CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database Article Swipe
Brian Alcock
,
William Huynh
,
Romeo Chalil
,
Keaton W Smith
,
Amogelang R. Raphenya
,
Mateusz A. Wlodarski
,
Arman Edalatmand
,
Aaron Petkau
,
Sohaib A Syed
,
Kara K. Tsang
,
Sheridan J.C. Baker
,
Mugdha Dave
,
Madeline C. McCarthy
,
Karyn M. Mukiri
,
Jalees A. Nasir
,
Bahar Golbon
,
Hamna Imtiaz
,
Xingjian Jiang
,
Komal Kaur
,
Megan W‐L Kwong
,
Zi Cheng Liang
,
Keyu C Niu
,
Prabakar Shan
,
Jasmine Y J Yang
,
Kristen L. Gray
,
Gemma R Hoad
,
Baofeng Jia
,
Timsy Bhando
,
Lindsey A. Carfrae
,
Maya A. Farha
,
Shawn French
,
Rodion Gordzevich
,
Kenneth Rachwalski
,
Megan M. Tu
,
Emily Bordeleau
,
Damion Dooley
,
Emma Griffiths
,
Haley L. Zubyk
,
Eric D. Brown
,
Finlay Maguire
,
Robert G. Beiko
,
William Hsiao
,
Fiona S. L. Brinkman
,
Gary Van Domselaar
,
Andrew G. McArthur
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkac920
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkac920
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.
Related Topics
Concepts
Resistome
Biology
Database
Data curation
Genetics
Computational biology
Antibiotic resistance
Gene nomenclature
Genome
Gene
Antibiotics
Computer science
Mobile genetic elements
World Wide Web
Taxonomy (biology)
Botany
Nomenclature
Metadata
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkac920
- https://academic.oup.com/nar/article-pdf/51/D1/D690/48441073/gkac920.pdf
- OA Status
- gold
- Cited By
- 1543
- References
- 28
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4306871314
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4306871314Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gkac920Digital Object Identifier
- Title
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CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance DatabaseWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-10-20Full publication date if available
- Authors
-
Brian Alcock, William Huynh, Romeo Chalil, Keaton W Smith, Amogelang R. Raphenya, Mateusz A. Wlodarski, Arman Edalatmand, Aaron Petkau, Sohaib A Syed, Kara K. Tsang, Sheridan J.C. Baker, Mugdha Dave, Madeline C. McCarthy, Karyn M. Mukiri, Jalees A. Nasir, Bahar Golbon, Hamna Imtiaz, Xingjian Jiang, Komal Kaur, Megan W‐L Kwong, Zi Cheng Liang, Keyu C Niu, Prabakar Shan, Jasmine Y J Yang, Kristen L. Gray, Gemma R Hoad, Baofeng Jia, Timsy Bhando, Lindsey A. Carfrae, Maya A. Farha, Shawn French, Rodion Gordzevich, Kenneth Rachwalski, Megan M. Tu, Emily Bordeleau, Damion Dooley, Emma Griffiths, Haley L. Zubyk, Eric D. Brown, Finlay Maguire, Robert G. Beiko, William Hsiao, Fiona S. L. Brinkman, Gary Van Domselaar, Andrew G. McArthurList of authors in order
- Landing page
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https://doi.org/10.1093/nar/gkac920Publisher landing page
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https://academic.oup.com/nar/article-pdf/51/D1/D690/48441073/gkac920.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://academic.oup.com/nar/article-pdf/51/D1/D690/48441073/gkac920.pdfDirect OA link when available
- Concepts
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Resistome, Biology, Database, Data curation, Genetics, Computational biology, Antibiotic resistance, Gene nomenclature, Genome, Gene, Antibiotics, Computer science, Mobile genetic elements, World Wide Web, Taxonomy (biology), Botany, NomenclatureTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1543Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 804, 2024: 563, 2023: 175, 2020: 1Per-year citation counts (last 5 years)
- References (count)
-
28Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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