rename 33252 to "atomic nucleus"

[muthuvenkat]

Hello,

One of the principles discussed at the OBO Foundry Summit is that we shouldn't have names clashing between ontologies. So could we have nucleus CHEBI:33252 renamed to "atomic nucleus" to avoid the clash with GO?

I will be asking GO to rename theirs to "cell nucleus".

best wishes, Colin.

Reported by: batchelorc

[muthuvenkat]

Logged In: YES user_id=802919 Originator: NO

I agree that the terms have to be made completely unambiguous within given domain (ontology). There is no way that all ontologies in the world should constantly checking each other for homonyms. Therefore, it is perfectly valid to call atomic nucleus just "nucleus" within ChEBI namespace (even though I am not particularly opposed to adding "atomic nucleus" as a synonym). Similarly, it is valid to call ChEBI's "L-valine residue" simply "valine" within sequence ontology because sequence people do not care about anything that is not found in sequences. It is unacceptable to name "L-valine" just "valine" within GO though because GO deals with both small and macromolecules.

Kirill

Original comment by: kiri11

[muthuvenkat]

Logged In: YES user_id=1473024 Originator: YES

"nucleus" is not unambiguous within chemistry, as a quick search for "pyrrole nucleus", "pyridine nucleus", "thiophene nucleus", etc., will attest.

Colin.

Original comment by: batchelorc

[muthuvenkat]

Logged In: YES user_id=802919 Originator: NO

Standalone "nucleus" in chemical text is unambiguous: it always means "atomic nucleus". In "pyrrole nucleus", "nucleus" on its own does not mean much. (On the contrary, in "pyrrole ring", "ring" has its own standalone meaning.)

But, just to make you happy, I've renamed "nucleus" to "atomic nucleus", that will appear in next ChEBI release.

Original comment by: kiri11

[muthuvenkat]

• status: open --> closed

Original comment by: kiri11