Ontology meeting 2015-07-30: Difference between revisions

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Cytokine production terms are designed to record gene function where a genotype or stimulation of a cell believed to mimic endogenous activity of some gene product leads to observed changes in (extracellular) production of a cytokine by a cell. It is not clear if the change is due to increased expression or increased secretion. At the Barcelona meeting, it was decided, rightly I think, that most or all annotations to production terms should be annotations to regulation of production.  
Cytokine production terms are designed to record gene function where a genotype or stimulation of a cell believed to mimic endogenous activity of some gene product leads to observed changes in (extracellular) production of a cytokine by a cell. It is not clear if the change is due to increased expression or increased secretion. At the Barcelona meeting, it was decided, rightly I think, that most or all annotations to production terms should be annotations to regulation of production.  


The July 16th decision appears to be that there should be no annotation at all in these cases.  But, from the point of view of an immunologist, the inference that a particular gene product functions to the amount of some specific cytokine that a B-cell releases is a very important part of recording its cannonical function - irrespective of what we know about the mechanism.  Surely we should be recording this - Isn't this what the whole BP branch is for!
The July 16th decision appears to be that there should be no annotation at all in these cases.  But, from the point of view of an immunologist, the inference that a particular gene product functions to regulate the amount of some specific cytokine that a B-cell releases is a very important part of recording its cannonical function - irrespective of what we know about the mechanism.  Surely we should be recording this - Isn't this what the whole BP branch is for!


Assuming we move most existing annotation to regulation of production, this still  leaves the question of what to do with the existing terms - do we retain them and add a do not annotate tag, or at least a warning about their use.  The terms are also problematic in that, where there is regulation of translation or secretion of the factors in question, these annotations will not be grouped under regulation of production.  We need to think about better formalisation to overcome some of these issues...
Assuming we move most existing annotations to regulation of production, this still  leaves the question of what to do with the existing terms - do we retain them and add a do not annotate tag, or at least a warning about their use.  The terms are also problematic in that, where there is regulation of translation or secretion of the factors in question, these annotations will not be grouped under regulation of production.  We need to think about better formalisation to overcome some of these issues...


=== Follow-up: no more merges ===
=== Follow-up: no more merges ===

Revision as of 11:03, 29 July 2015

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General Guidance ?

Cytokine production and its regulation

DOS: Ruth and I are concerned about decisions taken regarding secretion/production terms at the July 16th editors meeting

First there seems to be some confusion between secretion terms and production terms. The ticket where this issue originated is clearly about production, not secretion:

https://sourceforge.net/p/geneontology/ontology-requests/10600/

So it is unclear to us why this should have any bearing on whether we make terms of the form 'X secretion' or not.

Cytokine production terms are designed to record gene function where a genotype or stimulation of a cell believed to mimic endogenous activity of some gene product leads to observed changes in (extracellular) production of a cytokine by a cell. It is not clear if the change is due to increased expression or increased secretion. At the Barcelona meeting, it was decided, rightly I think, that most or all annotations to production terms should be annotations to regulation of production.

The July 16th decision appears to be that there should be no annotation at all in these cases. But, from the point of view of an immunologist, the inference that a particular gene product functions to regulate the amount of some specific cytokine that a B-cell releases is a very important part of recording its cannonical function - irrespective of what we know about the mechanism. Surely we should be recording this - Isn't this what the whole BP branch is for!

Assuming we move most existing annotations to regulation of production, this still leaves the question of what to do with the existing terms - do we retain them and add a do not annotate tag, or at least a warning about their use. The terms are also problematic in that, where there is regulation of translation or secretion of the factors in question, these annotations will not be grouped under regulation of production. We need to think about better formalisation to overcome some of these issues...

Follow-up: no more merges

See http://wiki.geneontology.org/index.php/Ontology_meeting_2015-07-16#Follow-up:_no_more_merges