U24GM143402

BiPortal: An Expansive Knowledgebase of Biomedical Entities and Relations - 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 BiPortal, that provides a unique knowledgebase of nearly all the world’s publicly accessible biomedical ontologies. Adoption of BiPortal 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 BiPortal, according to Google Scholar.

We propose the following four specific aims:

(1) We will continue to govern and maintain the BiPortal 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 BiPortal 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 BiPortal 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 BiPortal to search, access, and browse knowledge in remote BiPortal 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.

The Leland Stanford Junior University

THE NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES (NIGMS) SUPPORTS BASIC RESEARCH THAT INCREASES OUR UNDERSTANDING OF BIOLOGICAL PROCESSES AND LAYS THE FOUNDATION FOR ADVANCES IN DISEASE DIAGNOSIS, TREATMENT, AND PREVENTION. NIGMS ALSO SUPPORTS RESEARCH IN SPECIFIC CLINICAL AREAS THAT AFFECT MULTIPLE ORGAN SYSTEMS: ANESTHESIOLOGY AND PERI-OPERATIVE PAIN, CLINICAL PHARMACOLOGY ?COMMON TO MULTIPLE DRUGS AND TREATMENTS, AND INJURY, CRITICAL ILLNESS, SEPSIS, AND WOUND HEALING.? NIGMS-FUNDED SCIENTISTS INVESTIGATE HOW LIVING SYSTEMS WORK AT A RANGE OF LEVELSFROM MOLECULES AND CELLS TO TISSUES AND ORGANSIN RESEARCH ORGANISMS, HUMANS, AND POPULATIONS. ADDITIONALLY, TO ENSURE THE VITALITY AND CONTINUED PRODUCTIVITY OF THE RESEARCH ENTERPRISE, NIGMS PROVIDES LEADERSHIP IN SUPPORTING THE TRAINING OF THE NEXT GENERATION OF SCIENTISTS, ENHANCING THE DIVERSITY OF THE SCIENTIFIC WORKFORCE, AND DEVELOPING RESEARCH CAPACITY THROUGHOUT THE COUNTRY.

93.859 - Biomedical Research and Research Training

National Institute of General Medical Sciences (NIGMS) [HHS - NIH]

Palo Alto, California 94304 United States

Single Zip Code

Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed) (PAR-20-097)

Amendment Since initial award the total obligations have increased 317% from $1,083,026 to $4,517,749.