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

Bioinformatics (Oxford, England) Pub Date : 2025-05-06 DOI:10.1093/bioinformatics/btaf173

Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luis Pedro Coelho

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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.

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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argNorm：抗生素耐药基因注释归一化到抗生素耐药本体（antibiotic resistance Ontology， ARO）。

摘要：目前可用和常用的基因组和宏基因组中抗生素耐药基因（ARGs）注释工具使用不一致的命名法提供结果。这使得比较不同的ARG注释输出具有挑战性。通过将基因名称及其类别映射到抗生素耐药性本体（ARO）等通用受控词汇表，可以提高ARG注释输出的可比性。我们开发了argNorm命令行工具和Python库，将6个ARG注释工具（8个数据库）中检测到的所有基因归一化到ARO。argNorm还使用相同的ARG分类向输出添加信息，以便它们可以跨工具进行比较。可用性和实现：argNorm是一个开源工具，可在https://github.com/BigDataBiology/argNorm上获得。它也可以作为PyPI包下载，并且可以在Bioconda上作为非核心模块使用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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