About Argos DataBase

The primary goal of the FDA-ARGOS project (Food and Drug Administration-dAtabase for Regulatory-Grade micrObial Sequences; NCBI BioProject Accession: PRJNA231221) was to provide researchers, clinicians, and public health officials with a comprehensive resource of high-quality genomic data for the identification and characterization of microbial pathogens. During the initial phase of the FDA-ARGOS project, experts at the FDA, University of Maryland, National Center for Biotechnology Information (NCBI) and others collaborated to conduct end-to-end genome assembly of clinically relevant organisms and emerging pathogens while establishing baseline quality control (QC) attributes of corresponding genomic data1. These data are available via the BioProject accession and publication referenced above, as well as in the ArgosDB under BCO IDs ARGOS_000009, ARGOS_000010, and ARGOS_000038. Guided by feedback from regulatory scientists and researchers, the FDA-ARGOS project objectives were expanded in September 2021 through additional funding and collaborating institutions including Embleema, The George Washington University, and Temple University. The primary aim was to harness state-of-the-art QC analytics to assist in infectious disease research and regulatory evaluations. The ArgosDB is a culmination of these phase 2 efforts by hosting: a) the development of a regulatory-grade data model that captures, annotates, and harmonization sequence and assembly data from the FDA BioProject and others b) a versioned data dictionary (DD) that supports robust QC protocols and comprehensive QC attributes per sequence and assembly data, and c) regulatory-grade sequence deposition and documentation, such as the availability of downloadable datasets accompanied with reproducible QC workflows via BioCompute Objects.

We invite you to explore our various datasets and protocols on the Home page.

Explore the Frequently Asked Questions (FAQs) tab to find helpful explanations about the project, datasets, and how to use and interpret the ArgosDB. If you have any questions or would like to report a bug, please reach out to Raja Mazumder at mazumder@email.gwu.edu. The research efforts and data products presented herein were funded by the U.S. Food and Drug Administration, Office of the Chief Scientist, Medical Countermeasures Initiative, under FDA contract 75F40121C00167. Please note that the ArgosDB reflects the views and efforts of the research team at The George Washington University and its collaborating partners and does not represent the views or policies of the FDA.

Relevant Publications

• Sichtig H, Minogue T, Yan Y, Stefan C, Hall A, Tallon L, Sadzewicz L, Nadendla S, Klimke W, Hatcher E, Shumway M, Aldea DL, Allen J, Koehler J, Slezak T, Lovell S, Schoepp R, Scherf U. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun. 2019 Jul 25;10(1):3313. doi: 10.1038/s41467-019-11306-6. PMID: 31346170; PMCID: PMC6658474.

• Simonyan V, Goecks J, Mazumder R. Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA J Pharm Sci Technol. 2017 Mar-Apr;71(2):136-146. doi: 10.5731/pdajpst.2016.006734. Epub 2016 Dec 14. PMID: 27974626; PMCID: PMC5510742.