An optimized relational database for querying structural patterns in proteins.

IF 3.4 4区生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Database: The Journal of Biological Databases and Curation Pub Date : 2024-01-17 DOI:10.1093/database/baad093

Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Ben Ingram

引用次数: 0

Abstract

A database is an essential component in almost any software system, and its creation involves more than just data modeling and schema design. It also includes query optimization and tuning. This paper focuses on a web system called GSP4PDB, which is used for searching structural patterns in proteins. The system utilizes a normalized relational database, which has proven to be inefficient even for simple queries. This article discusses the optimization of the GSP4PDB database by implementing two techniques: denormalization and indexing. The empirical evaluation described in the article shows that combining these techniques enhances the efficiency of the database when querying both real and artificial graph-based structural patterns.

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用于查询蛋白质结构模式的优化关系数据库。

数据库几乎是所有软件系统的重要组成部分，而数据库的创建不仅仅涉及数据建模和模式设计。它还包括查询优化和调整。本文重点介绍一个名为 GSP4PDB 的网络系统，该系统用于搜索蛋白质的结构模式。该系统使用的是规范化关系数据库，事实证明，即使是简单的查询，该数据库的效率也很低。本文讨论了通过实施去规范化和索引这两种技术对 GSP4PDB 数据库进行优化的问题。文章中描述的实证评估表明，在查询真实和人工基于图的结构模式时，结合这些技术可以提高数据库的效率。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Database: The Journal of Biological Databases and Curation MATHEMATICAL & COMPUTATIONAL BIOLOGY-

CiteScore

9.00

自引率

3.40%

发文量

100

审稿时长

>12 weeks

期刊介绍： Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories, large datasets will become even more prevalent. The archiving, curation, analysis and interpretation of all of these data are a challenge. Database development and biocuration are at the forefront of the endeavor to make sense of this mounting deluge of data. Database: The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users.