ROBOT: A Tool for Automating Ontology Workflows
ROBOT: A Tool for Automating Ontology Workflows
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DOI：
10.1186/s12859-019-3002-3
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发表时间：
2019-07-29
影响因子：
3
通讯作者：
Overton, James A.
中科院分区：
文献类型：
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作者：
Jackson, Rebecca C.;Balhoff, James P.;Overton, James A.
本体在生命科学中是非常宝贵的，但是构建和维护本体通常需要具有挑战性的任务，例如运行自动推理机和质量控制检查，提取依赖关系和特定于应用程序的子集，生成标准报告，以及生成多种格式的发布文件。与更一般的软件开发类似，自动化是有效执行和管理这些任务以及以标准形式发布更健壮产品的关键。对于使用Web本体语言（OWL）的本体，OWL API Java库是一系列软件工具（包括Protege本体编辑器）的基础。在开放的生物和生物医学本体（OBO）的社区，我们认识到有必要将广泛的低层次的OWL API功能打包成一个库的共同的更高层次的操作，并使这些操作可作为一个命令行tool.ResultsROBOT（ROBOT的递归缩写是一个OBO工具）是一个开源库和命令行工具，用于自动化本体开发任务。该库可以从Java虚拟机（JVM）上运行的任何编程语言调用。大多数使用是通过命令行工具，它在macOS，Linux和Windows上运行。ROBOT为各种任务提供本体处理命令，包括用于转换格式、运行推理器、创建导入模块、运行报告和各种其他任务的命令。这些命令可以组合成更大的工作流程，使用一个单独的任务执行系统，如GNU使，和工作流程可以自动执行内持续集成systems.ConclusionsROBOT支持自动化的本体开发任务的范围广泛，专注于OBO公约。它将常见的高级本体开发功能打包到一个方便的库中，并使其易于配置、联合收割机和在综合的自动化工作流中执行单个任务。这有助于本体开发人员有效地创建、维护和发布高质量的本体，以便他们可以将更多的时间集中在开发任务上。它还有助于保证发布的本体没有某些类型的逻辑错误，并符合标准的质量控制检查，提高本体开发生命周期的整体鲁棒性和效率。
BackgroundOntologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms.For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protege ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool.ResultsROBOT (a recursive acronym for ROBOT is an OBO Tool) is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems.ConclusionsROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.