RLS Version 0.5.0

Updated the 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 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.

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Unreleased
+## 0.5.0 - 26 June 2024
 
 ### Update drug categorization
 - confers_resistance_to() now gets drugs for the whole AMR gene family. For example, OXA-19 previously only returned cephalosporin and penam, but now will also return oxacillin (from AMR gene family).
@@ -18,9 +18,10 @@
 - megares_curation: MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD -> 3000557
 
 ### Handle AROs as string rather than int in get_aro_mapping_table()
+
 AROs were previously handled as 'int' in the get_aro_mapping_table() function and this posed challenges when ARO numbers such as 'ARO:0010004' (leading zeros are cut). To fix this, AROs are now treated as strings so leading zeros can be maintained.
 
-## 0.4.0 - 10 June
+## 0.4.0 - 10 June 2024
 
 - Bundle a specific version of ARO with the package instead of downloading it from the internet (ensures reproducibility)
 - Add missing ARO mappings to manual curation.

docs/whatsnew.md

@@ -1,5 +1,30 @@
 # What's New
 
+ArgNorm is under active development and outputs may change between versions. Particular versions of argNorm should, however, be reproducible as the databases are bundled with the tool.
+
+## 0.5.0 - 25 June 2024
+
+### 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 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.
+
 ## 0.4.0 - 10 June
 
 ### User-facing changes

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='argnorm',
-    version="0.4.0",
+    version="0.5.0",
     author='ArgNorm Developers',
     author_email='luispedro@big-data-biology.org',
     url="https://github.com/BigDataBiology/argNorm",