Ontology meeting 2023-09-25

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  • Group members: Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul
  • Present: Pascale, Raymond, Kimberly, Jim, Peter, Chris, Paul, Tanya
  • Regrets: Edith, David


Discussion points

Usage of 'has input' versus 'has primary input'

We wanted to decide whether to switch in the ontology all ‘has input’ for ‘has primary input’ (as appropriate). I have made a table of ‘pros and cons’ for the two options, see:

https://docs.google.com/spreadsheets/d/1tYXUa8RhnihwOVCokpgvARobZ9CmCHCvWrVWdjXRSC4/edit#gid=0

We also need to think about the decision process: which parameters weigh the most?

Cell to cell signaling terms

Request was to

  • Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with epiblast cell-extraembryonic ectoderm cell signaling (Single EXP to PMID:14511481)
  • Replace "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation GO:0021937, with: cerebellar Purkinje cell-granule cell precursor cell signaling (def: Any process that mediates the transfer of information from Purkinje cells to granule cell precursors.) (9 EXP)

Some example terms:

  • neuron-glial cell signaling
  • epithelial-mesenchymal cell signaling
  • mesenchymal-epithelial cell signaling
  • astrocyte-dopaminergic neuron signaling
  • ectoderm and mesoderm interaction
  • mesodermal-endodermal cell signaling
  • glial cell-neuron signaling

There are also terms for which the cells signaling to each other are not specified:

  • cell-cell signaling involved in amphid sensory organ development
  • cell-cell signaling involved in cardiac conduction
  • cell-cell signaling involved in cell fate commitment
  • cell-cell signaling involved in kidney development
  • cell-cell signaling involved in lung development

etc

  • The question is, is 'cell x to cell y' signaling a biological process relevant for GO?
  • Issues:
    • orthogonal to other signaling pathways
    • For example: neuron-glial cell signaling is defined as "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine."
      • acetylcholine receptor signaling pathway is not a child of cell-cell signaling
      • dopamine receptor signaling pathway is a has_part child, with the relation 'has part 'synaptic transmission, dopaminergic'
      • We dont have noradrenaline signaling, but we have synaptic transmission, noradrenergic
      • >> but none of these are linked to neuron-glial cell signaling, which is probably OK, since these pathways may be taking place in various cell types
      • >>> It seems these terms are BPs that contain CC information, and this information should be captured with 'occurs in'
  • Terms are not much used:
    • cell-cell signaling involved in cell fate commitment 9 EXP
    • epithelial-mesenchymal cell signaling 4 EXP
    • glutamate secretion, neurotransmission 4 EXP
    • mesenchymal-epithelial cell signaling 4 EXP
    • mesodermal-endodermal cell signaling 2 EXP
    • neuron-glial cell signaling 5 EXP
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