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A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets

Breuza, L; Arighi, CN; Argoud-Puy, G; Casals-Casas, C; Estreicher, A; Famiglietti, ML; Georghiou, G; ... IMEx Consortium, UniProt Consortium, .; + view all (2020) A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. Journal of Alzheimer's Disease 10.3233/JAD-200206. (In press). Green open access

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Abstract

BACKGROUND: The analysis and interpretation of data generated from patient-derived clinical samples relies on access to high-quality bioinformatics resources. These are maintained and updated by expert curators extracting knowledge from unstructured biological data described in free-text journal articles and converting this into more structured, computationally-accessible forms. This enables analyses such as functional enrichment of sets of genes/proteins using the Gene Ontology, and makes the searching of data more productive by managing issues such as gene/protein name synonyms, identifier mapping, and data quality. OBJECTIVE: To undertake a coordinated annotation update of key public-domain resources to better support Alzheimer's disease research. METHODS: We have systematically identified target proteins critical to disease process, in part by accessing informed input from the clinical research community. RESULTS: Data from 954 papers has been added to the UniProtKB, Gene Ontology, and the International Molecular Exchange Consortium (IMEx) databases, with 299 human proteins and 279 orthologs updated in UniProtKB. 7,45 binary interactions were added to the IMEx human molecular interaction dataset. CONCLUSION: This represents a significant enhancement in the expert curated data pertinent to Alzheimer's disease available in a number of biomedical databases. Relevant protein entries have been updated in UniProtKB and concomitantly in the Gene Ontology. Molecular interaction networks have been significantly extended in the IMEx Consortium dataset and a set of reference protein complexes created. All the resources described are open-source and freely available to the research community and we provide examples of how these data could be exploited by researchers.

Type: Article
Title: A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets
Location: Netherlands
Open access status: An open access version is available from UCL Discovery
DOI: 10.3233/JAD-200206
Publisher version: https://doi.org/10.3233/JAD-200206
Language: English
Additional information: © 2020 – IOS Press and the authors. All rights reserved This article is published online with Open Access and distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
Keywords: Alzheimer’s disease, Cytoscape network analysis, data curation, database, neurobiology, protein
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Cardiovascular Science
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Cardiovascular Science > Pre-clinical and Fundamental Science
URI: https://discovery.ucl.ac.uk/id/eprint/10107449
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