{"database":"biostudies-other","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Fernando Sola"],"funding":["MICIU/AEI/10.13039/501100011033 and FSE+","Spanish Ministry of Universities","MICIU/AEI/ 10.13039/501100011033 and ERDF/EU","Spanish Ministry of Science and Innovation (Health Institute Carlos III)"],"species":["Homo sapiens (human)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-BSST2698"],"repository":["biostudies-other"],"funding_grant_id":["PI23/01522","FPU23/04004","FPU22/00336","PID2022-139798OB-I00","RYC2023-045030-I"],"pubmed_authors":["Marina R. Pulido","Inma Hernández","Rafael Ayala","Lorena López-Cerero","David Ruiz","Daniel Ayala","Fernando Sola"],"additional_accession":[]},"is_claimable":false,"name":"BAKTA genome annotations and AMR gene profiles for ~20,000 NCBI bacterial isolates from NDARO","description":"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.\n\nData contents:\n- ncbi_isolates_bakta_annotations.7z: BAKTA genome annotations for all isolates, including GFF3, GenBank, and protein sequence files.\n- ndaro_baseline.csv: AMR gene presence/absence features from NDARO dataset.\n- UniRef50 and UniRef90 clustered gene annotations datasets: bakta50 and bakta90 (files .npz, _assemblies.pkl and _columns.pkl for each one).\n- UniRef50 and UniRef90 clustered AMRFinder genes annotations datasets: bakta50_amr and bakta90_amr (files .npz, _assemblies.pkl and _columns.pkl for each one).\n\nThe 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.\n\nNote: 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\".","dates":{"release":"2026-02-09T00:00:00Z","modification":"2026-06-19T13:58:24.126Z","creation":"2026-02-09T11:28:37.346Z"},"accession":"S-BSST2698","cross_references":{}}