Dataset Information

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

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 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.

SUBMITTER: Breuza L

PROVIDER: S-EPMC7592670 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

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

Breuza Lionel L Arighi Cecilia N CN Argoud-Puy Ghislaine G Casals-Casas Cristina C Estreicher Anne A Famiglietti Maria Livia ML Georghiou George G Gos Arnaud A Gruaz-Gumowski Nadine N Hinz Ursula U Hyka-Nouspikel Nevila N Kramarz Barbara B Lovering Ruth C RC Lussi Yvonne Y Magrane Michele M Masson Patrick P Perfetto Livia L Poux Sylvain S Rodriguez-Lopez Milagros M Stoeckert Christian C Sundaram Shyamala S Wang Li-San LS Wu Elizabeth E Orchard Sandra S

Journal of Alzheimer's disease : JAD 20200101 1

<h4>Background</h4>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 make ...[more]

PMID: 32716361

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Project description:BackgroundSince spring 2020, the SARS-CoV-2 virus has spread worldwide, causing dramatic global consequences in terms of medical, care, economic, cultural and bioethical dimensions. Although the resulting conflicts initially appeared to be quite similar in most countries, a closer look reveals a country-specific intensification and differentiation of issues. Our study focused on understanding and highlighting bioethical conflicts that were triggered, exposed or intensified by the COVID-19 pandemic in low and middle-income countries (LMICs) and high-income countries (HICs).MethodsWe conducted qualitative interviews with 39 ethics experts from 34 countries (Argentina, Australia, Austria, Brazil, Canada, Colombia, Denmark, Ecuador, Ethiopia, France, Germany, India, Italy, Israel, Japan, Kyrgyzstan, Mexico, Nigeria, Oman, Pakistan, Paraguay, Poland, Romania, Russia, Singapore, South Korea, Spain, Sweden, South Africa, Tunisia, Türkiye, United-Kingdom, United States of America, Zambia) from November 2020 to March 2021. We analysed the interviews using qualitative content analysis.ResultsThe scale of the bioethical challenges between countries differed, as did coping strategies for meeting these challenges. Data analysis focused on: a) Resource scarcity in clinical contexts: Scarcity of medical resources led to the need to prioritize the care of some COVID-19 patients in clinical settings globally. Because this entails the postponement of treatment for other patients, the possibility of serious present or future harm to deprioritized patients was identified as a relevant issue. b) Health literacy: The pandemic demonstrated the significance of health literacy and its influence on the effective implementation of health measures. c) Inequality and vulnerable groups: The pandemic highlighted the context-sensitivity and intersectionality of the vulnerabilities of women and children in LMICs and the aged in HICs. d) Conflicts surrounding healthcare professionals: The COVID-19 outbreak underscored the tough working conditions for nurses and other health professionals, raising awareness of the need for reform.ConclusionThe pandemic exposed pre-existing structural problems in LMICs and HICs. Without neglecting individual contextual factors in the observed countries, we created a mosaic of different voices of experts in bioethics across the globe, drawing attention to the need for international solidarity in the context of a global crisis.

Dataset Information

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

Background

Objective

Methods

Results

Conclusion

Publications

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

Similar Datasets

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