title: CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
abstract: The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis.
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Baofeng
authors: B
authors: Jia
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Amogelang R
authors: AR
authors: Raphenya
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Brian
authors: B
authors: Alcock
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Nicholas
authors: N
authors: Waglechner
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Peiyao
authors: P
authors: Guo
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Kara K
authors: KK
authors: Tsang
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Briony A
authors: BA
authors: Lago
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Biren M
authors: BM
authors: Dave
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Sheldon
authors: S
authors: Pereira
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Arjun N
authors: AN
authors: Sharma
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Sachin
authors: S
authors: Doshi
authors: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
authors: Mélanie
authors: M
authors: Courtot
authors: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
authors: Raymond
authors: R
authors: Lo
authors: Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS U.S. National Poultry Research Center, U.S. Department of Agriculture, Athens, GA 30605, USA.
authors: Laura E
authors: LE
authors: Williams
authors: Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS U.S. National Poultry Research Center, U.S. Department of Agriculture, Athens, GA 30605, USA.
authors: Jonathan G
authors: JG
authors: Frye
authors: School of Medicine, Royal College of Surgeons in Ireland, Dublin 2, Republic of Ireland.
authors: Tariq
authors: T
authors: Elsayegh
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Daim
authors: D
authors: Sardar
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Erin L
authors: EL
authors: Westman
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Andrew C
authors: AC
authors: Pawlowski
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Timothy A
authors: TA
authors: Johnson
authors: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
authors: Fiona S L
authors: FS
authors: Brinkman
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
authors: Gerard D
authors: GD
authors: Wright
authors: M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada mcarthua@mcmaster.ca.
authors: Andrew G
authors: AG
authors: McArthur
mesh_terms: D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods*; D066289:Data Curation; D030541:Databases, Genetic; D004352:Drug Resistance, Microbial; D008829:Microbiology; D064878:Web Browser