Ontology meeting 2023-10-16

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

Discussion points

Design patterns

• Any new logical definition should match a DP; otherwise create a new DP (in a new ticket)
• Create a new ticket with the label 'Design pattern'
• Ontology editors to request PR to be reviewed by another ontology editor
• Create regularly run reports for terms that don't match design patterns

Protégé 5.6.3

• Won't install, there is a bug.
• Everyone will need to switch at the same time, please wait for green light

Cryptic Travis errors

Added a new wiki page: Interpretation_of_Travis_checks_errors

Switching from has in/output to has primary in/output

• TBC OK to merge, in the sense that the inferences are no worse than current and no equivalent terms are being created
• Need decision on relation to use for receptor activity

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

• Chris's slides: Decomposition of macro biological processes in GO