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defense response

Jungwon Yoon jyoon at acoma.stanford.edu
Wed Aug 22 10:55:05 PDT 2001


Hello all,

Here at TAIR, I've been trying to modify 'response to external stimulus' part in 
process ontology for plant defense response.

The problem was 'defense response' is the child of both 'response to 
pest/pathogen/parasite' and 'response to wounding'.

%cell communication
   %response to external stimulus
      %response to biotic stimulus
         %response to pest/pathogen/parasite
            %defense response
               %immune response
                  %systemic acquired resistance
         %response to wounding
            %defense response
               %immune response
                  %systemic acquired resistance
						
'systemic acquired resistance GO:0009627' can not be a child of response to 
wounding.
Also I wanted to put other kinds of systemic resistance(jasmonic acid/ethylene 
dependent systemic resistance and induced sytemic resistance) under immune 
response(definition: A defense response triggered by the presence of a foreign 
body.).

To resolve this, I tried to take out defense response from both 'response to 
pest/pathogen/parasite' and 'response to wounding', and put it under 'response 
to biotic stimulus'.  Then I could add 'induced systemic resistance GO:0009682' 
and a new term 'jasmonic acid/ethylene dependent systemic resistance' under 
'immune response' together with 'systemic acquired resistance'.  Also some 
children terms of 'immune response' got imported to appropriate parent nodes 
like 'response to pest/pathogen/parasite' and 'response to wounding'.

The new term is;
jasmonic acid/ethylene dependent systemic resistance GO:0009681

The definition is;
the jasmonic acid, ethylene dependant process that confers broad spectrum 
systemic resistance to disease in response to wounding or a pathogen.

%cell communication
   %response to external stimulus
      %response to biotic stimulus
         %defense response
            %gene silencing
            %hypersensitive response
            %inflammatory response
            %immune response
               %activation of natural killer cell activity
               %cellular defense response
               %humoral defense mechanism
               %inhibition of natural killer cell activity
               %systemic acquired resistance
               %induced systemic resistance
               %jasmonic acid/ethylene dependent systemic resistance
         %response to bacteria
            %response to pathogenic bacteria
               %resistance to pathogenic bacteria
                  %systemic acquired resistance
                  %jasmonic acid/ethylene dependent systemic resistance
         %response to fungi
            %response to pathogenic fungi
               %resistance to pathogenic fungi
                  %systemic acquired resistance
                  %jasmonic acid/ethylene dependent systemic resistance
         %response to pest/pathogen/parasite
            %gene silencing
            %hypersensitive response
            %activation of natural killer cell activity
            %cellular defense response
            %humoral defense mechanism
            %inhibition of natural killer cell activity
            %inflammatory response
            %systemic acquired resistance
            %jasmonic acid/ethylene dependent systemic resistance
         %response to wounding
            %cellular defense response
            %inflammatory response
            %jasmonic acid/ethylene dependent systemic resistance
            
Obviously this is very truncated showing of a whole DAG.
I just outlined main changes.
All kinds of feedback will be appreciated.
Thank you.

Sincerely,
J Yoon
            
                                                                                   
                                                                 
                             
         



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