Extending gene ontology in the context of extracellular RNA and vesicle communication.

Journal: Journal of biomedical semantics
Published Date: Jan 1, 2016

Abstract

BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research.

Authors

  • Kei-Hoi Cheung
    Department of Emergency Medicine, Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT USA ; VA Connecticut Healthcare System, West Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Shivakumar Keerthikumar
    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Paola Roncaglia
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. paola@ebi.ac.uk.
  • Sai Lakshmi Subramanian
    Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Matthew E Roth
    Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Monisha Samuel
    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia.
  • Sushma Anand
    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia.
  • Lahiru Gangoda
    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia.
  • Stephen Gould
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; American Society for Exosomes and Microvesicles (ASEMV), ᅟ, ᅟ
  • Roger Alexander
    Pacific Northwest Diabetes Research Institute, Seattle, WA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • David Galas
    Pacific Northwest Diabetes Research Institute, Seattle, WA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, 06520, CT, USA. mark.gerstein@yale.edu.
  • Andrew F Hill
    The Department of Biochemistry and Chemistry La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria Australia.
  • Robert R Kitchen
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Jan Lötvall
    University of Gothenburg, Gothenburg, Sweden ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
  • Tushar Patel
    Mayo Clinic, Jacksonville, FL USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Dena C Procaccini
    Division of Neuroscience and Behavior, National Institute on Drug Abuse (NIDA), Rockville, MD USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Peter Quesenberry
    University Medicine Comprehensive Cancer Center, Providence, RI USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
  • Joel Rozowsky
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Robert L Raffai
    Department of Surgery, University of California San Francisco and VA Medical Center, San Francisco, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Aleksandra Shypitsyna
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Andrew I Su
    Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA, USA.
  • Clotilde Théry
    Institut Curie, PSL Research University, INSERM U932, Paris, France ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
  • Kasey Vickers
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Marca H M Wauben
    Department of Biochemistry & Cell Biology, Utrecht University, Utrecht, Netherlands ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
  • Suresh Mathivanan
    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
  • Aleksandar Milosavljević
    University of Niš, Faculty of Electronic Engineering, Aleksandra Medvedeva 14, 18000 Niš, Serbia.
  • Louise C Laurent
    Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ

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