Ontology meeting 2016-01-21: Difference between revisions

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   build to break, we can now examine them. The problem described in  
   build to break, we can now examine them. The problem described in  
   [[GH12235|https://github.com/geneontology/go-ontology/issues/12235]] was one result that was troubling.  See this ticket.   
   [[GH12235|https://github.com/geneontology/go-ontology/issues/12235]] was one result that was troubling.  See this ticket.   
   Basic pattern is 'negative regulation of xx by negative regulation of yy'.
   Basic pattern is 'negative regulation of xx by negative regulation of yy' inferred SubClassOf: positive regulation of xx. 
  This was due to a badly designed TG template (since removed by Heiko). But the bigger problem is that this is just too
  much complexity to pack into a term.  All agreed ee should get rid of the terms we have and not allow more.  


   DavidH/KMV are annotating in LEGO but GAFs produced are not being consumed. Heiko working on tweaking GAF DOS suggests 
   There are 22 terms following this pattern.  We have decided to obsolete all that have no annotations ASAP.
  making LEGO diagrams for the annotations using each of the xx outstanding terms (see GH ticket) to clarify.  Inference
  For those that have annotations,  as a temporary measure we will delete the Equivalence axioms
  from the GAF would give multiple relevant parent classes. Remove those terms.  It is possible to roll a whole pathway
  that cause the problem and manually assert classification.  We will then request re-annotation for all existing annotations,
   into a term like this but it doesn't really make sense to do that. In the meantime, assert two is_a parents, both negative,
  preferably via construction of a LEGO model -> production of inferred annotations in GAF would give annotation to  the relevant  
  delete the equivalent class expression and work out what assertions to add directly.  In cases w/o anntotaions, just send
  parent classes.
  out obsoletion notice.
    
 
  Discussion of practicality of doing this in LEGO:
  GAF from LEGO status:  Most primitive thing is there. Sometimes we want more than just the basic inference.  The whole part
  When will be able to do this?  
  where we go to deeper terms, use inferencing features, is taking longer.  What do we state in the model and what do we infer?
  GAF from LEGO status:  Basic inference already works. This is probably sufficient for the models we need for this issue.
  Needs discussion. Something stable is needed by the end of the month will be out for KMW to consume.  Less than 2 weeks to the
  But sometimes we want more than just the basic inference.  T
  basic version.
  The whole part where we go to deeper terms, use inferencing features, is taking longer.  What do we state in the model and what do we infer?
  Needs discussion. Something stable is needed by the end of the month will be out for KMW to consume.  Less than 2 weeks to the
  basic version.


== DNA methylation and gene expression ==
== DNA methylation and gene expression ==

Revision as of 13:59, 21 January 2016

Attendees: DavidH, DavidOS, Harold, Heiko, Melanie, Paola, Tanya

Minutes: Tanya


Fun with regulates axioms

https://github.com/geneontology/go-ontology/issues/12235 

 400 some new inferences after Chris added some regulates axioms before the holiday break. After fixing what was causing the
 build to break, we can now examine them. The problem described in 
 https://github.com/geneontology/go-ontology/issues/12235 was one result that was troubling.  See this ticket.  
 Basic pattern is 'negative regulation of xx by negative regulation of yy' inferred SubClassOf: positive regulation of xx.  
 This was due to a badly designed TG template (since removed by Heiko). But the bigger problem is that this is just too 
 much complexity to pack into a term.  All agreed ee should get rid of the terms we have and not allow more. 

 There are 22 terms following this pattern.  We have decided to obsolete all that have no annotations ASAP.
  For those that have annotations,  as a temporary measure we will delete the Equivalence axioms 
  that cause the problem and manually assert classification.  We will then request re-annotation for all existing annotations, 
  preferably via construction of a LEGO model -> production of inferred annotations in GAF would give annotation to  the relevant 
  parent classes.
 
 Discussion of practicality of doing this in LEGO:
  When will be able to do this?  
  GAF from LEGO status:  Basic inference already works. This is probably sufficient for the models we need for this issue.
  But sometimes we want more than just the basic inference.  T
  The whole part  where we go to deeper terms, use inferencing features, is taking longer.  What do we state in the model and what do we infer?
  Needs discussion. Something stable is needed by the end of the month will be out for KMW to consume.  Less than 2 weeks to the
  basic version.

DNA methylation and gene expression

Stemming from latest assert report (the same one with the negative by negative terms) 

 ADD	GO:1901535 'regulation of DNA demethylation' GO:0010468 'regulation of gene expression'

because 'DNA demethylation' (and 'DNA methylation') is_a 'regulation of gene expression, epigenetic'. Should it be part_of instead? 

 DOS: I have a mini project going on this topic.  From discussion with Ruth and Karen, we agreed that a regulates relation should apply between 'chromatin modification' and 'epigenetic regulation of gene expression'
 Long confusing umbrella ticket here:  https://github.com/geneontology/go-ontology/issues/11628

 How about: DNA methylation is_a regulates gene expression?
 DNA methylation part_of regulation of gene expression, epigenetic
 Disentangle 'regulation of gene expression, epigenetic' into its parts.
 DNA methylation vs. DNA demethylation and their relationships to regulation of gene expression, epigenetic.
 DOS: Looking at definition of 'reg of gene expression', the definition is consistent with the current placement of DNA 
 methylation.
 For now, go with part_of. 'DNA de/methylation' part_of 'regulation of gene expression, epigenetic'
 DH: Discomfort with regulates o part_of. Imagines that this will be disastrous in LEGO models. Where molecular functions
 that are part of the same signal transduction pathway may have a directly activates relation between them. We wouldn't want to
 infer that they regulate the pathway. 
 Consult with Val?
 Use 'causally upstream of' as a solution? More general than 'regulates' and won't have grouping.
 DH: another example, restriction enzyme system in bacteria, methylation causes inability for REs to cut - DNA methylation 
 is not always linked to 'regulation of gene expression, epigenetic' - Kills the part_of solution as this is not always true.
 PMID:6243774

Latest assertions

The list in yesterday's assert report (email "[go-ontology] build-go-assert-inferences - Build # 173 - Fixed!") is really long, 402 added axioms presumably as a result of the synapse branch merge. Has anyone had a chance to review them all? 


 DOS: Inferences from synapse branch merge reviewed.
 Many inferences also come from the change to regulation axiomatisation.
 I have reviewed these briefly.  Some problematic ones are flagged in
 https://github.com/geneontology/go-ontology/issues/12235

 AI: Everyone else look through report for odd references.

Logical definitions for 'response to chemical' terms

Logical defs for 'response to chemical' terms point to 'response to stimulus', while 'cellular response to chemical' points to 'cellular response to chemical stimulus':

id: GO:1903842

name: response to arsenite ion

intersection_of: GO:0050896 ! response to stimulus

intersection_of: has_input CHEBI:22633 ! arsenite ion

relationship: has_input CHEBI:22633 {is_inferred="true"} ! arsenite ion

but

id: GO:1903843

name: cellular response to arsenite ion

intersection_of: GO:0070887 ! cellular response to chemical stimulus

intersection_of: has_input CHEBI:22633 ! arsenite ion

relationship: has_input CHEBI:22633 {is_inferred="true"} ! arsenite ion

Was this intentional - shouldn't the former point more specifically to 'response to chemical'? (which is_a 'response to stimulus') Of course, the 'response to chemical' parentage is inferred anyway.

DOS RESPONSE: [note - DH suggested the same]

Non-redundant classification is correct:

This equivalence axioms takes care of the correct classification of 'response to arsenite ion' under 'response to chemical':

  • 'response to chemical' EquivalentTo 'response to stimulus' and ('has input' some 'chemical entity')

We don't yet have axiomatisation to deal with the 'cellular bit' - hence the more specific genus in this case. But if we agree that all cellular response occurs in some cell we could have:

  • 'cellular response to stimulus' EquivalentTo: 'response to stimulus' and occurs in some cell
  • 'cellular response to chemical stimulus' EquivalentTo: 'response to stimulus' and occurs in some cell and has_input some 'chemical entity'
  • 'cellular response to arsenite ion' EquivalentTo: 'response to stimulus' and occurs in some cell and has_input some 'arsenite ion'

The reasoner would then look after classification completely. 

 AI: DOS will check with Val whether she's comfortable with 'occurs in' some cell.

movement, transport, establishment of localization

See this document that DOS put together: https://docs.google.com/document/d/1mLuIbLGo9MApOVBeELzqaalKDcLG0xZthWnporGVkCg/edit?usp=sharing

also:

https://github.com/geneontology/go-ontology/issues/9189 which brings up issues with 'establishment of localization' and 'transport'

DOS' work in this area should clear up that issue as well. More discussion needed. 

 Melanie suggests using synonyms and using 'community of usage' as a property. "you can them extract specific slims for your users
 with their preferred labels" Might that be a solution?
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