Difference between revisions of "Annotation Call July 22 2014"

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(Col-16 Questions)
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==Agenda==
 
==Agenda==
  
===Col-16 Questions===
+
===Col-16 Questions (SGD)===
 
* PMID: 11486005
 
* PMID: 11486005
 
** Snf1 requires Snf4 for full kinase activity - it's unclear how Snf4 contributes to full Snf1 activity) is_regulated_by is not allowed any more. In this case I could use in_presence_of or dependent_on. Which one is correct?
 
** Snf1 requires Snf4 for full kinase activity - it's unclear how Snf4 contributes to full Snf1 activity) is_regulated_by is not allowed any more. In this case I could use in_presence_of or dependent_on. Which one is correct?
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  has_input: [ID of ubiquitin ligase enzyme]
 
  has_input: [ID of ubiquitin ligase enzyme]
 
  has_regulation_target: [ID of protein being ubiquitinated]
 
  has_regulation_target: [ID of protein being ubiquitinated]
 
  
 
===IPI evidence code for annotating CC complex formation===
 
===IPI evidence code for annotating CC complex formation===

Revision as of 14:03, 16 July 2014

Agenda

Col-16 Questions (SGD)

  • PMID: 11486005
    • Snf1 requires Snf4 for full kinase activity - it's unclear how Snf4 contributes to full Snf1 activity) is_regulated_by is not allowed any more. In this case I could use in_presence_of or dependent_on. Which one is correct?
    • Snf1 doesn't phosphorylate Mig1 during during salt stress) not_happens_during is not an option any more. What is the correct relationship for this? independent_of doesn't seem right
  • PMID: 15652479
    • ste20 is localized to the nucleus when cells are treated with H2O2.

This was originally captured as: Ste20 - nucleus - during:GO:0070301 (cellular response to hydrogen peroxide)

"During" is not allowed in this case, the suggested replacement is exists_during, which doesn't sound right. Does localization_dependent_on fit here or should we use exists_during?


  • Can we can specify both the direct target and the downstream modified protein for BP terms such as this example from PMID:24899725:
negative regulation of protein ubiquitination ; GO:0031397
has_input: [ID of ubiquitin ligase enzyme]
has_regulation_target: [ID of protein being ubiquitinated]

IPI evidence code for annotating CC complex formation

Are we annotating consistently with the guidelines for IPI? The documentation says:

Examples where the IPI evidence code should not be used:
Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA, not IPI with the ID corresponding to the tagged subunit in the with/from  column because not all subunits of the complex interact directly with the tagged subunit. Thus this type of assay can provide IDA for annotation to a component term for the specific complex because it is a direct assay for a complex, but it would not necessarily be true to say that all members of the complex interact directly with the tagged subunit.

But there are alot of (some recent) annotations to protein complexes using the IPI evidence code.


rehousing annotations to Cell cycle phase term

We are trying a new approach to help groups rehouse annotations. We will deal with one term at a time. Highlight what the issues are etc so the groups can focus and not be overwhelmed. We can also highlight this term on the GOC website (why we can't have direct anotations to this term etc).

Cell cycle phase should not be used any more for manual annotations.