Ontology meeting 2012-02-22
Jump to navigation Jump to search
Moving biological_process_xp_cellular_component into live GO
- Chris wants to start discussions on moving the logical definitions from scratch to the live GO.
[Term] id: GO:0070072 ! vacuolar proton-transporting V-type ATPase complex assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0016471 ! vacuolar proton-transporting V-type ATPase complex
ChEBI changes: modified amino acid
I've been thinking again about our use of the term 'modified amino acid', which both ChEBI and (from what you said earlier) GO seem to have used as a repository for any derivative of an amino acid. I now really need to tidy this up within ChEBI, but I need to know whether the changes that I'm thinking of would have an effect on the GO.
I would like the term 'modified amino acid' to be renamed in accordance with its original intended meaning, probably as 'modified canonical amino-acid residue' and then to populate it accordingly. The vast majority of the entries currently under 'modified amino acid' could be conveniently moved into one or other of two new disjoint classes of 'canonical amino-acid derivative' or 'non-canonical amino-acid derivative', both is_a children of 'amino-acid derivative'. (However, just what the parent of 'amino-acid derivative' would be I'm not quite sure about yet - we certainly couldn't use 'amino-acid derivative' is_a 'amino acid' because of the the inclusion of amides etc here. The 'canonical amino-acid derivative' and 'non-canonical amino-acid derivative' classes could have 'has_functional_parent' relationships to 'canonical amino acid' and 'non-canonical amino acid' terms respectively, both children of 'amino acid'.
<snip> What do you think? If I can make this work within ChEBI, would it also work within the GO?
One other thing that worries me, and that is with the terminology. Is 'canonical amino acid' synonymous with 'proteogenic amino acid' and if so which is generally preferred within the world of biology? If they are in fact subtly different, which would be the more appropriate term to use within our ontologies?
Meeting postponed since neither David nor Chris is available.