BioPortal: An Expansive Knowledgebase of Biomedical Entities and Relations

点击翻译按钮获取中文摘要

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.