Sequence Ontology terminology for gene regulation.

Journal: Biochimica et biophysica acta. Gene regulatory mechanisms
PMID: 34389511

Abstract

The Sequence Ontology (SO) is a structured, controlled vocabulary that provides terms and definitions for genomic annotation. The Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) initiative has gathered input from many groups of researchers, including the SO, the Gene Ontology (GO), and gene regulation experts, with the goal of curating information about how gene expression is regulated at the molecular level. Here we discuss recent updates to the SO reflecting current knowledge. We have developed more accurate human-readable terms (also known as classes), including new definitions, and relationships related to the expression of genes. New findings continue to give us insight into the biology of gene regulation, including the order of events, and participants in those events. These updates to the SO support logical reasoning with the current understanding of gene expression regulation at the molecular level.

Authors

  • David W Sant
    Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Sciences, Noorda College of Osteopathic Medicine, Provo, UT, USA. Electronic address: david.sant@utah.edu.
  • Michael Sinclair
    Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Stefan Schulz
    Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria.
  • Daniel Zerbino
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK. Electronic address: zerbino@ebi.ac.uk.
  • Ruth C Lovering
    Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK. r.lovering@ucl.ac.uk.
  • Colin Logie
    Molecular Biology Department, Faculty of Science, Radboud University, PO box 9101, 6500HB Nijmegen, the Netherlands.
  • Karen Eilbeck
    Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, 84112-5775 USA.

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