{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T16:54:57Z","timestamp":1773161697239,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T00:00:00Z","timestamp":1744761600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000193","name":"International Development Research Centre","doi-asserted-by":"publisher","award":["109304-001"],"award-info":[{"award-number":["109304-001"]}],"id":[{"id":"10.13039\/501100000193","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf173","type":"journal-article","created":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T15:41:17Z","timestamp":1744818077000},"source":"Crossref","is-referenced-by-count":8,"title":["argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7907-1597","authenticated-orcid":false,"given":"Svetlana","family":"Ugarcina Perovic","sequence":"first","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai, 200433,","place":["China"]},{"name":"Department of Cellular, Computational and Integrative Biology \u2013 CIBIO, University of Trento , Trento, 38123 Povo,","place":["Italy"]}]},{"given":"Vedanth","family":"Ramji","sequence":"additional","affiliation":[{"name":"APL Global School , Chennai, 600097, Tamil Nadu,","place":["India"]},{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , 37 Kent St. , Brisbane, Queensland, 4102 Woollongabba,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7676-7975","authenticated-orcid":false,"given":"Hui","family":"Chong","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai, 200433,","place":["China"]}]},{"given":"Yiqian","family":"Duan","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai, 200433,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1203-9514","authenticated-orcid":false,"given":"Finlay","family":"Maguire","sequence":"additional","affiliation":[{"name":"Faculty of Computer Science, Dalhousie University , Halifax, Nova Scotia, B3H 4R2,","place":["Canada"]},{"name":"Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University , Halifax, Nova Scotia, B3H 4R2,","place":["Canada"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9280-7885","authenticated-orcid":false,"given":"Luis Pedro","family":"Coelho","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai, 200433,","place":["China"]},{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , 37 Kent St. , Brisbane, Queensland, 4102 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