A Common Dialect for Infrastructure and Services in Translator

Translator 中基础设施和服务的通用方言

• 批准号: 10546806
• 负责人: Christopher Bizon
• 金额: $ 113.23万
• 依托单位: UNIVERSITY OF COLORADO DENVER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2022-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10546806
• 关键词: Infrastructure; Services; Text

1) We will build a robust, dynamic Translator Standards and Reference Implementations Component (SRI) that integrates the collaborations and investments that the NCATS Translator has made to date. This component will consist of a suite of standards and products, a model for their governance, and processes to coordinate integration and shared implementation: ● Community governance coordination will be developed with community buy-in to ensure an effective collaborative environment, and drive consortium-wide consensus on the other components. ● Architecture and API specifications will drive community efforts to define details of project architecture and communication protocols across Translator Knowledge Providers (KPs), Autonomous Relay Agents (ARAs), and the Autonomous Relay System (ARS). ● The BioLink model will define the standard entity types, relationship types, and a schema shared by all Translator components. This includes related utility libraries and a novel approach to accommodate multiple alternate data modeling perspectives. ● Integrated reference ontologies will provide BioLink-compliant terms and relationships. We will draw on the ROBOKOP Ubergraph framework [1] , the Monarch integrated ontologies, and other ontologies from Open Biological and Biomedical Ontologies (OBO) [2] . ● A continually-updated knowledge graph and data lake will provide Translator with a standardized and integrated global view of the whole information landscape. ● Next-generation Shared Translator Services will integrate features of ROBOKOP [3] , Monarch [4] , BioLink [5] , and the reasoner APIs to remove integration barriers. These services will provide validation, lookup, and mapping functionality for use across Translator. ● A registry of Translator KPs, ARAs, and shared services will increase efficiency, eliminate duplication of effort, and promote collaboration. 2) Our proposed SRI will address the problem of connecting together different components and data/information sources at scale, with community buy-in, and with a plan for sustainability. 3) For the development of the standards component of the SRI, our plan will begin with accepted Translator standards, and we will work with the ARS, ARAs, and KPs to identify gaps. We will have a community process for contributing to the standards, making use of GitHub pull requests and voting, to help everyone contribute effectively and fairly with clear attribution. We will ensure rigorous documentation and testing. For the reference implementation component, we will stand up core Translator services, and will include additional services if they are useful to more than one Translator component rather than used by only one. 4) Consensus-building is hard. Our team has proven expertise and resources to identify needs, refine solutions, and find agreement , thereby successfully bringing infrastructure to fruition. Our team also has the technical and biological expertise to design and test the necessary standards, having been at the forefront of multiple ontology, data standards, and large enterprise software initiatives. 5) The Translator infrastructure is by nature heterogeneous, distributed, and growing; consequently, the most significant data and infrastructure challenge is managing the validity, currency, equivalency, and typing of entities (diseases, phenotypes, drugs, etc.). Our group has developed several innovative algorithms for managing this and related problems; these algorithms are in use for other integration projects and will be modified to suit Translator needs.

1) 我们将建立一个强大的、动态的翻译标准和参考实现 集成 NCATS 翻译器的协作和投资的组件 (SRI) 迄今为止，该组件将包含一套标准和产品，一个模型。 他们的治理以及协调整合和共享实施的流程： ● 社区治理协调将在社区的支持下进行，以确保 有效的协作环境，并推动联盟范围内的共识 成分。 ● 架构和 API 规范将推动社区努力定义项目细节 译者知识提供者 (KP) 的架构和通信协议， 自主中继代理 (ARA) 和自主中继系统 (ARS)。 ● BioLink 模型将定义标准实体类型、关系类型和模式 由所有翻译器组件共享，这包括相关的实用程序库和小说。 适应多种替代数据建模视角的方法。 ● 集成参考本体将提供符合BioLink 的术语和关系。 将利用 ROBOKOP Ubergraph 框架 [1]、Monarch 集成本体， 以及来自开放生物和生物医学本体论 (OBO) 的其他本体论 [2]。 ● 不断更新的知识图谱和数据湖将为Translator提供 整个信息格局的标准化和集成的全球视图。 ● 下一代共享翻译服务将集成ROBOKOP [3]的功能， Monarch [4] 、BioLink [5] 和 Reasoner API 可消除集成障碍。 服务将提供验证、查找和映射功能以供跨 Translator 使用。 ● 翻译者 KP、ARA 和共享服务的注册将提高效率、 消除重复工作，促进协作。 2）我们提出的 SRI 将解决将不同组件连接在一起的问题 大规模的数据/信息来源，得到社区的支持，并制定可持续发展计划。 3) 对于 SRI 标准部分的开发，我们的计划将从 接受译者标准，我们将与 ARS、ARA 和 KP 合作找出差距。 我们将有一个社区流程来为标准做出贡献，利用 GitHub pull 请求和投票，以帮助每个人做出贡献并公平地明确归属。 将确保参考实施组件的严格记录和测试。 我们将提供核心翻译服务，并将包括额外的服务（如果它们对翻译有用） 多个转换器组件而不是仅由一个组件使用。 4) 建立共识是很困难的，我们的团队拥有公认的专业知识和资源来确定需求， 完善解决方案并达成一致，从而成功实现我们的基础设施。 团队还拥有技术和生物专业知识来设计和测试必要的标准， 一直处于多种本体、数据标准和大型企业软件的前沿 建议。 5) Translator 基础设施本质上是异构的、分布式的且不断增长的； 因此，最重要的数据和基础设施挑战是管理有效性， 我们的团队有货币、等价性和实体类型（疾病、表型、药物等）。 开发了几种创新算法来管理此问题及相关问题； 算法正在用于其他集成项目，并将进行修改以满足翻译器的需求。