NodeNorm has always calculated the preferred name for a clique itself, even though we need to calculate this in Babel so we can use it in NameRes:
https://github.com/TranslatorSRI/NodeNormalization/blob/13ba01efc06ba73d0e9ebacb7c8d277c8f4e680b/node_normalizer/normalizer.py#L707-L736
This means we need to manually keep this in sync with Babel.
As we redesign NodeNorm's database to add clique-level properties (#302), we should see if we can use the preferred name from the compendium files instead of having to recalculate them here.
Update: PR #386 updated NodeNorm to use the Babel preferred name where available, but we fallback to the old (buggy -- see #396) logic if a preferred name is not present. Once I confirm that everything has a preferred name (NCATSTranslator/Babel#940), we can remove this code entirely.
NodeNorm has always calculated the preferred name for a clique itself, even though we need to calculate this in Babel so we can use it in NameRes:
https://github.com/TranslatorSRI/NodeNormalization/blob/13ba01efc06ba73d0e9ebacb7c8d277c8f4e680b/node_normalizer/normalizer.py#L707-L736
This means we need to manually keep this in sync with Babel.
As we redesign NodeNorm's database to add clique-level properties (#302), we should see if we can use the preferred name from the compendium files instead of having to recalculate them here.
Update: PR #386 updated NodeNorm to use the Babel preferred name where available, but we fallback to the old (buggy -- see #396) logic if a preferred name is not present. Once I confirm that everything has a preferred name (NCATSTranslator/Babel#940), we can remove this code entirely.