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#11495 query parent GO:0000297 spermine transmembrane transporter activit

PomBase
closed
5
2015-03-09
2015-02-02
No

GO:0000297 spermine transmembrane transporter activity
has
ammonium transmembrane transporter activity
as a parent, is that correct? it seems odd?

Discussion

  • Paola Roncaglia

    Paola Roncaglia - 2015-02-04

    Hi Val,

    I'm attaching a screenshot of the explanation in Protege.

    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2015-02-04
    • labels: --> Other term-related request, transport, chemicals
    • Description has changed:

    Diff:

    --- old
    +++ new
    @@ -1,4 +1,3 @@
    -
    
      GO:0000297 spermine transmembrane transporter activity
     has 
    
    • assigned_to: Paola Roncaglia
    • Group: None --> PomBase
     
  • Valerie Wood

    Valerie Wood - 2015-02-06

    OK I expected it to follow CHEBI spermine rather than spermine(4+)?
    attached, do you know why we don't?

    But, I would also expect CHEBI to class spermine as a polyamine
    http://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:51349

     
  • Paola Roncaglia

    Paola Roncaglia - 2015-03-09

    Hi Val,

    Back to your question

    “I expected it to follow CHEBI spermine rather than spermine(4+) attached, do you know why we don’t?”

    It follows both… spermine and spermine(4+) are the conjugate acid/base pair. Similar issue as reported elsewhere, see e.g. the very bottom of https://sourceforge.net/p/geneontology/ontology-requests/11524/

    As for your other question

    “But, I would also expect CHEBI to class spermine as a polyamine”

    ChEBI classifies spermine as a tetraamine, but tetraamine (CHEBI:39166) is a organic amino compound (CHEBI:50047). I think that’s the missing link. I’ll add this comment to the ChEBI SF tracker you already opened:

    https://sourceforge.net/p/chebi/curator-requests/2424/

    Would you be ok with me closing this ontology ticket?

    Cheers,

    Paola

     
  • Valerie Wood

    Valerie Wood - 2015-03-09

    yep!

     
  • Paola Roncaglia

    Paola Roncaglia - 2015-03-09
    • Description has changed:

    Diff:

    --- old
    +++ new
    @@ -1,4 +1,3 @@
    -
      GO:0000297 spermine transmembrane transporter activity
     has 
     ammonium transmembrane transporter activity
    
    • status: open --> closed
     

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