Services to support the OBO foundry standards

支持 OBO 铸造标准的服务

• 批准号: 9385259
• 负责人: CHRISTOPHER J MUNGALL
• 金额: $ 48.45万
• 依托单位: LA JOLLA INSTITUTE FOR IMMUNOLOGY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-21 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9385259
• 关键词: Address; Anatomy; Basic Science; Biological Assay; Biological Process; Biology; Clinical Research; Code; Collaborations; Communities; Computer software; Development; Disease; Documentation; Education and Outreach; Electronic Mail; Ensure; Funding; Gene Components; Genes; Goals; Guidelines; Human; Individual; Investigation; Investments; Knowledge; Language; Licensing; Maintenance; Measures; Mediating; Metadata; Mission; Molecular; Monitor; Ontology; Phenotype; Publishing; Quality Control; Registries; Reporting; Research Infrastructure; Research Personnel; Resources; Running; Services; Software Engineering; Software Tools; Standardization; System; Teleconferences; Testing; Time; Training; Translational Research; United States National Institutes of Health; Update; base; biomedical ontology; cost; design; disease phenotype; experience; gene function; gene product; improved; information organization; interoperability; member; open source; outreach; public health relevance; success; tool; volunteer

PROJECT SUMMARY/ABSTRACT The Open Biomedical Ontologies (OBO) Foundry is a community organized project that aims to facilitate the discovery, development, application, harmonization, interoperability and sharing of ontologies. OBO ontologies are widely used as a standard for knowledge representation in a broad range of domains relevant to the NIH basic, translational, and clinical research mission. They cover for example gene functions (Gene Ontology, GO), diseases and phenotypes (Disease Ontology, DO; Human Phenotype Ontology, HP; Uberon Anatomy Ontology), assay types (Ontology for Biomedical Investigations, OBI), and relationships connecting these entities, both within and across ontologies (Relationship Ontology, RO). For over a decade, OBO has provided a variety of widely used services to the community, including 1) the OBO registry, which collects standardized metadata for each member ontology such as domain, scope, license, point of contact, etc., thus enhancing findability of each ontology, 2) configurable Persistent URLs (PURLs), which provide an unchanging address for ontologies and ontology classes, enhancing accessibility and reuse, 3) optional content hosting for OBO ontologies that want to take advantage of centrally managed versioning, 4) standardized software tools that make it easy to follow best practices for ontology development, 5) OBO principles, guidelines and best practices, designed to enhance quality and interoperability, and 6) an outreach and coordination effort to mediate between different member ontologies with the goal to coordinate and reduce overlap, through a central email list and regular teleconferences. The present proposal will provide time-limited, catalytic support to increase robustness of existing services by upgrading critical infrastructure on which they are based, by defining and applying standards for metadata and PURL management, and by applying best practices from software engineering to increase maintainability of the codebase. Second, we will introduce new capabilities into our service infrastructure to add automated quality controls to ontologies (individually and in groups), enhance the integration between our services and standardized tools, and add monitoring and metrics. Third, we will perform outreach and training efforts to increase the ability of the community to participate in the OBO project. In accomplishing these aims we will continue to keep our operating costs extremely low, and to freely share the tools and resources we build.

项目概要/摘要 开放生物医学本体 (OBO) Foundry 是一个社区组织的项目，旨在促进 本体的发现、开发、应用、协调、互操作性和共享。 OBO本体 被广泛用作与 NIH 相关的广泛领域的知识表示标准 基础、转化和临床研究任务。它们涵盖例如基因功能（基因本体论， GO）、疾病和表型（疾病本体论，DO；人类表型本体论，HP；Uberon Anatomy 本体）、分析类型（生物医学研究本体，OBI）以及连接这些的关系 本体内部和跨本体的实体（关系本体，RO）。十多年来，OBO 提供了 为社区提供各种广泛使用的服务，包括 1) OBO 注册表，该注册表收集标准化信息 每个成员本体的元数据，例如领域、范围、许可证、联系点等，从而增强 每个本体的可查找性，2) 可配置的持久 URL (PURL)，提供不变的地址 用于本体和本体类，增强可访问性和重用性，3) OBO 的可选内容托管 想要利用集中管理版本控制的本体，4）标准化软件工具 使遵循本体开发的最佳实践变得容易，5) OBO 原则、指南和最佳实践 旨在提高质量和互操作性的实践，以及 6) 外展和协调工作 通过协调和减少重叠的目标，在不同的成员本体之间进行调解 中央电子邮件列表和定期电话会议。本提案将提供有时限的、催化性的 支持通过升级现有服务所依赖的关键基础设施来提高现有服务的稳健性 基于，通过定义和应用元数据和 PURL 管理标准，并通过应用最佳 来自软件工程的实践，以提高代码库的可维护性。其次，我们将推出新的 能力融入我们的服务基础设施中，以向本体添加自动化质量控制（单独和在 组），增强我们的服务和标准化工具之间的集成，并添加监控和 指标。第三，我们将开展外展和培训工作，以提高社区的能力 参与OBO项目。为了实现这些目标，我们将继续保持运营成本 极低，并自由共享我们构建的工具和资源。