Response to and signaling: Difference between revisions

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See slides 20 and 24 in the following [http://wiki.geneontology.org/images/6/62/Signaling_LA_May2011.pdf presentation] (from the GOC meeting, LA, May 2011)
See slides 20 and 24 in the following [http://wiki.geneontology.org/images/6/62/Signaling_LA_May2011.pdf presentation] (from the GOC meeting, LA, May 2011)


Please note that because ligands are considered participants in the signaling pathway, and pathways are part_of/an_instance_of the response, then this means that ligands will inherit 'cellular response to x' annotations.


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Latest revision as of 08:59, 14 April 2015

PROBLEM

  • It would seem sensible to have 'cellular response to x' terms as parents of 'x signaling pathway' terms, since the signaling pathway is one part/instance of the cellular response.
  • BUT there isn't a 1:1 relationship between receptors and their ligands, and many pathways are defined based on their receptor.

OUTCOME

  • 'RESPONSE TO X' involves everything from detection of the stimulus, the signaling pathway AND the downstream cellular response.
  • The signaling pathways REGULATE the downstream cellular response.
  • Therefore the signaling pathways are part of the cellular response.
  • Therefore the signaling pathway terms should be children of the response_to terms.
  • Splitting some of the signaling pathways into ligand-activated, and receptor-activated pathways, will allow the response to terms to be correctly linked to the signaling pathway terms.

See slides 20 and 24 in the following presentation (from the GOC meeting, LA, May 2011)

Please note that because ligands are considered participants in the signaling pathway, and pathways are part_of/an_instance_of the response, then this means that ligands will inherit 'cellular response to x' annotations.


STILL TO DO

  • Is the signaling pathway PART_OF the response, or an INSTANCE of a response?
    • NB: At the moment, the signaling pathways are is_a children of the response terms, but we need to think if this is correct.



Related SF items

Response to stimulus: SF:1601609