Loci ID correspondence and loci subsets for the schemas deposited in Chewie-NS

This dataset includes files with the loci ID correspondence and loci subsets for the schemas deposited in Chewie-NS. Each ZIP archive includes files for the schemas of a specific species. The contents of each ZIP archive are the following:

species1_Spyogenes.zip -- contains the files for the schemas of the species with ID=1 (Streptococcus pyogenes).

species1_Spyogenes_schema1 -- contains the files for the schema with ID=1.

species1_Spyogenes_schema1_loci_IDs_mapping.tsv -- contains the loci ID correspondence between the loci IDs used by the current instance of Chewie-NS and the original loci IDs.

species1_Spyogenes_schema1_cgMLST95_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for the core loci defined based on a loci presence threshold of 95%.

species1_Spyogenes_schema1_cgMLST95_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the core loci, defined based on a loci presence threshold of 95%, used by the current instance of Chewie-NS and the original loci IDs.

species1_Spyogenes_schema1_cgMLST99_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for the core loci defined based on a loci presence threshold of 99%.

species1_Spyogenes_schema1_cgMLST99_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the core loci, defined based on a loci presence threshold of 99%, used by the current instance of Chewie-NS and the original loci IDs.

species1_Spyogenes_schema1_cgMLST100_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for the core loci defined based on a loci presence threshold of 100%.

species1_Spyogenes_schema1_cgMLST100_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the core loci, defined based on a loci presence threshold of 100%, used by the current instance of Chewie-NS and the original loci IDs.

species1_Spyogenes_schema1_Transcriptional_Regulators_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for a set of transcriptional regulators.

species1_Spyogenes_schema1_Transcriptional_Regulators_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the transcriptional regulators used by the current instance of Chewie-NS and the original loci IDs.

species1_Spyogenes_schema1_Virulence_Factors_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for a set of virulence factors.

species1_Spyogenes_schema1_Virulence_Factors_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the virulence factors used by the current instance of Chewie-NS and the original loci IDs.

species10_Ecoli.zip -- contains the files for the schemas of the species with ID=10 (Escherichia coli).

species10_Ecoli_schema1 -- contains the files for the schema with ID=1 (more information about the schema creation process and the definition of the loci subsets is available here).

species10_Ecoli_schema1_loci_IDs_mapping.tsv -- contains the loci ID correspondence between the loci IDs used by the current instance of Chewie-NS, the original loci IDs, and the loci IDs used in the first instance of Chewie-NS (discontinued on July 2025).

species10_Ecoli_schema1_cgMLST99_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for the core loci defined based on a loci presence threshold of 99%.

species10_Ecoli_schema1_cgMLST99_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the core loci, defined based on a loci presence threshold of 99% as described here, used by the current instance of Chewie-NS, the original loci IDs, and the loci IDs used in the first instance of Chewie-NS (discontinued on July 2025).

species14_Senterica.zip -- contains the files for the schemas of the species with ID=14 (Salmonella enterica).

species14_Senterica_schema1 -- contains the files for the schema with ID=1 (more information about the schema creation process and the definition of the loci subsets is available here).

species14_Senterica_schema1_loci_IDs_mapping.tsv -- contains the loci ID correspondence between the loci IDs used by the current instance of Chewie-NS, the original loci IDs, and the loci IDs used in the first instance of Chewie-NS (discontinued on July 2025).

species14_Senterica_schema1_cgMLST99_loci_IDs.txt -- contains the list of loci IDs used by the current instance of Chewie-NS for the core loci defined based on a loci presence threshold of 99%.

species14_Senterica_schema1_cgMLST99_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the core loci, defined based on a loci presence threshold of 99% as described here, used by the current instance of Chewie-NS, the original loci IDs, and the loci IDs used in the first instance of Chewie-NS (discontinued on July 2025).

species18_Lmonocytogenes.zip -- contains the files for the schemas of the species with ID=18 (Listeria monocytogenes).

species18_Lmonocytogenes_schema1 -- contains the files for the schema with ID=1 (corresponding to the Institut Pasteur Listeria moncytogenes cgMLST schema described in Moura et al, 2016, available at https://bigsdb.pasteur.fr/listeria/).

species18_Lmonocytogenes_schema1_loci_IDs_mapping.tsv -- contains the correspondence between the loci IDs for the core loci used by the current instance of Chewie-NS, the original loci IDs, and the loci IDs used in the first instance of Chewie-NS (discontinued on July 2025).