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A Note on Ongoing Revisions of the Antibiotic Resistance Ontology
| NAME | INFO | VERSION | FILE FORMAT | DATE | ACTION |
|---|---|---|---|---|---|
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | April 2017 patch - corrected mutation download file | 1.1.7 | JSON, TAB ,OBO, FASTA | 2017-04-12 11:31:30.894574 | DOWNLOAD |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | 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 |
| CARD | Removes models with missing parameters | 1.0.8 | JSON, TAB ,OBO, FASTA | 2016-06-16 13:11:22.136803 | DOWNLOAD |
| CARD | 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 |
| CARD | 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 |
| CARD | Ontological improvements for RGI functional categories. | 1.0.5 | JSON, TAB ,OBO, FASTA | 2016-04-06 11:55:19.278521 | DOWNLOAD |
| CARD | Improved model cut-offs for beta-lactamases. | 1.0.4 | JSON, TAB ,OBO, FASTA | 2016-03-31 14:14:00.32158 | DOWNLOAD |
| CARD | 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 |
| CARD | Additional beta-lactamases and membrane AMR proteins. | 1.0.2 | JSON, TAB ,OBO, FASTA | 2016-03-23 13:53:47.74496 | DOWNLOAD |
| CARD | Numerous annotation improvements and additions, most notably MCR-1. | 1.0.1 | JSON, CSV, OBO, FASTA | 2015-12-14 11:05:47.411141 | DOWNLOAD |
| CARD | 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 |
|---|---|---|---|---|
| 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 |
|---|---|---|---|---|---|
| CARD 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 |
| CARD 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 |
| CARD 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 | 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