TypeTaxonScript:糖化和增强生物系统学和生物多样性研究中的数据结构

IF 2.5 Q3 BIOCHEMICAL RESEARCH METHODS
Lucas S B Jordão, M. P. Morim, J. F. Baumgratz, Marcelo Fragomeni Simon, André L C Eppinghaus, Vicente A Calfo
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引用次数: 0

摘要

面向对象编程(OOP)体现了一种软件开发范式,它将现实世界中的实体表示为对象,从而促进了一种更高效、更结构化的建模方法。在本文中,我们探索了 OOP 原则与 TypeScript(TS)编程语言之间的协同作用,以创建一个 JSON 格式的数据库,用于存储生物特征数组。这种技术融合促进了可控的模块化代码脚本,简化了生物数据的整合、操作、扩展和分析,同时通过使用点符号等方式增强了语法,提高了人类的可读性。我们提倡生物学家采用 Git 技术,类似于程序员和编码员的做法,以启动版本控制和协作项目。利用广受欢迎的集成开发环境 Visual Studio Code 还能带来额外的优势。它不仅支持运行 TS 所必需的 Node.js 环境,还能有效管理 GitHub 版本控制。我们提供了一个涉及分类学数据结构的用例,重点是被子植物豆科植物。这种方法的特点是简单,因为所使用的工具都是完全免费的,而且被专业程序员社区广泛采用。此外,我们还致力于通过全面的教程、GitHub 上随时可用的预建数据库和 npm 上的新软件包来促进实际应用和理解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research
Object-Oriented Programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modeling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.
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来源期刊
Biology Methods and Protocols
Biology Methods and Protocols Agricultural and Biological Sciences-Agricultural and Biological Sciences (all)
CiteScore
3.80
自引率
2.80%
发文量
28
审稿时长
19 weeks
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