GlyGen growth and evolution into a central resource for glycans and glycoconjugates

GlyGen 生长并进化为聚糖和复合糖的核心资源

• 批准号: 10494610
• 负责人: Raja Mazumder
• 金额: $ 109.41万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-27 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10494610
• 关键词: 5 year old; Anabolism; Binding; Binding Proteins; Biology; Biomedical Research; Cells; Communities; Complex; Computer software; Consumption; Coupled; Data; Data Analyses; Data Set; Databases; Development; Discipline; Disease; Education and Outreach; Educational Curriculum; Ensure; Event; Evolution; Feedback; Funding; Future; Gene Expression; Gene Proteins; Generations; Genes; Genetic Transcription; Genomics; Glycobiology; Glycoconjugates; Glycoproteins; Growth; Health; Individual; International; Intuition; Investigation; Knowledge; Licensing; Link; Lipids; Malignant Neoplasms; Manuals; Maps; Mediating; Metadata; MicroRNAs; Mission; Modeling; Mutation; Neurosciences; Pathway interactions; Pattern; Persons; Polysaccharides; Procedures; Process; Professional Organizations; Prokaryotic Cells; Proteins; Quality Control; Regulatory Pathway; Research Personnel; Resource Informatics; Resources; Science; Site; Societies; Specificity; Structure; System; Testing; Tissues; Training; Translations; Visualization; base; cell type; data communication; data format; data harmonization; data modeling; data portal; data visualization; design; disease phenotype; experience; glycosylation; glycosyltransferase; improved; knowledgebase; lipidomics; machine learning algorithm; meetings; metabolomics; next generation; novel; outreach; preference; protein expression; social media; specific biomarkers; text searching; tool; training opportunity; transcription factor; transcriptome sequencing; transcriptomics; undergraduate student; web portal; webinar

ABSTRACT GlyGen is a maturing (five years old) knowledgebase that accumulates data in the glycobiology domain and connects it with other data types. GlyGen is unique; no other present or prior informatic resource has undertaken such an integrative mission. In part, the lagging growth of accessible knowledge in the glycobiology domain, compared to other -omics or biomedical research fields, reflects the inherent complexity of glycan structures, which, unlike genes and proteins, exist in branched and isomeric forms whose biosynthesis is not attributable to well-characterized, template-driven processes such as transcription or translation. Rather, glycan biosynthesis is mediated by the regulated expression of ensembles of glycosyltransferases, substrate transporters, and secretory pathway regulatory mechanisms that together generate dynamic cell- and tissue-specific patterns of protein and lipid glycosylation. In addition, each glycosylation site on a glycoprotein may routinely be modified by one of an ensemble of glycan structures, a glycoprotein feature called microheterogeneity. Importantly, microheterogeneity is not random, but reflects the intrinsic biosynthetic capacity of specific cells and tissues and may be modified by disease. These structural and biosynthetic complexities are essential contributors to the tissue- and disease-specific functions of glycans and glycosylation, and, therefore, need to be captured and represented in knowledgebases in a way that they can be queried and linked to other types of data. GlyGen aims to expand its underlying data model to accommodate new and more complex datatypes, augmenting and integrating new data types, and implementing robust modeling, unified procedures, and tools to improve discovery and exploration of glycan and glycoconjugate data. Enhancement of the overall resource functionality will be achieved through front-end improvements to accommodate user preferences and ensure exceptional data communication and visualization. Improving the interconnectivity of GlyGen and its partner databases as well as enhancing data-sharing across resources will continue to be core principles of the GlyGen project. All resulting harmonized data will be available through highly permissive licenses for easy integration into other resources, such as NCBI, EBI, SIB and other international efforts, as well as for easy repurposing by independent researchers, educators, bioinformaticians, and commercial entities. By the end of the next project period GlyGen expects to become the go-to, well-integrated resource for glycoscience data, similar to existing protein and genomic resources and serving the same broad community of biomedical researchers.

摘要 GlyGen是一个成熟的（五岁）知识库，积累了糖生物学领域的数据， 将其与其他数据类型连接起来。GlyGen是独一无二的;没有其他目前或以前的信息资源已经承担 这样一个综合性的使命。在某种程度上，糖生物学领域可获得的知识增长滞后， 与其他组学或生物医学研究领域相比，反映了聚糖结构的固有复杂性， 与基因和蛋白质不同，它们以分支和异构形式存在，其生物合成不能归因于 良好表征的模板驱动过程，如转录或翻译。相反，聚糖生物合成 由糖基转移酶、底物转运蛋白和 分泌途径调节机制，共同产生动态的细胞和组织特异性模式， 蛋白质和脂质糖基化。此外，糖蛋白上的每个糖基化位点可以常规地被修饰 通过一系列聚糖结构中的一种，一种称为微异质性的糖蛋白特征。重要的是， 微异质性不是随机的，而是反映了特定细胞和组织的内在生物合成能力， 可能会因疾病而改变。这些结构和生物合成的复杂性是重要的贡献者， 聚糖和糖基化的组织和疾病特异性功能，因此需要被捕获， 在知识库中以一种可以查询和链接到其他类型数据的方式表示。甘精 旨在扩展其基础数据模型，以适应新的和更复杂的数据库， 集成新的数据类型，并实施健壮的建模、统一的过程和工具，以提高 聚糖和糖缀合物数据的发现和探索。增强总体资源功能 将通过前端改进来实现，以适应用户的偏好，并确保提供出色的数据 沟通和可视化。改善GlyGen及其合作伙伴数据库的互连性， 加强跨资源的数据共享将继续是GlyGen项目的核心原则。所有由此产生 统一的数据将通过高度许可证提供，以便于整合到其他资源中， 例如NCBI、EBI、SIB和其他国际努力，以及独立的 研究人员、教育工作者、生物信息学家和商业实体。到下一个项目期结束时， 有望成为糖科学数据的首选，整合良好的资源，类似于现有的蛋白质和 基因组资源并为同一广泛的生物医学研究人员社区服务。