Restructured project: Moved files into case_studies/CARD, removed red… #107
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| # CARD README | ||||||
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| ## Source: | ||||||
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| This dataset was downloaded from the Comprehensive Antibiotic Resistance Database (CARD) in 2024-10 at https://card.mcmaster.ca/download/0/broadstreet-v3.3.0.tar.bz2 | ||||||
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| CITATION: | ||||||
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| Alcock et al. 2023. "CARD 2023: expanded curation, support for machine learning, and resistome | ||||||
| prediction at the Comprehensive Antibiotic Resistance Database" Nucleic Acids Research, | ||||||
| 51, D690-D699. https://pubmed.ncbi.nlm.nih.gov/36263822/ | ||||||
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| ## CARD SHORT NAMES | ||||||
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| The CARD database uses standardized abbreviations, known as CARD Short Names, for AMR gene names associated with Antibiotic Resistance Ontology terms. These names are created for compatibility across data files and outputs from the Resistance Gene Identifier (RGI). Short Names for genes with 15 or fewer characters retain the original gene name, while longer names are abbreviated to uniquely represent each gene or protein. All CARD Short Names replace whitespace with underscores. For pathogen names, CARD follows the convention of capitalizing the first letter of the genus followed by the first three letters of the species in lowercase. Where applicable, CARD Short Names adopt formats such as “pathogen_gene,” “pathogen_gene_drug,” or “gene_drug.” Full lists of these abbreviations are available in the provided files: | ||||||
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| shortname_antibiotics.tsv | ||||||
| shortname_pathogens.tsv" | ||||||
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| ## FASTA | ||||||
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| The FASTA files included here contain retrieved sequences of antimicrobial resistance genes. | ||||||
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| ## Data Files Downloaded | ||||||
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| aro_index.tsv | ||||||
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| This file contains an index of ARO (Antibiotic Resistance Ontology) identifiers with associated GenBank accessions. Each entry includes information used to link antibiotic resistance genes to GenBank sequences. | ||||||
| shortname_antibiotics.tsv | ||||||
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| Contains standardized abbreviations for antibiotics used in CARD’s short names. These abbreviations, which follow conventions from the American Society for Microbiology (ASM) and additional custom terms, provide a uniform naming system for antibiotics referenced within CARD data. | ||||||
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| shortname_pathogens.tsv | ||||||
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| Lists standardized abbreviations for pathogens used in CARD. Each abbreviation represents pathogen names in a condensed format, commonly the first letter of the genus followed by the first three letters of the species. This abbreviation system simplifies pathogen referencing in CARD outputs. | ||||||
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| AAC Abbreviation Molecule | ||
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There was a problem hiding this comment. can use this for short nomenclature, e.g., spp_dru_... |
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| AMG Aminoglycosides | ||
| AMK Amikacin | ||
| AMU Aminocoumarin | ||
| AMX Amoxicillin | ||
| ATM Aztreonam | ||
| AVI Avibactam | ||
| AZM Azithromycin | ||
| BDQ Bedaquiline | ||
| BLA Beta-lactams | ||
| CAP Capreomycin | ||
| CEF Ceftazidime | ||
| CZA Ceftazidime-Avibactam | ||
| CHL Chloramphenicol | ||
| CIP Ciprofloxacin | ||
| CLI Clindamycin | ||
| CLR Clarithromycin | ||
| CST Colistin | ||
| DAO Dapsone | ||
| DAP Daptomycin | ||
| DCS D-cycloserine | ||
| EDN Edeine | ||
| ELF Elfamycin | ||
| EMB Ethambutol | ||
| EMCM Ethambutol & Capreomycin | ||
| ENC Enacyloxin IIa | ||
| ENR Enrofloxacin | ||
| ERY Erythromycin | ||
| ETO Ethionamide | ||
| FA Fusidic acid | ||
| FLO Fluoroquinolones | ||
| FOF Fosfomycin | ||
| G418 G418 | ||
| GE2A GE2270A | ||
| GEN Gentamicin | ||
| GENC Gentamicin C | ||
| HGM Hyrgomycin B | ||
| INH Isoniazid | ||
| IPM Imipenem | ||
| KAN Kanamycin | ||
| KAS Kasugamicin | ||
| KIR Kirromycin | ||
| LEV Levofloxacin | ||
| LYS Lysocin (E) | ||
| LZD Linezolid | ||
| MAC Macrolides | ||
| MULT Multiple antibiotics | ||
| MUP Mupirocin | ||
| MTZ Metronidazole | ||
| MXF Moxifloxacin | ||
| NEO Neomycin | ||
| NIT Nitrofurantoin | ||
| OFX Ofloxacin | ||
| OXZ Oxazolidinone | ||
| PAC Pactamycin | ||
| PAR Paromomycin | ||
| PAS Para-aminosalicylic acid | ||
| PCL Perchlozone | ||
| PLM Pleuromutilin | ||
| PLV Pulvomycin | ||
| PTO Prothionamide | ||
| PZA Pyrazinamide | ||
| RFB Rifabutin | ||
| RIF Rifampicin | ||
| SLF Sulfonamides | ||
| SPT Spectinomycin | ||
| STR Streptomycin | ||
| TMP Trimethoprim | ||
| TET Tetracycline | ||
| TOB Tobramycin | ||
| TRC Triclosan | ||
| TYL Tylosin | ||
| VAN Vancomycin | ||
| VIO Viomycin | ||
| ZOL Zoliflodacin | ||
| CAP capreomycin | ||
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| Abbreviation Pathogen | ||
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| Abau Acinetobacter baumannii | ||
| Acla Alkalihalobacillus clausii | ||
| Afab Agrobacterium fabrum | ||
| Bado Bifidobacterium adolescentis | ||
| Bbac Bartonella bacilliformis | ||
| Bbif Bifidobacterium bifidum | ||
| Bbur Borreliella burgdorferi | ||
| Bdol Burkholderia dolosa | ||
| Bhyo Brachyspira hyodysenteriae | ||
| Bpse Burkholderia pseudomallei | ||
| Bpum Bacillus pumilus | ||
| Bsub Bacillus subtilis | ||
| Bsui Brucella suis | ||
| Ccol Campylobacter coli | ||
| Cacn Cutibacterium acnes | ||
| Cbut Clostridium butyricum | ||
| Cspo Clostridium sporogenes | ||
| Cdif Clostridioides difficile | ||
| Cgin Capnocytophaga gingivalis | ||
| Cjej Campylobacter jejuni | ||
| Cmen Chryseobacterium meningosepticum | ||
| Cper Clostridium perfringens | ||
| Cpsi Chlamydophila psittaci | ||
| Crei Chlamydomonas reinhardtii | ||
| Cstr Corynebacterium striatum | ||
| Ctra Chlamydia trachomatis | ||
| Eclo Enterobacter cloacae | ||
| Ecol Escherichia coli | ||
| Efac Enterococcus faecium | ||
| Efae Enterococcus faecalis | ||
| Erhu Erysipelothrix rhusiopathiae | ||
| Hhal Halobacterium halobium | ||
| Hinf Haemophilus influenzae | ||
| Hpin Haemophilus parainfluenzae | ||
| Hpyl Helicobacter pylori | ||
| Hsal Halobacterium salinarum | ||
| Kaer Klebsiella aerogenes | ||
| Kleb Klebsiella | ||
| Kpne Klebsiella pneumoniae | ||
| Lhon Laribacter hongkongensis | ||
| Lmon Listeria monocytogenes | ||
| Lreu Limosilactobacillus reuteri | ||
| Mabs Mycobacteroides abscessus | ||
| Mavi Mycobacterium avium | ||
| Mbov Mycobacterium tuberculosis variant bovis | ||
| Mcat Moraxella catarrhalis | ||
| Mche Mycobacteroides chelonae | ||
| Mfer Mycoplasmopsis fermentans | ||
| Mgal Mycoplasma gallisepticum | ||
| Mgen Mycoplasma genitalium | ||
| Mhom Mycoplasma hominis | ||
| Mint Mycobacterium intracellulare | ||
| Mkan Mycobacterium kansasii | ||
| Mlep Mycobacterium leprae | ||
| Mmor Morganella morganii | ||
| Mpne Mycoplasma pneumoniae | ||
| Msme Mycolicibacterium smegmatis | ||
| Mtub Mycobacterium tuberculosis | ||
| Ngon Neisseria gonorrhoeae | ||
| Nmen Neisseria meningitidis | ||
| Nvir Neobacillus vireti | ||
| Nfar Nocardia farcinica | ||
| Paer Pseudomonas aeruginosa | ||
| Pmir Proteus mirabilis | ||
| Pmul Pasteurella multocida | ||
| Prop Propionibacteria | ||
| Pros Planobispora rosea | ||
| Rfas Rhodococcus fascians | ||
| Rsph Rhodobacter sphaeroides | ||
| Saga Streptococcus agalactiae | ||
| Samb Streptomyces ambofaciens | ||
| Saur Staphylococcus aureus | ||
| Scin Streptomyces cinnamoneus | ||
| Scoh Staphylococcus cohnii | ||
| Sent Salmonella enterica | ||
| Sfle Shigella flexneri | ||
| Sfra Streptomyces fradiae | ||
| Sven Streptomyces venezuelae | ||
| Sint Staphylococcus intermedius | ||
| Sliv Streptomyces lividans | ||
| Smar Serratia marcescens | ||
| Smit Streptococcus mitis | ||
| Spne Streptococcus pneumoniae | ||
| Spyo Streptococcus pyogenes | ||
| Sris Streptomyces rishiriensis | ||
| Sser Salmonella serovars | ||
| Ssui Streptococcus suis | ||
| Tthe Thermus thermophilus | ||
| Uure Ureaplasma urealyticum | ||
| Vcho Vibrio cholerae | ||
| Vang Vibrio anguillarum | ||
| Vvul Vibrio vulnificus | ||
| Yent Yersinia enterocolitica | ||
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@Cateline, thanks for adding this README. Out of curiosity, are these descriptions already paraphrased from the original source (CARD), or yet to be?
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The descriptions are from the original source (CARD) and have not been paraphrased yet