Ontology meeting 2016-11-10: Difference between revisions

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===Modified Proteins Proposal===
===Modified Proteins Proposal===
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives.
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives.  
 


# Continue to add these terms by hand. Unsustainable?
# Continue to add these terms by hand. Unsustainable?
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# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.
We discussed three possible semantic interpretations of modified protein binding terms:
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h
Number 2 in this list - binds to the modified part of a protein - had the most support.  Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is).


[[Category:Ontology]]
[[Category:Ontology]]
[[Category:Meetings]]
[[Category:Meetings]]

Revision as of 10:10, 8 November 2016

Attendees:

Minutes:

Regrets:

GoToMeeting invite: https://global.gotomeeting.com/join/859015101

Debrief from GOC meeting: ontology group update and breakout session on ontology priorities

For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#

Discussion of 'positive regulation' and 'maintenance' from last annotation call

See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2

Modified Proteins Proposal

The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives.


  1. Continue to add these terms by hand. Unsustainable?
  2. Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.
  3. Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.
  4. Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.

We discussed three possible semantic interpretations of modified protein binding terms:

https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h

Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain

For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is).