ABRomics Platform

The ABRomics project aims to develop an online community-driven platform to scale up and improve surveillance and research on antibiotic resistance from a One Health perspective.

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 answer generic and specific research questions related to AMR. There is also a need to develop a user-friendly Web interface for data deposit and for the presentation and retrieval of results.

Overview

The ABRomics platform is made of three essential components :

• A data warehouse made of (i) a filesystem space containing AMR public resources, raw data sequences and raw datafile results, and (ii) the ABRomics database to structure metadata on (meta)genome sequences and projects, part of the analysis results, and knowledge on ABR gene.  API (Application Programming Interface) functions will allow data interoperability with other epidemiological resources and databases (WP2).
• A Galaxy server which includes, in the first version of ABRomics, standard tools and pipelines for (semi) automatic analysis of NGS data from pathogenic strains (WP2). Further versions of the platform will include mathematical and bioinformatics tools to analyze and interpret user-submitted multi-omics data, and to model the evolution of antibiotic resistance, the transmission and dissemination of clones and genes within and between sectors (WP3).
• A web application allowing to upload and analyse (meta)genomic data and to explore the ABRomics database. Graphical User Interfaces (GUI) are also made available for the visualization of result analysis.

The three components of the ABRomics platform are running on the French Bioinformatics Institute (IFB) IT infrastructure: it offers high capacity of data storage and data analysis, accessible to users under defined rules (free to strict depending on the sensitivity of the data), and offering a general software environment, both HPC and Cloud environments.