Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns
Abstract
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.
- Authors:
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[1];
[2];
[1];
[3];
[4];
[5];
[6];
[1];
[7];
[7];
[3];
[7];
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[2]
- Univ. of Cambridge (United Kingdom)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. College London (United Kingdom)
- Stanford Univ., CA (United States)
- The Jackson Lab., Bar Harbor, ME (United States)
- California Institute of Technology (CalTech), Pasadena, CA (United States)
- Swiss Inst. of Bioformatics, Geneva (Switzerland)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Wellcome Trust; National Human Genome Research Institute (NHGRI); UK Medical Research Council; UK Biotechnology and Biological Sciences Research Council; Alzheimer’s Research UK
- OSTI Identifier:
- 1713252
- Grant/Contract Number:
- AC02-05CH11231; 104967/Z/14/Z; U41 HG002273; U41 HG001315; U24 HG010859; U24 HG002223; MR/S000453/1; BB/P024602/1; MR/N030117/1; ARUK-NAS2017A-1
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Open Biology
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 2046-2441
- Publisher:
- The Royal Society
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; gene ontology; quality control; annotation; biocuration
Citation Formats
Wood, Valerie, Carbon, Seth, Harris, Midori A., Lock, Antonia, Engel, Stacia R., Hill, David P., Van Auken, Kimberly, Attrill, Helen, Feuermann, Marc, Gaudet, Pascale, Lovering, Ruth C., Poux, Sylvain, Rutherford, Kim M., and Mungall, Christopher J. Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. United States: N. p., 2020.
Web. doi:10.1098/rsob.200149.
Wood, Valerie, Carbon, Seth, Harris, Midori A., Lock, Antonia, Engel, Stacia R., Hill, David P., Van Auken, Kimberly, Attrill, Helen, Feuermann, Marc, Gaudet, Pascale, Lovering, Ruth C., Poux, Sylvain, Rutherford, Kim M., & Mungall, Christopher J. Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. United States. https://doi.org/10.1098/rsob.200149
Wood, Valerie, Carbon, Seth, Harris, Midori A., Lock, Antonia, Engel, Stacia R., Hill, David P., Van Auken, Kimberly, Attrill, Helen, Feuermann, Marc, Gaudet, Pascale, Lovering, Ruth C., Poux, Sylvain, Rutherford, Kim M., and Mungall, Christopher J. Wed .
"Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns". United States. https://doi.org/10.1098/rsob.200149. https://www.osti.gov/servlets/purl/1713252.
@article{osti_1713252,
title = {Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns},
author = {Wood, Valerie and Carbon, Seth and Harris, Midori A. and Lock, Antonia and Engel, Stacia R. and Hill, David P. and Van Auken, Kimberly and Attrill, Helen and Feuermann, Marc and Gaudet, Pascale and Lovering, Ruth C. and Poux, Sylvain and Rutherford, Kim M. and Mungall, Christopher J.},
abstractNote = {Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.},
doi = {10.1098/rsob.200149},
journal = {Open Biology},
number = 9,
volume = 10,
place = {United States},
year = {Wed Sep 02 00:00:00 EDT 2020},
month = {Wed Sep 02 00:00:00 EDT 2020}
}
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