Data for "A Hybrid Pipeline for Feature Reduction, and Ordinal Classification to Predict Antimicrobial Resistance from Genetic Profiles"

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.