Ontology meeting 2012-06-20

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Minutes: Jane

CHEBI alignment

Following up from call of June 6th:

  • Do we need 'carbohydrate derivative metabolism' and such in GO so that we can group the CHO-phosphate terms under these as they will not go under carbohydrate metabolism anymore?
  • We think that the best course of action for the EXISTS, NOT ENTAILED links is for a couple of GO curators to work these out with the ChEBI curators. Tanya and David have spreadsheet to show EBI curators along with some issues encountered along the way. Ideally, someone at the EBI can meet with a ChEBI curator and resolve the outstanding issues in person instead of long email back and forth or SF discussions.


'Transports' relationship for RO

For ChEBI alignment, bio-chebi doesn't include equivalence GCIs for the results_in_transport_of relation, so it won't bridge the conjugate base path.

Example of resulting problem (bunch of lines in reasoner-diff report like this):

  EXISTS, NOT-ENTAILED    SubClassOf(GO:0000101    sulfur amino acid transport    GO:0006865    amino acid transport
  even when sulfur-containing aa is_a aa in ChEBI.  
  [Term]
  id: GO:0000101 ! sulfur amino acid transport
  intersection_of: GO:0006810 ! transport
  intersection_of: results_in_transport_of CHEBI:26834 ! sulfur-containing amino acid
  http://www.ebi.ac.uk/chebi/searchId.do;5345C2899EA5516DAE172F14D6816380?chebiId=CHEBI:26834

We need to get the generic transport relation into RO and then we'll put the axioms in bio-chebi.owl. We need something that can be used for both transport and localization.

Candidates:

  "transports_or_maintains_localization_of"

Cell Cycle Meeting?