argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).

Journal: Bioinformatics (Oxford, England)
PMID: 40238188

Abstract

SUMMARY: Currently available and frequently used tools for annotating antibiotic resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challenging. The comparability of ARG annotation outputs can be improved by mapping gene names and their categories to a common controlled vocabulary such as the Antibiotic Resistance Ontology (ARO). We developed argNorm, a command line tool and Python library, to normalize all detected genes across six ARG annotation tools (eight databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.

Authors

  • Svetlana Ugarcina Perovic
    Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
  • Vedanth Ramji
    APL Global School, Chennai, 600097, Tamil Nadu, India.
  • Hui Chong
    MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
  • Yiqian Duan
    Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China.
  • Finlay Maguire
    Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
  • Luis Pedro Coelho
    Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia. Electronic address: luispedro@big-data-biology.org.

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