December 9th 2010: Difference between revisions

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[[Category:Signaling]]
=='''MINUTES'''==
=='''MINUTES'''==



Latest revision as of 18:57, 22 April 2014

MINUTES

Present:

Rebecca Foulger, Andrew Chatr-aryamontri (BioGRID), Midori Harris, Peter D'Eustachio, Ruth Lovering, Val Wood


Key Points

  • The general structure of the proposal is an improvement.
  • The term 'intercellular ligand transport ; GO:NEW' is not needed. It would be better to have 'x transport involved in signaling' for specific ligands as-and-when we need them. Becky will zap 'intercellular ligand transport' from the proposal.
  • Cascade is confusing to use for the shared intracellular components as it implies amplification. It is correct for some (eg protein kinase cascades) but not for all.
  • It's ok to change all 'x signaling pathway involved in y process' to 'x signaling pathway involved in REGULATION OF y process'.
  • We should retain 'pathway' nomenclature for all signaling pathways.
  • We don't need to link up trancytosis with signaling for now.
  • AI: Becky will add a comment to 'multicellular organismal signaling ; GO:NEW' to suggest annotating to one of the more specific children terms instead, to make it clearer it's a grouping term.
  • RECEPTOR-MEDIATED ENDOCYTOSIS AND SIGNALING
    • The role of receptor mediated endocytosis (RME) is to bring stuff into the cell (Peter). It can be:
      • part of a larger signaling process
      • part of a larger transport process
    • Therefore, it looks like we do need to split the receptors into signaling receptors, and transport receptors. Some receptors may play a role in both. And RME can have a positive/negative effect on signaling pathways, so 'RME involved in signaling' may be the most accurate way to go. With children 'receptor internalization involved in negative regulation of signal transduction'.


Unresolved Points/Questions to put to GO

  • Which of the current 'cascade' terms can stay as 'cascades' and which need to be renamed as they don't imply amplification?
  • Where does 'creation/generation of a signal' start: transcription of the gene encoding the signal, translation, processing?
  • Does it make sense to have a paracrine/autocrine/endocrine split for terms? (The autocrine term already exists. Rebecca proposed creating the paracrine and endocrine terms to replace the 'signal transmission by diffussion', 'signal transmission via vascular system' terms'.
  • Should receptor terms go under 'signaling'. Or just 'regulation of signaling'? (It makes most sense to have them under regulation of signaling'. E.g. 'receptor clustering involved in positive regulation of signal transduction'.



AGENDA

1/ Rebecca will go through the proposal to remove the pathway/process split in the signaling node. They key points of the proposal are:

    • Merging signaling process and signaling, to remove the process/pathway split
    • Merging signaling pathway and signal transduction, to remove the process/pathway split
    • Removed 'behavioral signaling' from the tree.
    • Split the signaling node into cellular, multicellular organism, and multi-organismal signaling nodes
    • OBSOLETION of 'signal transmisison' and its children
    • OBSOLETION of 'consequence of signal transmission' and its children
    • Creation of some new signaling terms to replace the signal transmission obsoletions

NB: THIS MEANS THAT LIGAND IS PART OF THE SIGNALING PATHWAY, AND WOULD GET A SIGNAL TRANSDUCTION ANNOTATION.



2/ Go through issues arising from the proposal, to reach conclusions

    • Can endocrine signaling be used for plants?
    • Is endocrine signaling restricted to hormones?
    • How does trancytosis affect signaling?
    • Definition of cascades (Val)
    • Where should a 'regulation of biological process/cellular process' link be added to the signaling node?
    • What is meant by 'termination of signal transduction?'
    • Should the receptor metabolism/processing terms go under 'signaling'?
    • Naming of pathway terms: signaling pathway, signal transduction, signal transduction pathways



3/ How to deal with non 1:1 receptor-ligand combinations.

    • First thing is to deal with our definitions of receptor-mediated signaling pathways