Use or reproduction of these materials, in whole or in part, by any non-academic organization whether or not for non-commercial (including research) or commercial purposes is prohibited, except with written permission of McMaster University. See the Use or Download Copyright & Disclaimer.
Exception: Ontologies at the Comprehensive Antibiotic Resistance Database are freely available under the Creative Commons CC-BY license version 4.0 
The Antibiotic Resistance Ontology (ARO), draft Mobilome Ontology (MOBIO), draft Virulence Ontology (VIRO), and Resistance Gene Identifier (RGI) are also available at GitHub. The ARO is registered at the OBO Foundry.
A Note on Ongoing Revisions of the Antibiotic Resistance Ontology
| NAME | INFO | VERSION | FILE FORMAT | DATE | ACTION |
|---|---|---|---|---|---|
| Ontology | October 2018 release - updated curation of the ATP-binding cassette protein superfamily (ribosomal protection). Public release of preliminary draft Mobilome (MOBIO) and Virulence (VIRO) ontologies. | 3.0.0 | OBO, OWL, TSV, JSON | 2018-10-11 14:00:44.515203 | DOWNLOAD |
| Ontology | August 2018 release - addition of colistin resistance gene ICR-Mc & phenicol-oxazolidinone-tetracycline resistance gene poxtA. Extensive categorical improvements. | 2.0.3 | OBO, OWL, TSV, JSON | 2018-08-22 13:50:23.436335 | DOWNLOAD |
| Ontology | June 2018 release - Improved classification of chloramphenicol acetyltransferases. | 2.0.2 | OBO, OWL, TSV, JSON | 2018-06-28 11:39:10.317136 | DOWNLOAD |
| Ontology | April 2018 release - Addition of HERA, TRU, & ACI beta-lactamases, sul4, new quinolone efflux pumps. Entirely new Antibiotic Resistance Ontology branch describing AMR phenotypic testing methods. | 2.0.1 | OBO, OWL, TSV, JSON | 2018-04-12 15:06:19.047356 | DOWNLOAD |
| Ontology | February 2018 release - 37 new ADC beta-lactamases, 21 PDC beta-lactamases, new MCR proteins, resistant isoleucyl-tRNA synthetases, and more. Ontolological improvements for AMR Gene Family classification. | 2.0.0 | OBO, OWL, TSV, JSON | 2018-01-29 09:25:26.824373 | DOWNLOAD |
| NAME | INFO | VERSION | FILE FORMAT | DATE | ACTION |
|---|---|---|---|---|---|
| Data | October 2018 release - updated curation of the ATP-binding cassette protein superfamily (ribosomal protection), plus flagging of partial AMR gene sequences throughout CARD and download files (in progress). | 3.0.0 | JSON, TAB , FASTA | 2018-10-11 14:05:28.718122 | DOWNLOAD |
| Data | August 2018 release - colistin resistance gene ICR-Mc, phenicol-oxazolidinone-tetracycline resistance gene poxtA, categorical improvements, correction of 5'-3' sequence orientation errors. | 2.0.3 | JSON, TAB , FASTA | 2018-08-22 13:52:14.884883 | DOWNLOAD |
| Data | June 2018 release - Improved curation of chloramphenicol acetyltransferases, reference sequence updates throughout CARD. | 2.0.2 | JSON, TAB , FASTA | 2018-06-28 11:41:00.414304 | DOWNLOAD |
| Data | April 2018 release - A variety of reference sequences updates, addition of HERA, TRU, & ACI beta-lactamases, sul4, new quinolone efflux pumps. | 2.0.1 | JSON, TAB , FASTA | 2018-04-12 15:10:27.172153 | DOWNLOAD |
| Data | February 2018 release - 37 new ADC beta-lactamases, 21 PDC beta-lactamases, new MCR proteins, 23 rRNA mutations, resistant isoleucyl-tRNA synthetases, hundreds of new resistance mutations, and more. Entirely revised ARO classification of resistance determinants by AMR Gene Family, Drug Class, and Resistance Mechanism. | 2.0.0 | JSON, TAB , FASTA | 2018-02-01 11:57:13.64608 | DOWNLOAD |
| Data | October 2017 release - minor revisions, addition of MCR-1.2, beta-lactamases, APHs | 1.2.1 | JSON, TAB ,OBO, FASTA | 2017-10-10 15:51:53.778226 | DOWNLOAD |
| Data | September 2017 release - extensive curation of rRNA mutations conferring antimicrobial resistance | 1.2.0 | JSON, TAB ,OBO, FASTA | 2017-09-07 11:14:51.693779 | DOWNLOAD |
| Data | August 2017 release - detection model significance cut-offs based on bitscores (expectation values depreciated), extensive curation of porins, efflux proteins, beta-lactamases, rRNA mutations, MCR variants. Ontological and classification improvements. | 1.1.9 | JSON, TAB ,OBO, FASTA, OWL, XML | 2017-08-03 11:58:27.046356 | DOWNLOAD |
| Data | May 2017 release - Addition of bitscores to detection models, curation of chloramphenicol exporter proteins, ontology changes, JSON file format changes | 1.1.8 | JSON, TAB ,OBO, FASTA | 2017-05-04 10:35:26.647001 | DOWNLOAD |
| Data | April 2017 patch - corrected mutation download file | 1.1.7 | JSON, TAB ,OBO, FASTA | 2017-04-12 11:31:30.894574 | DOWNLOAD |
| Data | April 2017 release - continued curation of efflux proteins, ribosomal RNA mutations, added bitscore cutoffs for models and revised determinant branch | 1.1.6 | JSON, TAB ,OBO, FASTA | 2017-04-05 15:22:43.542391 | DOWNLOAD |
| Data | March 2017 release - continued curation of efflux proteins and ribosomal RNA mutations, plus extensive Antibiotic Resistance Ontology revisions | 1.1.5 | JSON, TAB ,OBO, FASTA, OWL, XML | 2017-03-06 11:12:32.574235 | DOWNLOAD |
| Data | February 2017 release - curation of trimethoprim resistant dihydrofolate reductases, chloramphenicol acetyltransferases, glycopeptide resistance clusters, and beta-lactamases. New mutation data added for many resistance genes. Notable revisions to the Antibiotic Resistance Ontology | 1.1.4 | JSON, TAB ,OBO, FASTA, OWL, XML | 2017-02-06 10:37:39.495444 | DOWNLOAD |
| Data | December 2016 release - Added 16S rRNA mutations, more AMR efflux subunits curation | 1.1.3 | JSON, TAB ,OBO, FASTA | 2016-12-05 15:17:52.170359 | DOWNLOAD |
| Data | November 2016 release - extensive curation of AMR efflux subunits, fluoroquinolone resistance mutations | 1.1.2 | JSON, TAB ,OBO, FASTA | 2016-11-07 22:07:02.913263 | DOWNLOAD |
| Data | September and October 2016 release - Added reference sequences and mutation data for fluoroquinolone resistance genes, improved detection models for aminoglycoside resistance genes, improved curation of a variety of beta-lactamases. | 1.1.1 | JSON, TAB ,OBO, FASTA | 2016-10-05 09:26:03.965223 | DOWNLOAD |
| Data | August 2016 release - Improved curation of polymyxin resistance mechanisms, additional mutation data for fosfomycin resistance, a few new beta-lactamases. | 1.1.0 | JSON, TAB ,OBO, FASTA | 2016-08-04 13:39:13.970861 | DOWNLOAD |
| Data | July 2016 release - Updated GI numbers with accession numbers, added more TB mutations and added ADC beta-lactamase class | 1.0.9 | JSON, TAB ,OBO, FASTA | 2016-07-13 11:23:06.398322 | DOWNLOAD |
| Data | Removes models with missing parameters | 1.0.8 | JSON, TAB ,OBO, FASTA | 2016-06-16 13:11:22.136803 | DOWNLOAD |
| Data | Continued review and updating of SNP data throughout all drug resistance mechanisms, with specific focus on fluoroquinolone and aminocoumarin resistant DNA topoisomerases. Improved curation of daptomycin and defensin resistant mprF, mupirocin resistance genes, fusidic acid resistance genes, and ethambutol resistance genes. Detection model improvements and overal curation upgrades for glycopeptide resistance clusters. Continued improvements in detection model cut-offs. | 1.0.7 | JSON, TAB ,OBO, FASTA | 2016-06-06 17:10:15.081235 | DOWNLOAD |
| Data | Extensive curation of SNP data, improved curation of vancomycin resistance clusters, update of fusidic acid resistance reference sequences, extensive improvement of detection model cut-offs. | 1.0.6 | JSON, TAB ,OBO, FASTA | 2016-05-03 14:47:26.109227 | DOWNLOAD |
| Data | Ontological improvements for RGI functional categories. | 1.0.5 | JSON, TAB ,OBO, FASTA | 2016-04-06 11:55:19.278521 | DOWNLOAD |
| Data | Improved model cut-offs for beta-lactamases. | 1.0.4 | JSON, TAB ,OBO, FASTA | 2016-03-31 14:14:00.32158 | DOWNLOAD |
| Data | Improved model cut-offs for beta-lactamases and efflux proteins. | 1.0.3 | JSON, TAB ,OBO, FASTA | 2016-03-24 09:01:11.519258 | DOWNLOAD |
| Data | Additional beta-lactamases and membrane AMR proteins. | 1.0.2 | JSON, TAB ,OBO, FASTA | 2016-03-23 13:53:47.74496 | DOWNLOAD |
| Data | Numerous annotation improvements and additions, most notably MCR-1. | 1.0.1 | JSON, CSV, OBO, FASTA | 2015-12-14 11:05:47.411141 | DOWNLOAD |
| Data | Migration of all data from the original CARD website into the new ARO- and model-centric "Broad Street" curation paradigm. | 1.0.0 | JSON, CSV, OBO, FASTA | 2015-09-29 10:58:58.525377 | DOWNLOAD |
| OLD | NEW | DATE | JSON | TAB |
|---|---|---|---|---|
| 2.0.3 | 3.0.0 | 2018-10-11 14:06:17.25016 | DOWNLOAD | DOWNLOAD |
| 2.0.2 | 2.0.3 | 2018-08-22 13:53:08.577451 | DOWNLOAD | DOWNLOAD |
| 2.0.1 | 2.0.2 | 2018-06-28 13:20:16.445273 | DOWNLOAD | DOWNLOAD |
| 2.0.0 | 2.0.1 | 2018-04-12 15:11:14.787874 | DOWNLOAD | DOWNLOAD |
| 1.2.1 | 2.0.0 | 2018-01-03 12:50:46.444515 | DOWNLOAD | DOWNLOAD |
| 1.2.0 | 1.2.1 | 2017-10-10 15:52:30.317199 | DOWNLOAD | DOWNLOAD |
| 1.1.9 | 1.2.0 | 2017-09-07 11:16:54.722682 | DOWNLOAD | DOWNLOAD |
| 1.1.8 | 1.1.9 | 2017-08-17 14:33:42.412334 | DOWNLOAD | DOWNLOAD |
| 1.1.7 | 1.1.8 | 2017-08-17 14:33:28.378386 | DOWNLOAD | DOWNLOAD |
| 1.1.6 | 1.1.7 | 2017-08-17 14:33:16.926088 | DOWNLOAD | DOWNLOAD |
| 1.1.5 | 1.1.6 | 2017-08-17 14:33:05.959052 | DOWNLOAD | DOWNLOAD |
| 1.1.4 | 1.1.5 | 2017-08-17 14:32:54.617083 | DOWNLOAD | DOWNLOAD |
| 1.1.3 | 1.1.4 | 2017-08-17 14:32:43.034068 | DOWNLOAD | DOWNLOAD |
| 1.1.2 | 1.1.3 | 2017-08-17 14:32:32.832956 | DOWNLOAD | DOWNLOAD |
| 1.1.1 | 1.1.2 | 2017-08-17 14:32:21.337571 | DOWNLOAD | DOWNLOAD |
| 1.1.0 | 1.1.1 | 2017-08-17 14:31:34.129394 | DOWNLOAD | DOWNLOAD |
| 1.0.9 | 1.1.0 | 2017-08-17 14:31:24.523124 | DOWNLOAD | DOWNLOAD |
| 1.0.8 | 1.0.9 | 2017-08-17 14:31:14.274363 | DOWNLOAD | DOWNLOAD |
| 1.0.7 | 1.0.8 | 2017-08-17 14:31:03.133199 | DOWNLOAD | DOWNLOAD |
| 1.0.6 | 1.0.7 | 2017-08-17 14:30:52.035576 | DOWNLOAD | DOWNLOAD |
| 1.0.5 | 1.0.6 | 2017-08-17 14:30:41.272991 | DOWNLOAD | DOWNLOAD |
| 1.0.4 | 1.0.5 | 2017-08-17 14:30:30.126761 | DOWNLOAD | DOWNLOAD |
| 1.0.3 | 1.0.4 | 2017-08-17 14:30:19.205167 | DOWNLOAD | DOWNLOAD |
| 1.0.2 | 1.0.3 | 2017-08-17 14:29:23.865885 | DOWNLOAD | DOWNLOAD |
| 1.0.1 | 1.0.2 | 2017-08-17 14:29:09.8992 | DOWNLOAD | DOWNLOAD |
| 1.0.0 | 1.0.1 | 2017-08-17 14:28:45.92905 | DOWNLOAD | DOWNLOAD |
| NAME | INFO | VERSION | FILE FORMAT | DATE | ACTION |
|---|---|---|---|---|---|
| Prevalence, Genomes, & Variants data | September 2018 incremental release - Expansion to 79 pathogens, 75,000+ resistomes, and 145,000+ AMR allele sequences based on sequence data acquired from NCBI on May & September, 2018, analyzed using RGI 4.2.0 (DIAMOND homolog detection) and CARD 2.0.3. Added: Brucella suis, Moraxella catarrhalis, Yersinia pestis. | 3.0.2 | TAB, FASTA | 2018-09-14 16:21:56.754543 | DOWNLOAD |
| Prevalence, Genomes, & Variants data | June 2018 release - Expansion to 76 pathogens, 70,000+ resistomes, and 130,000+ AMR allele sequences based on sequence data acquired from NCBI on May 28, 2018, analyzed using RGI 4.1.0 (DIAMOND homolog detection) and CARD 2.0.2. | 3.0.1 | TAB, FASTA | 2018-06-28 11:55:25.809338 | DOWNLOAD |
| Prevalence, Genomes, & Variants data | April 2018 release - Expansion to 67 important pathogens, with a focus on ESKAPEs, WHO Priority Pathogens, and agents of sepsis based on analysis using RGI 4.0.3 (DIAMOND homolog detection) and CARD 2.0.1. | 3.0.0 | TAB, FASTA | 2018-04-16 09:56:52.056473 | DOWNLOAD |
| Prevalence, Genomes, & Variants data | CARD Prevalence 2.0.0 is based on sequence data acquired from NCBI on August 28, 2017, analyzed using RGI 4.0.0 (DIAMOND homolog detection) and CARD 2.0.0. Now includes results for protein overexpression models and rRNA mutations. All results organized by revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Download files now include 35000+ genome annotations and all predicted sequence variants. | 2.0.0 | TAB, FASTA | 2018-01-29 14:41:13.878291 | DOWNLOAD |
| Prevalence | CARD Prevalence 1.0.2 is based on sequence data acquired from NCBI on August 28, 2017, analyzed using RGI 3.2.1 (DIAMOND homolog detection) and CARD 1.2.1. | 1.0.2 | TAB | 2017-10-12 15:05:34.356057 | DOWNLOAD |
| Prevalence | CARD Prevalence 1.0.1 is based on sequence data acquired from NCBI on August 28, 2017, analyzed using RGI 3.2.1 (DIAMOND homolog detection) and CARD 1.2.0. | 1.0.1 | TAB | 2017-09-07 11:16:31.524574 | DOWNLOAD |
| Prevalence | CARD Prevalence 1.0.0 is based on sequence data acquired from NCBI on June 13, 2017, analyzed using RGI 3.2.1 (DIAMOND homolog detection) and CARD 1.1.9. | 1.0.0 | TAB | 2017-08-01 13:32:23.711679 | DOWNLOAD |
| NAME | INFO | VERSION | FILE FORMAT | DATE | ACTION |
|---|---|---|---|---|---|
| RGI Software | Fixed indexing error | 4.2.2 | TAR | 2018-10-12 12:50:15.044004 | DOWNLOAD |
| RGI Software | Updated output json to include possible start and stop missed by Prodigal v2.6.3 and tests for heatmap | 4.2.1 | TAR | 2018-10-12 12:49:21.903041 | DOWNLOAD |
| RGI Software | New heat map tool to visualize multiple RGI results, updated documentation, fixed minor bugs involving missing keys, imports, and string comparison. | 4.2.0 | TAR | 2018-08-22 14:05:36.51466 | DOWNLOAD |
| RGI Software | Fixed bug causing protein variant model SNP under-reporting for a small number of cases. | 4.1.0 | TAR | 2018-07-05 00:05:51.235755 | DOWNLOAD |
| RGI Software | Updated LICENSE and minor fixes | 4.0.3 | TAR | 2018-04-11 15:05:12.606344 | DOWNLOAD |
| RGI Software | Added support for docker, added flag (--low_quality) to predict partial genes from short contigs, updated dependencies and added debug (--debug) flag | 4.0.2 | TAR | 2018-03-08 09:20:54.714457 | DOWNLOAD |
| RGI Software | Added support to store database in the working directory by using --local flag, --local flag added to rgi subcommands: main, load, clean and database. Compatible with CARD data (card.json) version 2.0.0 and up. | 4.0.1 | TAR | 2018-02-08 13:41:23.385986 | DOWNLOAD |
| RGI Software | Entirely new codebase, compatible with CARD data (card.json) version 2.0.0 and up (download separately). Open Reading Frame (ORF) prediction using Prodigal, homolog detection using BLAST (default) or DIAMOND, and Strict significance based on CARD curated bitscore cut-offs. Addition of rRNA mutation and efflux over-expression models. Hits of 95% identity or better are automatically listed as Strict. All results organized by revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Revised documentation, command line menu, and website graphical interface. | 4.0.0 | TAR | 2018-01-30 16:38:23.548345 | DOWNLOAD |
| RGI Software | Prodigal ORF calling, BLAST (default) or DIAMOND homolog detection, significance cut-offs based on bitscores (expectation values depreciated). | 3.2.1 | JSON, PYTHON,TXT, GZ | 2017-08-03 14:34:24.627865 | DOWNLOAD |
| RGI Software | Removed MetaGeneMark. RGI uses Prodigal with E-values | 3.2.0 | JSON, PYTHON,TXT, GZ | 2017-05-04 15:08:23.057335 | DOWNLOAD |
| RGI Software | Fixes error with version 3.1.0 when generating tab-delimited file. Added option to check RGI version. | 3.1.1 | JSON, PYTHON,TXT, GZ | 2016-07-13 12:06:21.355196 | DOWNLOAD |
| RGI Software | Added Prodigal open reading frame caller | 3.1.0 | JSON, PYTHON,TXT, GZ | 2016-07-13 12:04:04.526229 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - fixed clean to remove all draft files if option -c 1 is selected | 3.0.9 | JSON, PYTHON,TXT, GZ | 2016-04-07 10:54:59.388664 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - fixed error when creating tab-delimited output with _metadata and data_type included in the RGI JSON results | 3.0.8 | JSON, PYTHON,TXT, GZ | 2016-04-07 10:51:00.86481 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - added function to format RGI output json, fixed error with _metadata key, added logging option | 3.0.7 | JSON, PYTHON,TXT, GZ | 2016-04-01 15:54:07.949631 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - added optional data type flag for input type (i.e chromosome, plasmid, wgs), added ORF protein, updated conversion from FastQ to FastA | 3.0.6 | JSON, PYTHON,TXT, GZ | 2016-04-01 15:50:33.765525 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - fixed typo for file contigToORF.py | 3.0.5 | JSON, PYTHON,TXT, GZ | 2016-04-01 15:49:18.613531 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - observed E-value added to tab-delimited output, added predicted nucleotide (ORF) for contig type, clean temporary files | 3.0.4 | JSON, PYTHON,TXT, GZ | 2016-04-01 15:48:01.776976 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - fixes paths, added options to use gzip files, added nucleotide sequence from CARD to results | 3.0.3 | JSON, PYTHON,TXT, GZ | 2016-04-01 15:46:35.755574 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) - updates and bug fixes | 3.0.2 | JSON, PYTHON,TXT, GZ | 2016-04-01 15:39:53.584648 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) beta testing - updated documentation | 3.0.1 | JSON, PYTHON,TXT | 2015-09-29 11:10:02.880597 | DOWNLOAD |
| RGI Software | Resistance Gene Identifier (RGI) beta testing | 3.0.0 | JSON, PYTHON,TXT | 2015-09-29 11:07:30.701362 | DOWNLOAD |
# searches rgi package and show available versions
$ conda search --channel bioconda rgi
# install rgi package
$ conda install --channel bioconda rgi
# install rgi specific version
$ conda install --channel bioconda rgi=3.1.1
# remove rgi package
$ conda remove --channel bioconda rgi