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

被引：5

作者：

Breuza, Lionel ^{[1
]}

Arighi, Cecilia N. ^{[2
,3
]}

Argoud-Puy, Ghislaine ^{[1
]}

Casals-Casas, Cristina ^{[1
]}

Estreicher, Anne ^{[1
]}

Famiglietti, Maria Livia ^{[1
]}

Georghiou, George ^{[4
]}

Gos, Arnaud ^{[1
]}

Gruaz-Gumowski, Nadine ^{[1
]}

Hinz, Ursula ^{[1
]}

Hyka-Nouspikel, Nevila ^{[1
]}

Kramarz, Barbara ^{[5
]}

Lovering, Ruth C. ^{[5
]}

Lussi, Yvonne ^{[4
]}

Magrane, Michele ^{[4
]}

Masson, Patrick ^{[1
]}

Perfetto, Livia ^{[4
]}

Poux, Sylvain ^{[1
]}

Rodriguez-Lopez, Milagros ^{[4
]}

Stoeckert, Christian ^{[6
]}

Sundaram, Shyamala ^{[1
]}

Wang, Li-San ^{[6
]}

Wu, Elizabeth ^{[7
]}

Orchard, Sandra ^{[4
]}

机构：

[1] Ctr Med Univ Geneva, SIB Swiss Inst Bioinformat, Swiss Prot Grp, Geneva, Switzerland

[2] Georgetown Univ, Med Ctr, Prot Informat Resource, Washington, DC 20007 USA

[3] Univ Delaware, Prot Informat Resource, Newark, DE USA

[4] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Campus, Cambridge CB10 1SD, England

[5] Univ Coll London UCL, Funct Gene Annotat Preclin & Fundamental Sci, Inst Cardiovasc Sci, London, England

[6] Univ Penn, Perelman Sch Med, Philadelphia, PA 19104 USA

[7] Alzforum, Cambridge, MA USA

来源：

JOURNAL OF ALZHEIMERS DISEASE | 2020年 / 77卷 / 01期

基金：

美国国家卫生研究院; 英国惠康基金;

关键词：

Alzheimer's disease; Cytoscape network analysis; data curation; database; neurobiology; protein; AMYLOID-BETA-PEPTIDE; GENE ONTOLOGY; A-BETA; TAU; CLEARANCE; HYPOTHESIS; INTERACTOME; CYTOSCAPE; P25; P35;

D O I：

10.3233/JAD-200206

中图分类号：

Q189 [神经科学];

学科分类号：

071006 ;

摘要：

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, computationallyaccessible 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.

引用

页码：257 / 273

页数：17

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