10March09 Phone Conference

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Pascale, Judy, Kara, Susan, Ranjana, Kimberly, Mike, Stan, Doug, Ruth, Varsha, Donghui, Tanya

Agenda for Oregon Meeting



Paper got reviewed: there are a few relatively minor comments to address.

Action Items from electronic jamboree

  • GAF file generated from the wiki page: can everyone have a look and let us know if there are problems with the file?
  • Adding relationships to binding terms in the ontology for enzymes and their substrates : Pascale spoke to Jane- the ontology group will look into that.
  • modification-dependent protein catabolic process (GO:0019941) -Suggestion to add synonym as modification-initiated protein catabolic process ; also to add proteolysis as synonym to many terms as required
  • Karen: obsolete 'ATP-dependent proteolysis: Not closed yet, why? //Closed on 2009-03-13


  • Karen: Should we make organelle specific terms for processes [and functions?] that aren't mechanistically different but use different gene sets? This generated a long email discussion; is it resolved? Move to the GOC meeting. : Move to the GOC meeting.
  • Debbie : to circulate where in the documentation it says not to annotate to binding
  • Ruth: proteolysis synonyms: closed SF:


PAINT update

We dont know when we'll be able to use the tool for annotation yet.

TOP2 annotations

  • Explicit protocol for doing these types of annotations, what to put in evidence_with field, elaboration on the ppt document (doesn't have to be discussed in the call, if someone just wants to put up a document that we can all consult, that would be great) -requested by Tanya

IC from EXP versus IC from ISS

  • Stems from the electronic jamborees:
    • Mouse = carbamoyl-phosphate synthase (ammonia) activity (IMP) => urea cycle IC
    • Can we do = carbamoyl-phosphate synthase (ammonia) activity (ISS) => urea cycle IC
    • ie, does that give two meanings to IC? We can just be careful when we propagate annotations to use IC from EXP?
  • Agreement is that there is no need to annotate 'everything' if we are not sure that he pathways exist, for example.

Next conference call

Tuesday April 14, 2009, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST

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