Published June 29, 2022 | Version v1
Poster Open

EMERGEN-DB : The French database for SARS-CoV-2 genomic surveillance and research

Authors/Creators

  • 1. CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry, France
  • 2. CNRS UMR7104, Inserm U1258, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
  • 3. Sorbonne Université, CNRS FR3631, Inserm US037, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, Paris, France
  • 4. Santé Publique France, 12, rue du Val d'Osne 94 415 Saint-Maurice Cedex
  • 5. Inserm, Institut national de la santé et de la recherche médicale, 101 rue de Tolbiac 75013 Paris, France
  • 6. Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
  • 7. Sorbonne Université, CNRS, FR2424, ABiMS, Station Biologique, 29680, Roscoff, France

Description

In January 2021, the French Ministries of Health (MSS) and Research (MESRI) launched EMERGEN, a national plan for SARS-CoV-2 genomic surveillance, which aims at monitoring the evolution of the COVID-19 in France, detecting new variants and supporting the integration of viral genomic data and health data for both surveillance and research. We present two components of the EMERGEN-Bioinfo digital platform developed by the IFB (Institut Français de Bioinformatique): 

(a) EMERGEN-DB, the database that collects and manages non-sensitive metadata (sample collection, sequencing method, …) and consensus SARS-CoV-2 genomic sequences produced by the 55 sequencing platforms of the consortium. Developed under Django, it is equipped with both user-friendly and application programmatic interfaces (API) that currently offer over 121 entry points, enabling users to upload their data and query the database manually or in batch. EMERGEN-DB also offers numerous tools to facilitate real-time monitoring of variant evolution and expansion throughout France (alerts, etc.), data export via the APIs, data brokering services to curate and manage the metadata before submitting them to the international repositories such as GISAID and EBI-ENA, and finally data exploration and visualization (summary tables, figures, maps, …) through the interactive pages (activity, sampling, …). 

(b) Rtools4emergen, an R package enabling to query EMERGEN-DB, to visualize data and  to automatically generate reports. 

To date, EMERGEN-DB collects metadata from ~64 sequencing platforms and has gathered more than 520513 records, of which 120186 were submitted to GISAID via our brokering tool.

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Cites
Presentation: 10.5281/zenodo.6778708 (DOI)