工程科学学报2024，Vol.46Issue(2)：279-289,11.DOI:10.13374/j.issn2095-9389.2022.11.21.003
BioMGE——一个用于采集和分析生物医用材料和多组学数据的数据库
BioMGE:A database for biomedical material and multiomics data collection and analysis
摘要
Abstract
Biomedical materials scientific research is increasingly data-driven,thanks to advancements in machine learning technology.The application of biological sequencing technology for assessing the biological functions of biomedical materials demands further optimization.To facilitate comprehensive analysis,it is essential to establish an open,shared infrastructure for storing diverse scientific data from various research fields.This paper presents BioMGE,a case study in database construction,utilizing the flexible and user-defined NMDMS platform(National Materials Data Management and Service Platform).BioMGE is designed for the collection of biomedical materials and multiomics sequencing data.Leveraging NMDMS's dynamic container framework,users can tailor data submission schemas to their preferences and store data from the domains of biomedical materials and multiomics research.To ensure data interoperability,the data schema creation module is combined with data standards.We also propose a standard specification for biomedical materials data.Employing the dynamic container framework and standard specifications,data submission schemas were established for biomedical material and multiomics data,covering aspects such as material names,experimental design,grouping information for experimental materials,and high-throughput omics sequencing.Since 2019,BioMGE has amassed 1547100 datasets of biomedical material and multiomics data based on these schemas.In order to enable users to analyze this data,BioMGE provides a data export interface.For instance,the BioMGE-viewer module offers one-dimensional,two-dimensional,and three-dimensional visualizations for omics data.The one-dimensional visualization displays gene information in tabular form.The two-dimensional visualization exhibits the topologically associating domains of chromatin using a heatmap.The three-dimensional visualization offers a three-dimensional representation of chromatin structure,aiding users in exploring the relationship between gene function and gene structure.What sets BioMGE apart is that it was constructed directly by researchers,not database designers.This means that researchers without programming expertise in various fields can design personalized data schemas that align with their research characteristics.This approach maximizes the interoperability and usability of NMDMS data.BioMGE has the potential to foster collaborative research across different domains and the joint analysis of biomedical materials and biological sequencing data.It offers fresh insights for the advancement of cell therapy and,concurrently,introduces a novel idea and platform for data sharing in various cross-field research endeavors.关键词
生物医用材料/多组学/动态容器数据库/异构数据存储/可视化Key words
biomedical material/multi-omics/dynamic container database/heterogeneous data storage/visualization分类
医药卫生引用本文复制引用
龚海燕,张晓彤,张司臣,李铭鸿,赵赫,王婧宇,王秀梅,陈阳..BioMGE——一个用于采集和分析生物医用材料和多组学数据的数据库[J].工程科学学报,2024,46(2):279-289,11.基金项目
国家自然科学基金资助项目(61971031,31871343) （61971031,31871343）
中国博士后科学基金资助项目(2023M740219) （2023M740219）
国家资助博士后研究人员计划资助项目(GZC20230239) （GZC20230239）
国家重点研发计划资助项目(2018YFB0704300) （2018YFB0704300）
佛山市高等教育高层次人才资助项目(BKBS202203) （BKBS202203）
北京科技大学顺德研究生院科技创新基金项目(BK20BF009) （BK20BF009）
中国科学院医学科学创新基金资助项目(2020-RC310-009) （2020-RC310-009）
