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.

项目总结/摘要 开放生物医学本体（OBO）铸造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NIH相关领域的知识表示标准 基础、转化和临床研究使命。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解剖学 本体）、测定类型（生物医学研究本体，OBI）以及连接这些的关系 实体，包括本体内和本体之间的实体（关系本体，RO）。十多年来，OBO提供了 向社区提供各种广泛使用的服务，包括1）OBO注册表， 每个成员本体的元数据，例如域、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），其提供不变的地址 对于本体和本体类，增强可访问性和重用性，3）OBO的可选内容托管 希望利用集中管理的版本控制的本体，4）标准化软件工具， 使其易于遵循本体开发的最佳实践，5）OBO原则，指导方针和最佳实践 实践，旨在提高质量和互操作性，以及6）外联和协调工作， 通过协调和减少重叠，在不同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 通过升级现有服务所依赖的关键基础设施，支持加强现有服务的稳健性 通过定义和应用元数据和PURL管理标准， 从软件工程的实践，以提高代码库的可维护性。第二，我们将引进新的 将自动化质量控制添加到我们的服务基础设施中（单独和以 组），增强我们的服务和标准化工具之间的集成，并增加监控和 指标.第三，我们将开展外联和培训工作，以提高社区的能力， 参与OBO项目。在实现这些目标的过程中，我们将继续保持我们的运营成本 非常低，并免费共享我们构建的工具和资源。