experimental models to extend our coverage of the human glycome.Results: In this manuscript, we demonstrate the capability of UniCarbKB to store and query relative glycan abundance data using a set of published colorectal and prostate cancer cell lines as examples. Furthermore, we outline our strategy for managing large-scale glycoproteomics data, site-specific and glycan compositional data, and how this information is adding value to UniCarbKB. Finally, we summarise our efforts to improve the efficient representation of disease terms and associated changes in glycan heterogeneity by integrating the Disease Ontology.Conclusions: Updates and improvements to UniCarbKB have introduced unique features for storing and displaying glycosylation features of mammalian glycoproteins. The integration of site-specific glycosylation data obtained from large-scale glycoproteomics and introduction of cell line studies will improve the analysis of glycoproteins and entire glycomes.General significance: Continuing advancements in analytical technologies and new data types are advancing disease-related glycomics. It is increasingly necessary to ensure all the data are comprehensively annotated. UniCarbKB was established with the mission of providing a resource for human glycobiology by capturing a wide range of data with corresponding annotations. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc. (C) 2016 Elsevier B.V. All rights reserved.