ENH Update drug categorization logic #51
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Vedanth-Ramji
commented
Jun 17, 2024
Vedanth-Ramji
commented
- Navigate up entire ARO tree for genes so drugs of gene families can be included
- Antibiotic mixture ARO mapping is excluded except cases of antibiotic + adjuvant mixtures
- Use 'has_part' relationship to handle antibiotic mixtures and give drug class rather than 'antibiotic mixture'
- Navigate up entire ARO tree for genes so drugs of gene families can be included - Antibiotic mixture ARO mapping is excluded except cases of antibiotic + adjuvant mixtures - Use 'has_part' relationship to handle antibiotic mixtures and give drug class rather than 'antibiotic mixture'
luispedro
requested changes
Jun 17, 2024
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Besides the inline comments, there are no tests and no CHANGELOG entry.
Somewhere in the code, there should be some description of what the rules are because I thought we had agreed on something different than this is implementing. Ideally, this should be in the tests, so that it's actual code that checks the results not just English language text (e.g., Gramicidin should be aminoglycose only; the beta lactam+beta lactamase inhibitors should be beta lactam; ...)
Major changes: - navigate_superclasses() renamed to _get_drug_classes() - remove 'is_small_inhibitor_molecule_rel' and never return antibiotic mixture
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