BAKTA genome annotations and AMR gene profiles for ~20,000 NCBI bacterial isolates from NDARO

ABSTRACT: This dataset contains genome annotations and antimicrobial resistance (AMR) gene features for approximately 20,000 bacterial isolates obtained from the NCBI National Database of Antibiotic-Resistant Organisms (NDARO). Apart from that, derived datasets for AMR prediction are provided. Data contents: - ncbi_isolates_bakta_annotations.7z: BAKTA genome annotations for all isolates, including GFF3, GenBank, and protein sequence files. - ndaro_baseline.csv: AMR gene presence/absence features from NDARO dataset. - UniRef50 and UniRef90 clustered gene annotations datasets: bakta50 and bakta90 (files .npz, _assemblies.pkl and _columns.pkl for each one). - UniRef50 and UniRef90 clustered AMRFinder genes annotations datasets: bakta50_amr and bakta90_amr (files .npz, _assemblies.pkl and _columns.pkl for each one). The annotations were generated to evaluate alternative genomic feature representations for machine learning-based AMR prediction. The dataset enables reproducibility and extension of methods comparing compact AMR-focused features versus genome-wide representations for predicting antibiotic resistance. Note: The organism field was set to "Homo sapiens" due to form limitations, but this dataset contains bacterial isolates (multiple species) from NCBI NDARO, not "Homo sapiens".

ORGANISM(S): Homo sapiens (human)

SUBMITTER: Fernando Sola 

PROVIDER: S-BSST2698 | biostudies-other |

REPOSITORIES: biostudies-other