10March09 Phone Conference

From GO Wiki
Jump to navigation Jump to search


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

Return to Reference_Genome_Annotation_Project