Ontology meeting 2015-12-03

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Report on Synapse project progress

Overview https://docs.google.com/document/d/1jn6GssXPJyWPijq1BcGeMvfJh5Q20X1S4dsV0FOTRwI/edit?usp=sharing

Topics arising from Synpase project

Untangling NT secretion, synaptic vesicle exocytosis, synaptic vesicle secretory pathway

https://github.com/geneontology/synapse/issues/34

If all neurotransmitter secretion happens by 'synaptic vesicle exocytosis' (which is a type of secretion), then what distinguishes synaptic vesicle endocytosis from neurotransmitter secretion?

TODO: For now punt merging NT secretionand SV exocytosis
 Calcium dep and indep exocytosis of NT need to be under SV exocytosis
 could consider obsoleting calcium indep SV exocytosis 
 But it is used in one annotation for spontanteous release, so safest to change name to that
 - although could be regulation - check paper.

'transport' vs 'movement of cell or subcellular component'

transport: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore."^^string"

'movement of cell or subcellular component': "The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore."

  • Query: 'movement of cell or subcellular component' and transport"
  • * 'microtubule-based movement'
  • * 'mitochondrion migration along actin filament'
  • * 'nuclear migration along microfilament'
  • * 'vesicle transport along actin filament'
  • * 'anterograde axonal transport'
  • * 'anterograde dense core granule transport'
  • * 'anterograde synaptic vesicle transport'
  • * ... 52 subclasses

2 relations:

'transports or maintains localization of': "Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c" 'results in movement of': "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c " (Currently only used for cell migration)

SOLUTION
NTR transport
 < -- is_a NTR containing vesicle trafficking along microtubule
vesicle trafficking along microtubule
   <-- is_a NTR containing vesicle trafficking along microtubule

signal transduction from synapse to nucleus

https://github.com/geneontology/synapse/issues/51#issuecomment-161622401

 Eds agree that these terms can be added.  We have precedent with ER to nucleus and chloroplast to nucleus sig
 Should add without formalisation for now, but formalisation that allows grouping of annotations to this with annotations to known pathways would be useful.
 See ticket for implementation discussion and possible formalisation

regulation of BP by MF - possible patterns

In many cases I have recommended a 'MF involved in 'regulation of quality'" pattern where it would be more accurate to say that an MF regulates a quality. But the former is much easier to support and more effective for grouping than the latter. For example

ligand-gated ion channel activity involved in regulation of presynaptic membrane potential EquivalentTo: 'ligand-gated ion channel activity' that 'part of' some 'regulation of presynaptic membrane potential'

But VU originally asked for: regulation of presynaptic membrane potential by ligand-gated ion channel activity

This. I think, better captures the biology - the activity really does regulate membrane potential (ignoring any compensating currents). But how might we formalise it and still get grouping under the relevant regulation of quality process term?

'regulation of presynaptic membrane potential by ligand-gated ion channel activity' EquivalentTo: 'ligand-gated ion channel activity' that regulates some 'presynaptic membrane potential' (OBA) # Although note that genus is at end of name

For grouping do we now need to add a part_of relationship to the process?

Plan for now is not to worry about this and stick with involved_in pattern - but it would be nice to be able to support the direct regulation alternative if we can work out and agree on a pattern.

 TODO: DOS to make general ticket on design pattern tracker

import/export is relative

import is relative: 'Ca2+ export from sER to cytosol' is also 'Ca2+ import into cytosol' but we use import/export relations to record it.

This makes some patterns hard/impossible given that support the very general (and not very useful) terms like 'Ca2+ import'


  We may be able to get rid of this issue by getting rid of import/export relations, 
  defining import and export classes entirely via start and end.  But then how to define general import/export classes?
  TODO: DOS to make general ticket for this on design pattern tracker.
  This should include an example of how implementation fixes this issue wrt cytoslic import/IC organelle export

calcium ion transport and regulation of calcium ion concentration in cytosol

https://github.com/geneontology/synapse/issues/46#issuecomment-161320244

In GO, we embed the assumption that 'calcium ion transport into cytosol' increases the concentration of calcium ions in the cytosol:

  positive regulation of cytosolic calcium ion concentration
     <-- is_a calcium ion transport into cytosol
         <-- is_a  release of sequestered calcium ion into cytosol

This doesn't fit with the patterns proposed by VU

  positive regulation of cytosolic calcium ion concentration
     <-- part_of release of sequestered calcium ion into cytosol involved in positive regulation of cytosolic calcium ion concentration