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Updated: May 13, 2025

Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
Published on: March 3, 2023
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
Svetlana Ugarcina Perovic1,2, Vedanth Ramji3,4, Hui Chong1
1Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
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.
Availability And Implementation:
argNorm is available as an open-source tool at: https://github.com/BigDataBiology/argNorm. It can also be downloaded as a PyPI package and is available on Bioconda and as an nf-core module.
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