Lynx: a knowledge base and an analytical workbench for integrative medicine.

Journal: Nucleic acids research
Published Date: Nov 20, 2015

Abstract

Lynx (http://lynx.ci.uchicago.edu) is a web-based database and a knowledge extraction engine. It supports annotation and analysis of high-throughput experimental data and generation of weighted hypotheses regarding genes and molecular mechanisms contributing to human phenotypes or conditions of interest. Since the last release, the Lynx knowledge base (LynxKB) has been periodically updated with the latest versions of the existing databases and supplemented with additional information from public databases. These additions have enriched the data annotations provided by Lynx and improved the performance of Lynx analytical tools. Moreover, the Lynx analytical workbench has been supplemented with new tools for reconstruction of co-expression networks and feature-and-network-based prioritization of genetic factors and molecular mechanisms. These developments facilitate the extraction of meaningful knowledge from experimental data and LynxKB. The Service Oriented Architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.

Authors

  • Dinanath Sulakhe
    Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA sulakhe@uchicago.edu.
  • Bingqing Xie
    Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, USA.
  • Andrew Taylor
    From the Departments of Urology (T.C., M.U., H.C.C., M.S.) and Radiology and Biomedical Imaging (J.M., M.P.K., A.T., P.J., R.G., S.W.), University of California, San Francisco. 505 Parnassus Ave, M-391, San Francisco, CA 94143; and Division of Urology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, The Thai Red Cross Society, Bangkok, Thailand (M.U.).
  • Mark D'Souza
    Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
  • Sandhya Balasubramanian
    Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
  • Somaye Hashemifar
    Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL 60637, USA.
  • Steven White
    Department of Medicine, University of Chicago, 5841 S. Maryland Avenue, Chicago, IL 60637, USA.
  • Utpal J Dave
    Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA.
  • Gady Agam
    Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, USA.
  • Jinbo Xu
    Toyota Technological Institute at Chicago, Chicago, IL 60615, USA.
  • Sheng Wang
    Intensive Care Medical Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People's Republic of China.
  • T Conrad Gilliam
    Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA.
  • Natalia Maltsev
    Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA maltsev@uchicago.edu.

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