Sequence Ontology terminology for gene regulation |
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| Institution: | 1. Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA;2. Department of Biomedical Sciences, Noorda College of Osteopathic Medicine, Provo, UT, USA;3. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;4. Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria;5. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK;6. Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK;7. Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, Netherlands;1. Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan;2. Department of Onco-cardiology, Osaka International Cancer Institute, Osaka, Japan;3. Student Lab, Tokushima University Faculty of Medicine, Tokushima, Japan. |
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| 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. |
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