Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

Abstract

Background Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability, the utility lies dormant. Results In this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression knowledge base. To better justify the findings are transferable, for each Bgee interoperability experience, we also highlight similar implementations by major bioinformatics knowledge bases. Moreover, we discuss ten general main lessons learned. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability. Conclusions This work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.

Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions

“…Synthesis Centers (funded by the NSF) are examples of projects that highly promote data reuse and integration, demonstrating the economic efficiency of data exchange with incredible success 26 . Recent efforts have also been made to boost interoperability in the Bgee knowledge base by taking stock of file-based data exchange, programmatic interfaces, and automatic interoperability efforts 55 . The good news is that interoperability boosting seems to have a positive domino effect enabled by automation, which will hopefully lead to near total integration capabilities soon 55 .…”

“…Recent efforts have also been made to boost interoperability in the Bgee knowledge base by taking stock of file-based data exchange, programmatic interfaces, and automatic interoperability efforts 55 . The good news is that interoperability boosting seems to have a positive domino effect enabled by automation, which will hopefully lead to near total integration capabilities soon 55 .…”