ARAX: a graph-based modular reasoning tool for translational biomedicine.

Journal: Bioinformatics (Oxford, England)
PMID: 36752514

Abstract

MOTIVATION: With the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challenging computational reasoning problems have contributed tools and approaches, but progress has been hindered by the lack of an expressive analysis workflow language for translational reasoning and by the lack of a reasoning engine-supporting that language-that federates semantically integrated knowledge-bases.

Authors

  • Amy K Glen
    School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
  • Chunyu Ma
    Gansu University of Traditional Chinese Medicine, Lanzhou, Gansu 730000, China.
  • Luis Mendoza
    Institute for Systems Biology, Seattle, WA 98109, USA.
  • Finn Womack
    Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA.
  • E C Wood
    School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
  • Meghamala Sinha
    School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America.
  • Liliana Acevedo
    School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
  • Lindsey G Kvarfordt
    School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
  • Ross C Peene
    School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
  • Shaopeng Liu
    Department of Computer Science, Guangdong Polytechnic Normal University, Guangzhou, 510006, China; Guangdong Key Laboratory of Big Data Analysis and Processing, Guangzhou, 510006, China.
  • Andrew S Hoffman
    Human Centered Design & Engineering (HCDE), University of Washington, USA.
  • Jared C Roach
    Institute for Systems Biology, Seattle, WA 98109, USA.
  • Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98109, United States.
  • Stephen A Ramsey
  • David Koslicki
    Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA.

Keywords

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