Plateforme numérique pour l'antibiorésistance, ABRomics
Creators: name: Médigue, Claudine
name: Glaser, Philippe
name: Consortium ABRomics
Publisher: name: Zenodo
Year: 2021
Subjects: Bioinformatics, antibioresistance, FAIR data, database, multiomics

description: 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 clinical 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: <em>- WP1. Computing architecture, </em>aiming to provide the ABRomics consortium with the computing infrastructure and software environment. <em>- WP2. Integrated multi-omics microbiological database</em> aiming to collect, standardize, organize, integrate and give access to the different types of multi-omics data relevant to ABR and perform standard automatic analysis on this data. <em>- WP3. Mathematical and bioinformatics tool development</em> aiming to provide new mathematical and bioinformatics tools dedicated to (i) ABR multi-omics data integration, (ii) decipher mechanisms of ABR transmission (iii) model ABR emergence, selection and spread. <em>- WP6. Web portal</em> <em>open access, privacy-preserving Web tool to submit data, run programs and access results, transversal.</em> In order to ensure that the platform will respond to the needs of the communities, this development will be performed considering six use cases (WP4). The communication across the diversity of actors of ABR and towards the general public will be essential for the success of ABRomics (WP5). In order to perform this ambitious project, we will set up a rigorous management plan (WP0) involving different committees. It will ensure smooth communication and interaction between teams in order to best coordinate the tasks to reach our objectives<strong>.</strong>