Comparison, alignment, and synchronization of cell line information between CLO and EFO.

Journal: BMC bioinformatics
Published Date: Dec 21, 2017

Abstract

BACKGROUND: The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the EMBL-EBI resources. The Cell Line Ontology (CLO) is an OBO community-based ontology that contains information of immortalized cell lines and relevant experimental components. EFO integrates and extends ontologies from the bio-ontology community to drive a number of practical applications. It is desirable that the community shares design patterns and therefore that EFO reuses the cell line representation from the Cell Line Ontology (CLO). There are, however, challenges to be addressed when developing a common ontology design pattern for representing cell lines in both EFO and CLO.

Authors

  • Edison Ong
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Sirarat Sarntivijai
    European Bioinformatics Institute (EMBL-EBI),European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Simon Jupp
    European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
  • Helen Parkinson
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.

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