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@Vedanth-Ramji Vedanth-Ramji released this 02 Aug 16:38
· 21 commits to main since this release

Updated the drug categorization and improved manual curation

USER-FACING CHANGES

Improved drug categorization

  • drugs_to_drug_classes() also uses the 'has_part' ARO relationship now to get drug classes for antibiotic mixtures. In case of antibiotic mixtures, the drug classes of the drugs associated with 'has_part' are returned rather than 'antibiotic mixture' (ARO:3000707).
  • 'antibiotic mixture' will not be reported as a drug class, rather the individual antibiotic classes making up the antibiotic mixture will be reported.

Improved manual curation

  • manual curation (argannot): (Tet)tetH:EF460464:6286-7839:1554 was incorrectly annotated as ARO:3004797 which is a beta-lactamase due to a loose RGI hit. This was manually curated to ARO:3000175.
  • Improved curation:
    • resfinder_curation: grdA_1_QJX10702 -> 3007380 & EstDL136_1_JN242251 -> 3000557
    • megares_curation: MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD -> 3000557

Bugfixes

  • confers_resistance_to() now gets drugs information even if it is encoded at a higher level in the ARO. For example, OXA-19 previously only returned cephalosporin and penam, but now will also return oxacillin (from AMR gene family).
  • drugs_to_drug_classes() now correctly only returns the immediate child of 'antibiotic molecule' as the drug class (this was previously not the case for certain corner cases).
  • inconsistent ARO versions deeparg, megares, resfinderfg & sarg curation: ARO:3004445 -> ARO:3005440, this was due to a change in the ARO and the ARO number for the RSA2 gene changing, but the version of ARO bundled with argNorm was out of sync.

INTERNAL CHANGES

  • AROs were previously handled as integers in the get_aro_mapping_table() function and this posed challenges when ARO numbers such as 'ARO:0010004' (leading zeros leading to issues). To fix this, AROs are now treated as strings so leading zeros can be maintained.