Ontology meeting 2014-12-09: Difference between revisions

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Everyone please take a look at AIs here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-11-20
Everyone please take a look at AIs here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-11-20
=== Follow-up from last week as Chris and David OS were away: 'Response to' terms again ===
From this week's assert report:
ADD GO:0097044 'histone H3-K56 acetylation in response to DNA damage' GO:0043200 'response to amino acid'
This seems to come from GO:0097044 being descendant of 'response to stimulus' and having an amino acid as input... same as the logical def of 'response to amino acid'.
This is an interesting case. Is the inference too broad for our liking, or are we happy to keep it? If the former, how do we restrict the ancestor?
  Should not be 'response to amino acid.' Wrong genus is asserted for one of the terms between 'response to amino acid' and 'GO:0097044', fix that.
  The term 'peptidyl-amino acid modification' needs to be sorted out, has_input to 'amino acid residue.' 
  Action item:  Jane will consult with Gareth @ ChEBI about which
  ChEBI term to use for the logical def. What is the difference between 'peptidyl-amino acid' and 'amino-acid residue'?  In common usage, these would
  be the same.  What was ChEBI's intention?  Ex. ubiquitinated proteins vs. 'normal' protein chain (alpha peptide chain)?  What about amino acid
  derivative vs. modified amino acid?  Sort out implications for GO. 
  Problem is broader.  Has_input as a relationship for 'response to x' results in the inability to specify 'what' is being responded to.  In this example,
  we'd expect 'damaged DNA' as the input.  ChEBI is not likely to have 'damaged DNA' as an entry.  Need a different relationship, 'responds to' perhaps.
  Action Item (not Amelia Ireland):  Chris and DOS to comment on 'responds to'
  Chris emails:
  "Usual issue. Either: (1) make response and metabolic response disjoint (2) Make a distinct relation for every possible genus
  I favor (1)"




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

Revision as of 09:19, 8 December 2014

Attendees:

Minutes:


Enzyme binding PUNTED

We agreed to obsolete 'DNA methyltransferase binding' from the TG queue a couple of weeks ago, we need to follow up with a plan for how to handle the existing terms in this branch, and guidance as to whether annotators request these terms. They've asked for us to report back on an annotation call.

Axiomatizing multi-organism processes PUNTED

We've agreed it's a good idea to try and axiomatize at least some of these terms before I leave. We need to agree which relationship I should use - can I go ahead and use regulates or do we need the more specific regulates_in_other_species?

Follow-ups from last call PUNTED

Everyone please take a look at AIs here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-11-20

Follow-up from last week as Chris and David OS were away: 'Response to' terms again

From this week's assert report:

ADD GO:0097044 'histone H3-K56 acetylation in response to DNA damage' GO:0043200 'response to amino acid'

This seems to come from GO:0097044 being descendant of 'response to stimulus' and having an amino acid as input... same as the logical def of 'response to amino acid'.

This is an interesting case. Is the inference too broad for our liking, or are we happy to keep it? If the former, how do we restrict the ancestor?

  Should not be 'response to amino acid.' Wrong genus is asserted for one of the terms between 'response to amino acid' and 'GO:0097044', fix that.
  The term 'peptidyl-amino acid modification' needs to be sorted out, has_input to 'amino acid residue.'  
  Action item:  Jane will consult with Gareth @ ChEBI about which 
  ChEBI term to use for the logical def. What is the difference between 'peptidyl-amino acid' and 'amino-acid residue'?  In common usage, these would
  be the same.  What was ChEBI's intention?  Ex. ubiquitinated proteins vs. 'normal' protein chain (alpha peptide chain)?  What about amino acid
  derivative vs. modified amino acid?  Sort out implications for GO.  
  Problem is broader.  Has_input as a relationship for 'response to x' results in the inability to specify 'what' is being responded to.  In this example,
  we'd expect 'damaged DNA' as the input.  ChEBI is not likely to have 'damaged DNA' as an entry.  Need a different relationship, 'responds to' perhaps.
  Action Item (not Amelia Ireland):  Chris and DOS to comment on 'responds to'
  Chris emails: 
  "Usual issue. Either: (1) make response and metabolic response disjoint (2) Make a distinct relation for every possible genus
  I favor (1)"