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arpcard / aro

The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of an antibiotic
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Possible to download ARO with mechanisms? #13

Open merytouceda opened 7 months ago

merytouceda commented 7 months ago

Hi!

I was wondering if there is a way to download a table that contains the accession number or name of the gene and the mechanism of resistance. When I download the aro.tsv from the CARD site (https://card.mcmaster.ca/download) I only get the description, but not the broader classifications of each gene.

Thanks!

arpcard commented 7 months ago

@merytouceda maybe the file aro_index.tsv in the Download CARD Data section will help:

cat aro_index.tsv | head -10
ARO Accession   CVTERM ID   Model Sequence ID   Model ID    Model Name  ARO Name    Protein Accession   DNA Accession   AMR Gene Family Drug Class  Resistance Mechanism    CARD Short Name
ARO:3005099 43314   6143    3831    23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A)  23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A)  AAB60941.1  AF002716.1  Erm 23S ribosomal RNA methyltransferase lincosamide antibiotic;macrolide antibiotic;streptogramin antibiotic    antibiotic target alteration    Spyo_ErmA_MLSb
ARO:3002523 38923   8144    1781    AAC(2')-Ia  AAC(2')-Ia  AAA03550.1  L06156.2    AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-Ia
ARO:3002524 38924   85  746 AAC(2')-Ib  AAC(2')-Ib  AAC44793.1  U41471.1    AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-Ib
ARO:3002525 38925   4719    1246    AAC(2')-Ic  AAC(2')-Ic  CCP42991.1  AL123456.3  AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-Ic
ARO:3002526 38926   228 1415    AAC(2')-Id  AAC(2')-Id  AAB41701.1  U72743.1    AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-Id
ARO:3002527 38927   5510    2832    AAC(2')-Ie  AAC(2')-Ie  CAC32082.1  AL583926.1  AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-Ie
ARO:3004628 42613   5361    3327    AAC(2')-IIa AAC(2')-IIa BAM16262.1  AB669090.1  AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-IIa
ARO:3003988 40870   3860    2524    AAC(2')-IIb AAC(2')-IIb APB03221.1  KX531051.1  AAC(2') aminoglycoside antibiotic   antibiotic inactivation AAC(2')-IIb
ARO:3002528 38928   8360    39  AAC(3)-Ia   AAC(3)-Ia   AAG15269.1  U12338.3    AAC(3)  aminoglycoside antibiotic   antibiotic inactivation AAC(3)-Ia