DOI: 10.5281/zenodo.18665869
title: Data for "A Hybrid Pipeline for Feature Reduction, and Ordinal Classification to Predict Antimicrobial Resistance from Genetic Profiles"

description: Notation Rules for Variable Interpretation

We provide below the notation system used to encode gene-level features in the dataset:

{P,N}{A,P}#{R,P}#_{A,P}X#Y

The notation is divided by underscores (_). The symbol # represents a number composed of at least one digit. Curly braces {} indicate allowed options. For example, {P,N} means either P or N must appear in that position. Each entry consists of three or four components.

1. Genomic Location

Indicates whether the gene is located on a plasmid.





P – Located on a plasmid




N – Not located on a plasmid



2. Gene Function

Indicates the functional annotation source.





A – Function annotated in CARD




P – Function identified by Prokka




# – Function identifier



When the function type is A, # corresponds to a CARD ARO identifier.

When the function type is P, # corresponds to an autogenerated identifier that maps to a standardized functional annotation index provided in a companion file.

For example:





P0 → hypothetical protein


P1 → tRNA U34 carboxymethyltransferase



P2 → Cytosol non-specific dipeptidase




P3 → Proline/betaine transporter




P4 → ABC transporter glutamine-binding protein GlnH




P5 → Hippurate hydrolase


...


The complete mapping between Prokka-derived identifiers (P#) and their functional descriptions is provided in the accompanying file:

Prokka_Function_Reference_Table.txt

3. Molecule Type and Family

Indicates the type of gene product.





R – The gene produces an RNA




P – The gene produces a protein




# – Autogenerated identifier, unique within each function category



4. Optional Mutation Annotation

Indicates the presence of a mutation.





A – Mutation annotated in CARD




P – Mutation detected through gene family alignment




X – Reference nucleotide or amino acid





For P-type mutations, the reference corresponds to the most common nucleotide or amino acid within the alignment (or the first in alphabetical order in case of ties).




For A-type mutations, the reference corresponds to a CARD gene from a susceptible strain.




If X = "-", this indicates an insertion relative to the reference.






# – Position of the mutation in the RNA or protein sequence




Y – New nucleotide or amino acid





If Y = "-", this indicates a deletion relative to the reference.





Annotation Priority Rules





CARD annotations (functions and mutations) take precedence over Prokka and alignment-derived annotations, respectively.




CARD annotations replace Prokka or alignment annotations when all of the following conditions are met:





Same contig




Same strand




Same gene type (RNA or protein)




Overlap greater than 95%





Counting Rules





Gene counts and mutation counts are reported in separate columns.




Each column represents counts from a single gene family.




A gene family may appear across multiple columns.




Genes annotated as having unknown function are not guaranteed to be grouped consistently.



Example

P_A3008823_P0

A gene located on a plasmid that produces a protein with CARD ARO identifier 3008823 (PC1 protein).

Software and Annotation Pipeline

All genomic features and annotations were generated using standardized bioinformatic tools as follows:





Prokka was used for gene prediction and primary genome annotation (CDS and functional annotation).




RGI (Resistance Gene Identifier) was used to identify antimicrobial resistance genes and resistance-associated SNPs based on CARD.




Barrnap was used to detect ribosomal RNA (rRNA) genes.




Infernal was used to identify non-coding RNAs (ncRNAs).




Platon was used to determine plasmid origin (plasmid vs chromosomal classification).




Sourmash was used for genome-level taxonomic classification.



All tools were executed using consistent parameter settings across genomes.