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.

抽象的 近年来强调了聚糖在生物医学研究中的重大影响，尤其是在 免疫学，在生物学功能中的作用，在疾病中的影响等等。近年来技术进步 允许研究人员更准确，有效地进行糖蛋白酶和糖蛋白质组学分析 导致文献中数据量的快速增长，并且非常需要强大的循证基于证据 存档聚糖记录维护。这种需求至少可以由允许作者的存储库部分满足 在数据库开发人员提供数据归档的机制时提交和更新数据，而无需任何编辑。 我们建议开发一个原型聚糖档案（主要数据库）来存储注册的聚糖结构 并允许用户存入新的聚糖，这些聚糖将与现有资源共享。预计这项努力 将导致发展国际管理的聚糖档案合作，并平行于概念 协调和维护的国际核苷酸序列数据库合作（INSDC） GenBank，DDBJ，ENA等数据库用于核苷酸。 Glycan档案原型将由Glygen开发 在subdomain gsa.glygen.org下。它将容纳所有来自现有公共数据库的聚糖 Glytoucan，Pubchem，Chebi，Kegg Glycan等。强大的QC程序将提高 提交的记录和所有聚糖记录都将与一个唯一的ID相关联 其他数据库。新颖的基于信息的结构验证将标记包含意外的提交 功能，允许在档案或辅助数据库中合并之前或之后进行其他评估。 我们预计所提出的机制对于研究人员，数据策展人，生物信息学将非常有价值 数据库，还提供了何时发布特定聚糖的历史记录。

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

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

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