BioPortal: An Expansive Knowledgebase of Biomedical Entities and Relations

BioPortal：生物医学实体和关系的广泛知识库

• 批准号: 10494104
• 负责人: Mark A Musen
• 金额: $ 107.39万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-27 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10494104
• 关键词: Academia; Access to Information; Adopted; Adoption; Area; Biological Sciences; Businesses; Collection; Communities; Data; Discipline; Ensure; Environmental Science; Government; Graph; Growth; Healthcare; Industry; Information Management; Information Resources; Infrastructure; Knowledge; Knowledge Management; Laboratories; Link; Medical; Mission; Monitor; Natural Language Processing; Ontology; Paper; Recording of previous events; Research Personnel; Resources; Running; Science; Scientist; Semantics; Services; Source; Standardization; Suggestion; System; Technology; Text; Time; United States National Institutes of Health; Work; base; biomedical ontology; biomedical scientist; computer infrastructure; data integration; improved; knowledge graph; knowledge integration; knowledge of results; knowledgebase; natural language; phrases; point of care; programs; repository; systems research; web server; web services

ABSTRACT The most widely used and most general-purpose knowledgebases in biomedicine are the ontologies that define the entities and the relationships that are central to different aspects of health care or the life sciences. When ontologies are brought together in an integrated framework—enabling terms denoting the same or similar entities to be related to one another and allowing computational infrastructure to operate across ontologies—then the aggregate collection of ontologies provides additional capabilities for users. Our group has developed an enormously popular knowledge resource, known as BioPortal, that provides a unique knowledgebase of nearly all the world’s publicly accessible biomedical ontologies. Adoption of BioPortal has been remarkable. Each month, more than 75,000 unique users from academia, government, and industry access the contents of our ontology repository, and our API services more than 16 million requests. At least 7,850 scientific papers mention the use of BioPortal, according to Google Scholar. We propose the following four specific aims: (1) We will continue to govern and maintain the BioPortal knowledgebase by enhancing the services that the knowledgebase provides to the biomedical community. (2) We will improve the efficiency with which users interact with the knowledgebase by creating the BioPortal Knowledge Graph. The graph—which will be a queryable knowledge resource in its own right—will integrate all ontologies in the knowledgebase and it will provide links to other knowledge sources, allowing users to perform expanded queries across all ontologies. (3) We will enable users of BioPortal to make requests for changes or extensions to ontologies, and to view the history of changes and change requests when ontologies are managed in Git repositories. The result will be a much more efficient workflow for making suggestions to ontology developers and the ability to monitor the change history of component ontologies to inform ontology selection for particular end-user tasks. (4) We will provide enhanced mechanisms to enable users of BioPortal to search, access, and browse knowledge in remote BioPortal servers. Users no longer will need to know in advance where particular knowledge might be stored and they will have the ability to easily integrate knowledge from complementary scientific disciplines stored across a network of servers. The result will be the world’s most widely accessed knowledgebase of biomedical concepts and relationships— supporting all other work in semantic technology in biomedicine and making all biomedical knowledgebases more standardized, more easily integrated, and more FAIR.

抽象的 生物医学中使用最广泛和最通用的知识库是本体论 定义实体和关系对医疗保健或生命科学不同方面的核心。 当本体论在一个集成框架中汇总在一起时，可以说明相同的术语或 相似的实体彼此相关并允许计算基础架构跨越 本体论 - 然后，整体集合为用户提供了其他功能。 我们的小组已经开发了一种非常流行的知识资源，称为Bioportal，它提供了一个 世界上几乎所有公共可访问的生物医学本体论的独特知识库。采用生物条件 非常了不起。每个月，来自学术界，政府和行业的75,000多名唯一用户 访问我们的本体存储库的内容，以及我们的API服务超过1600万请求。至少 根据Google Scholar的说法，有7,850篇科学论文提到了生物规模的使用。 我们提出以下四个特定目标：（1）我们将继续管理和维护生物阶段 通过增强知识库为生物医学界提供的服务来通过增强知识基础。 （2） 我们将通过创建Bioportal来提高用户与知识库相互作用的效率 知识图。该图本身就是一个可查询的知识资源 - 将整合所有 知识库中的本体论，它将提供指向其他知识源的链接，使用户可以执行 在所有本体论中扩展查询。 （3）我们将使Bioportal的用户能够提出更改或 扩展到本体，并查看本体学是变化和变化请求的历史 在GIT存储库中管理。结果将是提出建议的更有效的工作流程 本体开发人员以及监视组件本体论的变化历史的能力，以告知本体论 选择特定最终用户任务。 （4）我们将提供增强的机制，以使生物属性用户 搜索，访问和浏览远程生物型服务器中的知识。用户不再需要知道 在可能存储特定知识的地方，他们将有能力轻松整合 来自跨服务器网络的完整科学学科的知识。 结果将是世界上最广泛访问的生物医学概念和关系的知识基础 - 支持生物医学语义技术的所有其他工作，并使所有生物医学知识库 更标准化，更容易整合，更公平。