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FDA-ARGOS: ARGOSDB

Repository for data files and schema definitions for ARGOS project. For additional details on project information and assembly QC see:

Introduction

FDA-ARGOS database updates may help researchers rapidly validate diagnostic tests and use qualified genetic sequences to support future product development

As of September 2021, Embleema and George Washington University have been conducting bioinformatic research and system development, focusing on expanding the FDA-ARGOS database. This project expands datasets publicly available in FDA-ARGOS, improves quality control by developing quality matrix tools and scoring approaches that will allow the mining of public sequence databases, and identifies high-quality sequences for upload to the FDA-ARGOS database as regulatory-grade sequences. Building on expansions during the COVID-19 pandemic, this project aims to further improve the utility of the FDA-ARGOS database as a key tool for medical countermeasure development and validation.

Data_files

The data files contains raw or processed code. It also contains templates and tables for the data files pushed to data.argosdb.org. It can be found here _

Docs

Documentation can be found in the docs directory.

Schema

Houses the ARGOS data schemas by release version:

Current: v1.6 v1.5
v1.4
v1.3
v1.2
v1.1
v1.0
v0.9
v0.8
v0.7
v0.6
v0.5
v0.4
v0.3
v0.1

lib

The lib directory contains the scripts, raw, processed code, and extras. Shell files, inside lib, can be found here.

covid-drdb

COVID-DRDB is created by the HIVDB team of Stanford University. It includes resistance data of SARS-CoV-2 for convalescent plasma, vaccinee plasma and monoclonal antibodies collected from published peer-reviewed/pre-print studies. The documents and files can be found here.

Validating a data file against a schema:

Assume you wanted to validate a file of the typeSRA_ngsQC(this same process should work for any of the types we have defined).

  • The data file is /data_files/test_SRA_ngsQC.tsv
  • The schema for a SRA_ngsQC data file is /schema/v0.5/non-core/SRA_ngsQC.json

For illitstration purposes cell T6 in our example data file has been modified. The schema says that the value has to be less than 1, as gc_ content is a percentage. The example data sheet has a value of 10.63682374 in that cell, and the following error should be thrown:

Line 5 failed. '10.63682374' does not match '^[+-]?([0]+\\.?[0-9]*|\\.[0-9]+)$

From the project root run:

> python lib/dictionary_utils.py validate -i data_files/test_SRA_ngsQC.tsv -s schema/v0.5/non-core/SRA_ngsQC.json

Validating a data file against a schema with remote files:

Both the schema [-s] and input file [-i] values can take a URL, assuming they are formatted correctly and resolvable.

For Example:

>  python lib/dictionary_utils.py validate -i https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/data_files/test_SRA_ngsQC.tsv -s https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/schema/v0.5/non-core/SRA_ngsQC.json

should give you the same results.

Citations

Sichtig, H., Minogue, T., Yan, Y. et al. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun 10, 3313 (2019). https://doi.org/10.1038/s41467-019-11306-6