The Knowledge Engine for Genomics Gains Momentum

Across the Midwest, summer is the season of growth. For KnowEnG, a Center of Excellence established by an NIH Big Data to Knowledge (BD2K) Initiative award to the University of Illinois in partnership with the Mayo Clinic, this summer’s activities have highlighted both how much has already been accomplished in the past two years and the promise of its newest directions.

KnowEnG stands for Knowledge Engine for Genomics, representing the center’s mission to develop analytical resources that will allow researchers to better interpret new genomic results by leveraging community knowledge of how genes interact with each other. Advances toward this goal were evident when members of the center’s External Advisory Committee and representatives of NIH visited Illinois this May to attend a two-day conference at the Carl R. Woese Institute for Genomic Biology, which houses the center.

Presentations by investigators highlighted research achievements, developed tools, plans for collaborator review, refinement, and dissemination, and new connections to related research efforts. Abel Bliss Professor of Engineering Jiawei Han, a Program Co-Director for the center, praised the rapid progress of the Center, which was founded in October 2014. Efforts at Illinois and the Mayo Clinic have focused on software development, and the creation of resources for bioinformatics education and training tailored to the needs of biomedical researchers, as well as establishing a cycle of feedback and refinement that will ensure the utility and accessibility of the resources under development.

“We need to bring computational genomic science together with biomedical science, and this [KnowEnG] is an excellent effort” said Richard Weinshilboum, M.D., Mary Lou and John H. Dasburg Professor of Cancer Genomics and director of the center’s Pharmacogenomics Translational Program. Weinshilboum praised the productivity of the partnership between Illinois and the Mayo Clinic within the center.

Since the center’s inception, researchers have developed a novel resource, the Knowledge Network that integrates many different high-quality public genomic information sources into a comprehensive theoretical landscape of gene functions and interactions. By placing their new results into the context of the Knowledge Network, biomedical researchers can produce a high-powered analysis of new genomic and transcriptomic datasets.

Another innovation of the KnowEnG Center is the Knowledge Engine (also called KnowEnG), an analytical platform that takes advantage of algorithms that are used successfully in other data mining endeavors, including Google’s search functions, but have not been previously applied to interpretation of genomic data. KnowEnG enables researchers to include the Knowledge Network, as well as more traditional resources, as part of their analytical workflow.

KnowEnG is being designed with a user-friendly interface and standardized analytical pipelines that guide investigators who are less familiar with computational aspects of bioinformatic analyses, and also offers varying levels of customization depending on the user’s expertise. The center has contracted with Amazon Cloud so that researchers can run analyses on the cloud, without requiring local resources, thereby increasing the tool’s usability and making it possible to run multiple variations or aspects of an analysis simultaneously.

“Cloud-based computing can be very helpful,” said Professor of Computer Science and Willett Faculty Scholar Saurabh Sinha, who serves as the second Program Co-Director for the center. “Users would like to run those interactions in parallel and be done with it, and a cloud computing network makes that happen very easily.”

KnowEnG’s user interface will also be connected with an extensive online suite of bioinformatics training modules that can improve understanding of both computational and biological aspects of genomic analyses. Founder Professor of Bioengineering and of Physics Jun Song leads training activities of the center, which include a new partnership with Fisk University to provide bioinformatics education and research opportunities to minority undergraduate students.

An important focus of the next phase of work will be ensuring that KnowEnG is accessible to biomedical researchers at all levels of computational skill. Partnership with the Mayo Clinic as well as bio-focused research groups at Illinois will provide opportunities for several rounds of user testing and feedback. And after another productive year, the KnowEnG Center is excited to share their progress with the wider world of genomic biomedical research.