10March09 Phone Conference: Difference between revisions

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* Adding relationships to binding terms in the ontology for enzymes and their substrates : Pascale spoke to Jane- the ontology group will look into that.  
* 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
* 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
* obsolete 'ATP-dependent proteolysis: Not closed yet, why?
* Karen: obsolete 'ATP-dependent proteolysis: Not closed yet, why?
https://sourceforge.net/tracker/index.php?func=detail&aid=2635152&group_id=36855&atid=440764
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? Should it be brought up at the GOC meeting?
* Debbie : to circulate where in the documentation it says not to annotate to binding
* Ruth: proteolysis synonyms
* Issue with terms 'peptidolysis v proteolysis and peptidase v protease'- did anyone look at those?


==PAINT update==
==PAINT update==

Revision as of 15:07, 9 March 2009

Present

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?

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? Should it be brought up at the GOC meeting?
  • Debbie : to circulate where in the documentation it says not to annotate to binding
  • Ruth: proteolysis synonyms
  • Issue with terms 'peptidolysis v proteolysis and peptidase v protease'- did anyone look at those?

PAINT update



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?

Annotating biochemical pathways

Setting up a working group


Next conference call

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


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