Cleaning up MAPKKK cascade

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BACKGROUND

MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier.


STILL TO DO

SourceForge item from Val sorting out the different types of MAPK cascades: https://sourceforge.net/p/geneontology/ontology-requests/10384/


REDEFINING 'MAPK CASCADE'DONE

Renamed (end 2011):

MAPKKK cascade ; GO:0000165
to
MAPK cascade ; GO:0000165

And redefined as a cascade containing at least MAPKKK, MAPKK and MAPK based on PMID 20811974 (from Paul Thomas's regulation proposal: http://gocwiki.geneontology.org/index.php/Ontology_meeting_2012-01-19. Also redefined the child terms accordingly.


PROCESS-FUNCTION RELATIONSHIPS'DONE

  • Created P/F links to connect the MAPK(n) activities to the downstream cascade components they activate (end 2011):
E.g:
MAPK cascade
--[partof]MAP kinase activity (new relationship)
----[pos_reg]positive regulation of MAP kinase activity
------[isa]activation of MAPK activity
--------[partof]MAP kinase kinase activity (new relationship)
----------[pos_reg]positive regulation of MAP kinase kinase activity
------------[isa] activation of MAP kinase kinase activity
--------------[partof]MAP kinase kinase kinase activity (new relationship)
etc etc
  • Note that this is a temporary solution because we can't yet say in GO that MF regulates MF. When we can, we will able to obsolete the redundant regulation process terms in this node.


MAPK FUNCTION TERMS

  • Need to sort out the distinction between MAPK/SAPK/JNK activities. Currently (May 2012):
MAP kinase activity ; GO:0004707
--[isa]SAP kinase activity ; GO:0016909
----[isa]JUN kinase activity ; GO:0004705



Relevant SourceForge Items