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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