Ontology meeting 2012-02-22

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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.

See: https://sourceforge.net/tracker/index.php?func=detail&aid=3487992&group_id=36855&atid=440764

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

From Marcus:

  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.