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.

项目摘要/摘要 开放的生物医学本体论（OBO）铸造厂是一个社区有组织的项目，旨在促进 发现，开发，应用，协调，互操作性和本体分享。 OBO本体论 被广泛用作与NIH相关的广泛领域中知识表示的标准 基本，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解剖结构 本体论），测定类型（生物医学研究的本体论，OBI）和将这些连接的关系 实体，无论是在本体方面和跨本体的内部学本体，RO）。十多年来，OBO提供了 社区的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 每个成员本体论的元数据，例如域，范围，许可证，联系点等，从而增强 每个本体的可发现性，2）可配置的持久性URL（purls），它提供了一个不变的地址 对于本体和本体课程，增强可访问性和重复使用，3）obo的可选内容托管 想要利用中央管理版本管理的本体论，4）标准化软件工具 使遵循本体发展的最佳实践变得容易，5）OBO原则，准则和最佳 实践，旨在提高质量和互操作性，以及6）外展和协调的努力 通过一个目标进行调解不同成员本体的目标，以协调和减少重叠 中央电子邮件列表和定期电视会议。目前的建议将提供时间限制的催化 通过升级其所在的关键基础架构来支持以提高现有服务的鲁棒性 通过定义和应用标准用于元数据和purl管理，并运用最佳 软件工程的实践以提高代码库的可维护性。第二，我们将介绍新的 在我们的服务基础架构中的功能，将自动质量控制添加到本体（单独和 组），增强我们的服务与标准化工具之间的集成，并添加监视和 指标。第三，我们将进行推广和培训工作，以提高社区的能力 参加OBO项目。在实现这些目标时，我们将继续保持运营成本 极低，并自由分享我们构建的工具和资源。