Plateforme numérique pour l'antibiorésistance, ABRomics [article]

Claudine Médigue, Philippe Glaser, Consortium ABRomics
2021 Zenodo  
Antibiotic resistance (ABR) is a major public health problem and a threat for the future. Genomics and other omics sciences are essential to improve surveillance of ABR from a One Health perspective and to develop new therapeutic strategies. In order to detect and understand emergence phenomena in time and space it is necessary to archive genomic and phenotypic data in a sustainable way. It is also essential to allow their analysis by all actors involved in the ABR issue: in microbiology and
more » ... nical laboratories, in surveillance and public health institutes and by researchers in the human, animal and environmental sectors. The integration and analysis of omics data with associated metadata requires the development of databases accessible to the community, the automatic use of standard pipelines for genomic and metagenomic data analysis, and the development of new bioinformatics and mathematical methods to meet the demands of the various communities. There is also a need to develop a user-friendly portal for data deposit and for the presentation and retrieval of results. The platform must ensure rigorous management of data access and confidentiality while facilitating collaboration between the various research and public health stakeholders. To meet these ambitious objectives, we have formed a consortium of 45 teams belonging to the main French research organizations. These teams bring together all the expertise required to build this platform. It covers the diversity of ABR research in clinical and fundamental fields, mathematical modeling methods and the whole range of expertise in computer science, bioinformatics, database and computer architecture. The informatics development of ABRomics-PF is organized around four technical work packages: - WP1. Computing architecture, aiming to provide the ABRomics consortium with the computing infrastructure and software environment. - WP2. Integrated multi-omics microbiological database aiming to collect, standardize, organize, integrate and give access [...]
doi:10.5281/zenodo.5230261 fatcat:lhtpmfwdjnddhi6cdilfpccc7q