Expanding BioThings as a community API gateway for sharing biomedical knowledge

Scripps Research Institute, The, La Jolla CA

Investigators

Abstract

In biomedical research, effective analysis of new experimental data depends on the contextualization of results using the totality of biomedical knowledge known to date. This existing knowledge is often organized in structured knowledge bases (KBs). These KBs are instrumental in interpreting new data, and subsequent conclusions are often integrated back into the KBs to stimulate future discoveries. This positive-feedback loop has benefited multiple areas of biomedical research, given the rich availability of both high-throughput data and derived knowledge in recent decades. While development of technologies for data generation remains a primary way to drive research forward, improvements to the efficiency of making available data/knowledge Findable, Accessible, Interoperable and Reusable (FAIR) also has a significant impact for the future advancement in biomedical research. In this proposal, we propose to build a distributed ecosystem of biomedical Application Programming Interfaces (APIs) for promoting FAIR data-sharing and knowledge integration. This ecosystem contains a framework for API creation; an API registry for API management and discovery; and a semantic annotation and integration framework to create cross-API interoperability for their reuse. Beyond promoting the FAIR principles, the distributed nature of this API-based data ecosystem also allows distributed implementation and maintenance efforts for its long-term sustainability. The utility of the ecosystem will be demonstrated in broad areas of research use-cases.