Difference between revisions of "Ontology meeting 2014-12-02"

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Attendees:
Attendees: Harold, DavidH, Paola, Heiko, Tanya, Jane


Minutes:
Minutes: Tanya


===Enzyme binding===
===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.
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===
===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?
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 ===
=== 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
Everyone please take a look at AIs here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-11-20
=== '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)"
=== Protein oligomerization ===
One bit of the proposal was about adding ‘protein homodimer’ and ‘protein heterodimer’ directly under ‘protein complex’. (This wasn’t my own idea, it came from others and was incorporated along.) Could we please pick your brains about persuading PRO to add these terms instead? Curators could then use them to annotate, e.g. has_quality = dimer?
For reference, here are the latest comments on this subject only:
Jane:
- Not ok with having 'protein homodimer' etc. live in GO ‘cellular component’. Is there any scope for persuading PRO to add 'protein heteromer' etc?
Val:
- Like Jane I would also be worried about classifying complexes by their stoichiometry. It sounds unmaintainable, it would definitely result in inconsistent annotation, and would not add much value for the effort it took. How would you cope with things which have a homo/hetero-dimer component but with additional subunits which are not always identified/associated? For instance Smc5-6 forms a heterodimer, but is part of the larger Smc5-6  complex with additional subunits. For me, it’s just too complicated to contemplate unless you have unlimited resources, and probably not a good use of editorial time... it could easily suck up an entire FTE...
(Even though I dislike them, I think the current MF binding terms are a better short term solution)
Peter:
- This stoichiometry issue sounds like something to add to the re-opened negotiation with PRO, on the general principle that GO covers classes of things while PRO takes on the job of covering specific instances like the variant forms of a complex that arise because it can sometimes (in some states, in some taxa) pick up an additional component or change its stoichiometry.
That doesn’t make the resulting data structure any easier to assemble or maintain, but PRO has definitely put a lot of effort into exactly this issue of capturing species- and state-specific differences in the exact makeup of a complex.
--------------
  For process terms, protein oligomerization, P will look and see how many bad annotations there are, where protein ends up as an oligomer, doesn't have
  that role.  Will send that out to the groups and will propose obsoletion of all children under protein complex assembly. P will look at split
  between DBs, may ask for help.  Poll the annotators for usage. If usage is different, proceed with plan to merge into protein binding. Looks
  like mostly Uniprot and MGI.  Uniprot will not be able to change them for
  months.  Perhaps we can ask for UniProtKB permission to change the annotations.  Will try to do this.
  New terms: 'protein heterodimer' and 'protein homodimer' not in GO but PRO?  Pragmatically, this might be the best solution.




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

Latest revision as of 07:35, 3 December 2014

Attendees: Harold, DavidH, Paola, Heiko, Tanya, Jane

Minutes: Tanya

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

'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)"

Protein oligomerization

One bit of the proposal was about adding ‘protein homodimer’ and ‘protein heterodimer’ directly under ‘protein complex’. (This wasn’t my own idea, it came from others and was incorporated along.) Could we please pick your brains about persuading PRO to add these terms instead? Curators could then use them to annotate, e.g. has_quality = dimer?

For reference, here are the latest comments on this subject only:

Jane: - Not ok with having 'protein homodimer' etc. live in GO ‘cellular component’. Is there any scope for persuading PRO to add 'protein heteromer' etc?

Val: - Like Jane I would also be worried about classifying complexes by their stoichiometry. It sounds unmaintainable, it would definitely result in inconsistent annotation, and would not add much value for the effort it took. How would you cope with things which have a homo/hetero-dimer component but with additional subunits which are not always identified/associated? For instance Smc5-6 forms a heterodimer, but is part of the larger Smc5-6 complex with additional subunits. For me, it’s just too complicated to contemplate unless you have unlimited resources, and probably not a good use of editorial time... it could easily suck up an entire FTE... (Even though I dislike them, I think the current MF binding terms are a better short term solution)

Peter: - This stoichiometry issue sounds like something to add to the re-opened negotiation with PRO, on the general principle that GO covers classes of things while PRO takes on the job of covering specific instances like the variant forms of a complex that arise because it can sometimes (in some states, in some taxa) pick up an additional component or change its stoichiometry. That doesn’t make the resulting data structure any easier to assemble or maintain, but PRO has definitely put a lot of effort into exactly this issue of capturing species- and state-specific differences in the exact makeup of a complex.


  For process terms, protein oligomerization, P will look and see how many bad annotations there are, where protein ends up as an oligomer, doesn't have
  that role.  Will send that out to the groups and will propose obsoletion of all children under protein complex assembly. P will look at split 
  between DBs, may ask for help.  Poll the annotators for usage. If usage is different, proceed with plan to merge into protein binding. Looks 
  like mostly Uniprot and MGI.  Uniprot will not be able to change them for 
  months.  Perhaps we can ask for UniProtKB permission to change the annotations.  Will try to do this.
  New terms: 'protein heterodimer' and 'protein homodimer' not in GO but PRO?  Pragmatically, this might be the best solution.