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TranslatorSRI / NodeNormalization

Service that produces Translator compliant nodes given a curie
MIT License
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Conflate Chirality? was: Two cliques for Coenzyme A #203

Open amykglen opened 1 year ago

amykglen commented 1 year ago

we noticed at the Relay today that the SRI Node Normalizer seems to have two cliques that both represent the concept 'Coenzyme A':

https://nodenorm.transltr.io/1.3/get_normalized_nodes?curie=PUBCHEM.COMPOUND:6816 https://nodenorm.transltr.io/1.3/get_normalized_nodes?curie=PUBCHEM.COMPOUND:87642

should these be merged to one clique?

cbizon commented 1 year ago

These are separate because they have differing inchikeys, i.e. different structures. In looking at the pubchem structures, it looks like the difference is in chirality. The 6816 has one bond that looks like it's being draw without chirality when the actual structure does have a chiral center. While we're looking at conflation, we could think about a chirality conflater. Of the chemical conflations that we've discussed chirality is maybe one where there is a large potential downside, since changes in chirality can have a large effect.

amykglen commented 1 year ago

Ah, interesting! Thanks. Hmm, should we close this issue? Or keep it open as a reminder to consider a chirality conflator?

cbizon commented 1 year ago

Yeah, good idea, let's leave it open. I updated the title to reflect the current state of the conversation.