peptide (MSO:0000104)

[nataled]

If ever there was a term I'd like to see retired forever, it's 'peptide'. Especially if used the way you're using it. That term has a loaded history, and one that has pretty much never been properly defined (being as it was based on a multitude of different length cut-offs). I went through that whole peptide vs. polypeptide vs protein vs protein complex mess in the early-to-mid days of PRO. I was quite unsatisfied with how ChEBI used it because it has 'protein polypeptide chain' as a descendent, and never in the history of the usage of 'peptide' could a protein be considered one. In the end I settled on a neutral term, "amino acid chain" (see definition here: http://purl.obolibrary.org/obo/PR_000018263 ).

By the way, there was once an issue raised many years ago about the fact that ChEBI even has 'protein' or similar terms. The issue was that the term was out of scope of that ontology. I met with them at that time and they agreed that PRO should own that term. They never did remove it though. Mostly that's because ChEBI the database needed it. Anyway, there might come a time when that issue is raised again, so just be aware of it.

[cmungall]

is there a CHEBI ticket to remove it?

[nataled]

This was the issue you raised close to 10 years ago. Not sure if there's a ticket for it anymore. There were a bunch of issues they mentioned at the time, one of which was that they had users that relied on those terms (at least the ones sitting below 'protein').

[mikebada]

I think that the provenance of the ChEBI modeling is chemistry nomenclature, specifically the IUPAC Gold Book, which defines peptides as chains of two or more amino-acid residues. MSO:peptide seems equivalent to PR:'amino acid chain'. I wouldn't particularly mind calling them amino acid chains instead (though I think it'd be good to at least have "peptide" as a synonym).

[nataled]

Indeed, we have "peptide" and "polypeptide" as narrow synonyms.