Ontology meeting 2015-07-30

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Minutes: David OS

Transition to GitHub

Migration of Images https://github.com/geneontology/go-ontology/issues/11985

THere are 600, so couldn't do all these by hand. Not trivial to script, but can be done.

AI: We should archive all of the attachments by SF ticket number. :Chris:

Labels - do we need to clean them up?


List includes: Quick, QuickFix, Quick Fix, Maybe Quick...

Easy to cleanup dodgy looking ones with no open issues. Just delete. After that we need more discussion of what we want.

  • Add more people to team? But be careful - they will end up watching everything by default.

General guidance for editors working with transferred tickets:

 Include all authors by @mention in comment.  They will then continue to be CC'd.
 Other advice:

Send out advice to users re transition:

   How to search by ticket number.
   How to search for tickets you have commented on.
   General Guidance ?
     Can we just rely on pointing users to generic GitHub user info?

Do we still need ticket summary emails?

  Who uses the ticket summaries?  Is it worth writing a new one for GitHub?

AI: Update links to tracker. Can we just use Purl? Chris would rather use a general page on GitHub for trackers.

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:


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...

  Alex: Immunologists are very concerned about cascades of release of cytokines.  
   This is important information understanding how the immune system functions.  
   If, say, you knock out a component of a signaling pathway and see an increase 
   in the release of some cytokine or the inhibition of release of another.
   Alex can provide some examples of this. He also agrees that the regulation terms 
   for these are the ones to use.

cytokine production "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels."^^string

  Alex: Intracellular is there as in some cases the data comes from flow cytometry, where 
   increased product is still in cells.
  AI: Alex to put together a few papers with examples. Focussing on cases where the 
  experimental evidence points to some important  conclusion about immune system function.

MF refactoring

Review Paul's emailed outline. (DOS to present).

 Got through to point 11 on Paul's email.  We will share results once finished.

Follow-up: no more merges

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