Enhanced ontology engineering through a Web-based, Cloud-based software architecture

项目总结/摘要 本提案是为了补充R 01 LM 013498 -01“元数据Powerwash -集成”而提交的 让生物医学数据变得公平的工具。”家长补助金建议研究方法，以标准化 在线数据集中的元数据，使相应的数据更容易查找、访问、互操作， 可重复使用。我们的目标是将在线注释实验数据集的元数据转换为 遵循标准报告指南，并使用标准本体中的术语。父母补助金 支持依赖于广泛的生物医学本体的可用性的研究-标准 描述不同应用领域中的实体的术语集合。在我们的工作中，几乎所有 我们使用的本体是通过一个名为Protégé的软件工具创建和维护的，Protégé是一个开发的系统， 在我们的实验室里，它是世界上本体工程中使用最广泛的开源工具。这些 本体表示第三方或参与的团队成员的开发工作， 由家长资助的研究。Protégé目前以两种形式存在：（1）桌面版本， 一个Java应用程序，以及（2）一个在Web上运行的版本。我们提出实质性的新软件 工程设计，以提高Protégé系统的性能和长期可持续性。 为了支持我们对本体工程的需求，结合我们现有的NLM R 01资助，我们提出了两个 具体目标：（1）我们将把WebProtégé转换为现代的、基于微服务的架构， 微服务-包括插件架构的可用性，该架构将允许第三方贡献新颖的 添加到WebProtégé代码库。我们将使用一种软件开发方法， 以可控的增量方式实现新的体系结构。(2)我们将使WebProtégé现代化， 让它成为云原生。我们将利用美国国立卫生研究院（NIH）的“生物多样性”计划，将该系统容器化， 在Google Cloud Platform（GPC）中部署，并调整软件以与基于云的第三方 用于数据存储、数据存储和搜索的第三方软件。我们还将迁移所有当前的WebProtégé用户 和他们的项目到基于云的系统。我们的工作将使整个生物医学界受益， 提高我们的能力，本体工程所需的我们现有的赠款。

PROJECT SUMMARY/ABSTRACT This proposal is submitted to supplement grant R01 LM013498-01, “The Metadata Powerwash - Integrated tools to make biomedical data FAIR.” The parent grant proposes to study methods to standardize the metadata in online datasets to make the corresponding data more findable, accessible, interoperable, and reusable. The goal is to transform the metadata that annotate experimental datasets online to a form that adheres to standard reporting guidelines and that uses terms from standard ontologies. The parent grant supports research that depends on the availability of a wide range of biomedical ontologies—standard collections of terms that describe the entities in different application areas. In our work, nearly all the ontologies that we use are created and maintained via a software tool known as Protégé, a system developed in our laboratory that is the most widely used open-source tool for ontology engineering in the world. These ontologies represent the development work of third parties or of members of the team participating in the research supported by the parent grant. Protégé currently exists in two forms: (1) a desktop version written as a Java application, and (2) a version that operates over the Web. We propose substantial, new software engineering to improve the performance and long-term sustainability of the Protégé system. To support our needs for ontology engineering in conjunction with our existing NLM R01 grant, we propose two specific aims: (1) We will convert WebProtégé to a modern, microservice-based architecture, adding new microservices—including the availability of a plug-in architecture that will allow third parties to contribute novel additions to the WebProtégé code base. We will use a software-development approach that will allow us to implement the new architecture in a controlled, incremental manner. (2) We will modernize WebProtégé to make it Cloud-native. We will take advantage of the NIH STRIDES initiative, containerizing the system for deployment in the Google Cloud Platform (GPC) and adapting the software to operate with Cloud-based third- party software for data storage, data queueing, and search. We also will migrate all current WebProtégé users and their projects to the Cloud-based system. Our work will benefit the biomedical community at large, while enhancing our capabilities for ontology engineering as required by our existing grant.