Metadata referential

Overview

The ABRomics analyses platform is designed to analyze the AMR genes content of bacterial samples using two types of data:

Genomic paired-end FASTQ files

Genomic FASTA files

How to fill metadata in the ABRomics analyses platform?

There are two ways to fill the metadata in the ABRomics analyses platform:

Directly on the upload form of platform
Or using an Excel document, that must follow a template of the platform

Metadata associated with templates on the platform

Genomic paired-end FASTQ

This metadata referential has 16 fields describing:

The biological sample
- 7 mandatory
- 5 optional

The isolated microorganism
- 1 mandatory

The sequencing data
- 3 mandatory

Biological sample metadata fields (12 fields)

Field name	Description	Status	Validation	Accepted values
Sample ID	ID of the sample	mandatory	Sample ID must be unique in the whole document	Free text
Strain ID	Name of the isolated strain	mandatory	Strain ID must be unique in the whole document	Free text
Sample type	Indicate if the sample is collected on human, on animal or in an environment	mandatory	Strain ID must be unique in the entire document	See “Fields values” of Metadata referentials
Sample source	Site of isolation of the sample	mandatory	One of the accepted values	See “Fields values” of Metadata referentials
Host species	Species of the host	mandatory	One of the accepted values	See “Fields values” of Metadata referentials
Country	Name of the country in which the sample has been collected	mandatory	Country english full name	See “Fields values” of Metadata referentials
Region	Region where the sample has been collected	optional	One of the accepted values	See on ABRomics analyses platform
Place	Place where the sample has been collected	optional	One of the accepted values	See on ABRomics analyses platform
Collected date	The date of sampling	mandatory	Must be a valid full date. For example: 07/10/2024	Must be a valid full date
Travel countries	Countries where the host traveled to in the last 3 months prior to the sampling	optional	Country english full name. If multiple countries, separate each by comma	See “Fields values” of Metadata referentials
Accession number	Accession numbers associated with the sample	optional	Multiple values should be split by ‘;’	Free text
Sample comment	Any comments on the sample	optional	Free text	Free text

Isolated microorganism field (1 field)

Field name	Description	Status	Validation	Accepted values
Microorganism scientific name	Scientific name of the isolated microorganism	mandatory	One of the accepted values	See “Fields values” of Metadata referentials

Sequencing data metadata fields (3 fields)

Field name	Description	Status	Validation	Accepted values
R1 fastq filename	Name of fastq forward file	mandatory	The filename must end by “.fastq.gz”	Free text
R2 fastq filename	Name of fastq reverse file	mandatory	The filename must end by “.fastq.gz”	Free text
Instrument model	The sequencing instrument model used in the experiment	mandatory	One of the accepted values	See “Fields values” of Metadata referentials

Genomic FASTA