Sequence Ontology terminology for gene regulation

David W Sant; Michael Sinclair; Christopher J Mungall; Stefan Schulz; Daniel Zerbino; Ruth C Lovering; Colin Logie; Karen Eilbeck

doi:10.1016/j.bbagrm.2021.194745

Sequence Ontology terminology for gene regulation

Biochim Biophys Acta Gene Regul Mech. 2021 Oct;1864(10):194745. doi: 10.1016/j.bbagrm.2021.194745. Epub 2021 Aug 11.

Authors

David W Sant¹, Michael Sinclair², Christopher J Mungall³, Stefan Schulz⁴, Daniel Zerbino⁵, Ruth C Lovering⁶, Colin Logie⁷, Karen Eilbeck⁸

Affiliations

¹ 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.
² Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
³ Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. Electronic address: cjmungall@lbl.gov.
⁴ Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria. Electronic address: stefan.schulz@medunigraz.at.
⁵ European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK. Electronic address: zerbino@ebi.ac.uk.
⁶ Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK. Electronic address: r.lovering@ucl.ac.uk.
⁷ Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, Netherlands. Electronic address: C.Logie@ncmls.ru.nl.
⁸ Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA. Electronic address: keilbeck@genetics.utah.edu.

PMID: 34389511
DOI: 10.1016/j.bbagrm.2021.194745

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.

Keywords: Gene regulation; Ontology.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Biological Ontologies*
Gene Expression Regulation*
Locus Control Region
Regulatory Elements, Transcriptional*

Grants and funding

T15 LM007124/LM/NLM NIH HHS/United States