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. 2015 Nov;22(6):1115-9.
doi: 10.1093/jamia/ocv090. Epub 2015 Jul 23.

KnowEnG: A Knowledge Engine for Genomics

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Free PMC article

KnowEnG: A Knowledge Engine for Genomics

Saurabh Sinha et al. J Am Med Inform Assoc. .
Free PMC article

Abstract

We describe here the vision, motivations, and research plans of the National Institutes of Health Center for Excellence in Big Data Computing at the University of Illinois, Urbana-Champaign. The Center is organized around the construction of "Knowledge Engine for Genomics" (KnowEnG), an E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. The scientist will come to KnowEnG with their own data sets in the form of spreadsheets and ask KnowEnG to analyze those data sets in the light of a massive knowledge base of community data sets called the "Knowledge Network" that will be at the heart of the system. The Center is undertaking discovery projects aimed at testing the utility of KnowEnG for transforming big data to knowledge. These projects span a broad range of biological enquiry, from pharmacogenomics (in collaboration with Mayo Clinic) to transcriptomics of human behavior.

Keywords: BD2K; Network analysis; big data; genomics; scalable.

Figures

Figure 1:
Figure 1:
The today figure illustrates a user’s gene set being tested for overlap with community gene sets. The future figure, KnowEnG, illustrates a user’s spreadsheets being analyzed in the light of a heterogeneous knowledge network, representing community data sets, leading to deeper insights.
Figure 2:
Figure 2:
Example of a knowledge-guided analysis. Prior knowledge that genes G1, G2, and G3 belong to the same pathway P allows discrimination of individuals I1, I2, and I3 from I4, I5, and I6 based on variants they carry (blue circles).
Figure 3:
Figure 3:
Rows in Analysis Matrix (user’s spreadsheet) map to nodes in Knowledge Network, making joint analysis possible.

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