10March09 Phone Conference
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:
We dont know when we'll be able to use the tool for annotation yet.
- 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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