Ochs Alexander R, Mehrabi Mehrsa, Becker Danielle, Asad Mira N, Zhao Jing, Zaragoza Michael V, Grosberg Anna
Department of Biomedical Engineering, University of California, Irvine; The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California, Irvine.
Pediatrics-Genetics & Genomics Division-School of Medicine, University of California, Irvine; Biological Chemistry-School of Medicine, University of California, Irvine.
J Vis Exp. 2019 Nov 22(153). doi: 10.3791/60038.
Science relies on increasingly complex data sets for progress, but common data management methods such as spreadsheet programs are inadequate for the growing scale and complexity of this information. While database management systems have the potential to rectify these issues, they are not commonly utilized outside of business and informatics fields. Yet, many research labs already generate "medium sized", low velocity, multi-dimensional data that could greatly benefit from implementing similar systems. In this article, we provide a conceptual overview explaining how databases function and the advantages they provide in tissue engineering applications. Structural fibroblast data from individuals with a lamin A/C mutation was used to illustrate examples within a specific experimental context. Examples include visualizing multidimensional data, linking tables in a relational database structure, mapping a semi-automated data pipeline to convert raw data into structured formats, and explaining the underlying syntax of a query. Outcomes from analyzing the data were used to create plots of various arrangements and significance was demonstrated in cell organization in aligned environments between the positive control of Hutchinson-Gilford progeria, a well-known laminopathy, and all other experimental groups. In comparison to spreadsheets, database methods were enormously time efficient, simple to use once set up, allowed for immediate access of original file locations, and increased data rigor. In response to the National Institutes of Health (NIH) emphasis on experimental rigor, it is likely that many scientific fields will eventually adopt databases as common practice due to their strong capability to effectively organize complex data.
科学的进步依赖于日益复杂的数据集,但诸如电子表格程序等常见的数据管理方法,已不足以应对这些信息不断增长的规模和复杂性。虽然数据库管理系统有潜力解决这些问题,但在商业和信息学领域之外,它们并不常用。然而,许多研究实验室已经在生成“中等规模”、低速度、多维度的数据,而实施类似系统将使这些数据受益匪浅。在本文中,我们提供了一个概念性概述,解释数据库的功能以及它们在组织工程应用中所具有的优势。利用来自携带核纤层蛋白A/C突变个体的结构成纤维细胞数据,在特定实验背景下进行示例说明。示例包括可视化多维数据、在关系数据库结构中链接表格、映射半自动数据管道以将原始数据转换为结构化格式,以及解释查询的底层语法。分析数据所得结果被用于创建各种排列的图表,并且在著名的核纤层蛋白病哈钦森-吉尔福德早衰症的阳性对照与所有其他实验组之间的对齐环境中,细胞组织的显著性得到了证明。与电子表格相比,数据库方法在时间效率上极高,一旦设置好就易于使用,允许立即访问原始文件位置,并提高了数据的严谨性。鉴于美国国立卫生研究院(NIH)对实验严谨性的重视,由于数据库具备有效组织复杂数据的强大能力,许多科学领域最终可能会将其作为常规做法采用。