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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.

TitleA Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.
Publication TypeJournal Article
Year of Publication2020
AuthorsBreuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti MLivia, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, San Wang L-, Wu E, Orchard S
Corporate AuthorsIMEx Consortium, UniProt Consortium
JournalJ Alzheimers Dis
Date Published2020
KeywordsAlzheimer Disease, Computational Biology, Databases, Protein, Expert Systems, Humans, Protein Interaction Maps, Public Sector

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 have 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. 745 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.

Pubmed Link
Alternate JournalJ Alzheimers Dis
PubMed ID32716361
PubMed Central IDPMC7592670
Grant List / WT_ / Wellcome Trust / United Kingdom
U24 HG007822 / HG / NHGRI NIH HHS / United States
212925/Z/18/Z / WT_ / Wellcome Trust / United Kingdom
/ DH_ / Department of Health / United Kingdom

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