[babel-tools] Re: Bug found with clique descriptions in NodeNorm 2.3.27 on RENCI Dev, to be fixed on Monday

Hi everybody,

With everything going on in end-Nov, I completely forgot to actually merge this. Thanks to Evan for pointing out the descriptions are still broken. I’ve just deployed NodeNorm v2.4.1 to RENCI Dev [1] with those fixes as well as some new features (see full release notes [2]):

• Set DrugChemical conflation to be active by default
• Remove leading/trailing whitespace from CURIEs before normalization
• (v2.3.27) NEW BUG: description accidentally moved from result['id']['description'] to result['description']
  • (v2.3.28) Fixed description bug introduced in NodeNorm v2.3.27
• Add an include_taxa field (default: True) that will return the list of taxa for a clique and equivalent identifiers
• Load a particular version of Biolink Model as per BIOLINK_MODEL_TAG
• Replaced RDB reader to support newer versions of Redis.
• Improved documentation:
  • Improve conflation documentation on API endpoints
  • Added NCBIGene:1756 to the list of examples
  • Update NodeNorm Jupyter Notebook
  • Added an "Open in Colab" button to NodeNorm Jupyter Notebook
  • Add Zenodo button

Please let me know if anybody runs into any problems with the new NodeNorm!

cheers, Gaurav

[1] https://nodenormalization-sri.renci.org/docs [2] https://github.com/NCATSTranslator/NodeNormalization/blob/master/releases/v2...

On Nov 26, 2025, at 3:05 PM, Vaidya, Gaurav <gaurav@renci.org> wrote:

Hi everybody!

Hina Shah found a bug in NodeNorm 2.3.27 (currently deployed to RENCI Dev [1]) -- when I added the include_taxa flag, I accidentally moved the description field [2] so that it moved from result['id']['description'] to result['description’]. Sorry about that!

I'm not going to modify NodeNorm Dev the day before Thanksgiving, but I'll fix this on Monday (Dec 1, 2025) and release this as NodeNorm v2.3.27 unless there any objections. My planned fix is:

1. To move the description field back into id.
2. To add a root-level descriptions (not description) field that includes all the descriptions known for a particular clique.

Please let me know if you disagree with this fix (either here or on the issue), or if you would like me to hold off on this update.

cheers, Gaurav

[1] https://nodenormalization-sri.renci.org/docs [2] https://github.com/NCATSTranslator/NodeNormalization/issues/345