10March09 Phone Conference

Present

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

Agenda for Oregon Meeting

http://wiki.geneontology.org/index.php/Oregon_Reference_Genomes_Meeting

Paper

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

https://sourceforge.net/tracker/index.php?func=detail&aid=2635152&group_id=36855&atid=440764

• 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:

https://sourceforge.net/tracker/index.php?func=detail&aid=2654263&group_id=36855&atid=440764

PAINT update

• http://wiki.geneontology.org/index.php/RefGenProgress_2009-02

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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