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Genes 2018, 9(12), 593; https://doi.org/10.3390/genes9120593

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data

1
UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK
2
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
3
Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK
4
UCL Queen Square Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, 1 Wakefield Street, London WC1N 1PJ, UK
*
Author to whom correspondence should be addressed.
Received: 31 October 2018 / Revised: 22 November 2018 / Accepted: 23 November 2018 / Published: 29 November 2018
(This article belongs to the Special Issue Systems Analytics and Integration of Big Omics Data)
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Abstract

The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. The aim of this project, funded by the Alzheimer’s Research United Kingdom (ARUK) foundation and led by the University College London (UCL) biocuration team, was to enhance the GO resource by developing new neurological GO terms, and use GO terms to annotate gene products associated with dementia. Specifically, proteins and protein complexes relevant to processes involving amyloid-beta and tau have been annotated and the resulting annotations are denoted in GO databases as ‘ARUK-UCL’. Biological knowledge presented in the scientific literature was captured through the association of GO terms with dementia-relevant protein records; GO itself was revised, and new GO terms were added. This literature biocuration increased the number of Alzheimer’s-relevant gene products that were being associated with neurological GO terms, such as ‘amyloid-beta clearance’ or ‘learning or memory’, as well as neuronal structures and their compartments. Of the total 2055 annotations that we contributed for the prioritised gene products, 526 have associated proteins and complexes with neurological GO terms. To ensure that these descriptive annotations could be provided for Alzheimer’s-relevant gene products, over 70 new GO terms were created. Here, we describe how the improvements in ontology development and biocuration resulting from this initiative can benefit the scientific community and enhance the interpretation of dementia data. View Full-Text
Keywords: Alzheimer’s disease; dementia; cognitive impairment; neurodegeneration; Gene Ontology; annotation; biocuration; amyloid-beta; microtubule-associated protein tau Alzheimer’s disease; dementia; cognitive impairment; neurodegeneration; Gene Ontology; annotation; biocuration; amyloid-beta; microtubule-associated protein tau
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Kramarz, B.; Roncaglia, P.; Meldal, B.H.M.; Huntley, R.P.; Martin , M.J.; Orchard, S.; Parkinson, H.; Brough, D.; Bandopadhyay, R.; Hooper, N.M.; Lovering, R.C. Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data. Genes 2018, 9, 593.

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