Glycan Structure Archive (GSA) prototype in support of GlyGen's data integration - Yr 5 Admin Supp

支持 GlyGen 数据集成的聚糖结构档案 (GSA) 原型 - 第 5 年级管理补充

• 批准号: 10440061
• 负责人: Raja Mazumder
• 金额: $ 15.06万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10440061
• 关键词: Archives; Asia; Base Sequence; Bioinformatics; Biological Process; Biomedical Research; Characteristics; Chemicals; Collaborations; Communities; Consensus; DNA Data Bank of Japan; Data; Databases; Deposition; Development; Disease; Ensure; Europe; Evaluation; Feedback; Foundations; Funding; Future; Genbank; Genes; Genome; Glycoconjugates; Goals; Immunology; Individual; Informatics; Intelligence; International; Intuition; Knowledge; Libraries; Link; Literature; Maintenance; Maps; Metadata; Methodology; Monosaccharides; Names; Nucleotides; Polysaccharides; Procedures; Process; PubChem; Publications; Publishing; Quality Control; Records; Reporting; Research Personnel; Resources; Retrieval; Role; Source; Structure; Time; United States; Update; Validation; archive data; base; data archive; data integration; design; evidence base; glycoproteomics; graphical user interface; member; molecular sequence database; novel; prototype; rapid growth; repository; tool

ABSTRACT Recent years have highlighted the significant impact of glycans in biomedical research especially in aspects of immunology, role in biological functions, impact in diseases, and more. Technical advancements in recent years have allowed researchers to perform glycomics and glycoproteomics analysis more accurately and efficiently, resulting in rapid growth of the volume of data in the literature and a great need for robust evidence-based archival glycan record maintenance. This need can be at least partially met by a repository that allows authors to submit and update data while database developers provide mechanisms for data archiving without any editing. We propose to develop a prototype glycan archive (a primary database) to store registered glycan structures and allow users to deposit new glycans which will be shared with existing resources. It is expected that this effort will lead to the development of an internationally managed glycan archive collaboration, parallel in concept to the International Nucleotide Sequence Database Collaboration (INSDC) that harmonizes and maintains databases like GenBank, DDBJ, ENA for nucleotides. The glycan archive prototype will be developed by GlyGen under subdomain gsa.glygen.org. and it will house all glycans sourced from existing public databases like GlyTouCan, PubChem, ChEBI, KEGG glycan, and others. Robust QC procedures will enhance the value of the submitted records and all glycan records will be associated with an unique ID that will be cross-referenced to other databases. Novel informatic-based structural validation will flag submissions that contain unexpected features, allowing additional evaluation before or after incorporation into the archive or secondary databases. We anticipate that the proposed mechanism will be highly valuable for researchers, data curators, bioinformatics databases, and also provide a historical record of when a particular glycan was published.

摘要 近年来，已经突出了聚糖在生物医学研究中的显著影响，特别是在以下方面： 免疫学、生物功能中的作用、疾病中的影响等等。近年来的技术进步 使研究人员能够更准确和有效地进行糖组学和糖蛋白质组学分析， 导致文献中的数据量快速增长，并且非常需要基于证据的强大的 档案聚糖记录维护。这种需求至少可以通过一个允许作者 提交和更新数据，而数据库开发人员提供无需任何编辑的数据存档机制。 我们建议开发一个原型聚糖档案（一个主要的数据库）来存储注册的聚糖结构 并允许用户存款新的聚糖，这些聚糖将与现有资源共享。预计这一努力 将导致国际管理的聚糖档案合作的发展，在概念上与 国际核苷酸序列数据库合作组织（INSDC），协调和维护 数据库如GenBank、DDBJ、ENA用于核苷酸。聚糖档案原型将由GlyGen开发 在子域gsa.glygen.org下，它将包含来自现有公共数据库的所有聚糖， GlyTouCan、PubChem、ChEBI、KEGG聚糖等。强大的质量控制程序将提高 提交的记录和所有聚糖记录将与一个唯一ID相关联，该ID将交叉引用到 其他数据库。新的基于信息的结构验证将标记包含意外的提交 功能，允许在纳入存档或二级数据库之前或之后进行额外评估。 我们预计，提出的机制将是非常有价值的研究人员，数据管理员，生物信息学， 数据库，并且还提供特定聚糖何时发表的历史记录。

项目成果

The international glycan repository GlyTouCan version 3.0.

• DOI: 10.1093/nar/gkaa947
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Fujita A;Aoki NP;Shinmachi D;Matsubara M;Tsuchiya S;Shiota M;Ono T;Yamada I;Aoki-Kinoshita KF
• 通讯作者: Aoki-Kinoshita KF

Meeting Report of the International Life Science Integration Workshop 2018.

2018年国际生命科学整合研讨会会议报告。

• DOI: 10.1093/glycob/cwy056
• 发表时间: 2018
• 期刊: Glycobiology
• 影响因子: 4.3

CarbArrayART: a new software tool for carbohydrate microarray data storage, processing, presentation, and reporting.

• DOI: 10.1093/glycob/cwac018
• 发表时间: 2022-06-13
• 期刊: Glycobiology
• 影响因子: 4.3

SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures.

• DOI: 10.3390/molecules26237149
• 发表时间: 2021-11-25
• 期刊: Molecules (Basel, Switzerland)
• 作者: Tsuchiya S;Matsubara M;Aoki-Kinoshita KF;Yamada I
• 通讯作者: Yamada I

The Glycan Structure Dictionary-a dictionary describing commonly used glycan structure terms.

聚糖结构词典 - 描述常用聚糖结构术语的词典。

• DOI: 10.1093/glycob/cwad014
• 发表时间: 2023
• 期刊: Glycobiology
• 影响因子: 4.3
• 作者: Vora,Jeet;Navelkar,Rahi;Vijay-Shanker,K;Edwards,Nathan;Martinez,Karina;Ding,Xiying;Wang,Tianyi;Su,Peng;Ross,Karen;Lisacek,Frederique;Hayes,Catherine;Kahsay,Robel;Ranzinger,Rene;Tiemeyer,Michael;Mazumder,Raja
• 通讯作者: Mazumder,Raja