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allergene annotation

Jane Lomax jane at ebi.ac.uk
Tue Mar 14 06:18:17 PST 2006


But I think when you're talking about interactions between organisms, 
there really isn't a 'normal' or 'abnormal' - the interaction just 
occurs. And remember that you'll record two taxon ids; one for the species 
producing the allergen, and one for the 'allergic' species. So it isn't 
the usual case of 'is it normal for the species I'm annotating' because 
you're annotating both.

jane

On Tue, 14 Mar 2006, Harold Drabkin wrote:

> 
> Yes, a new term would work much better.  However, it may or may not be 
> the "normal " function or process.
> A virus or symbiont host interaction is a bit different, because those 
> interactions are most likely critical for the life cycle (eg, if you 
> don't have a host, the virus can't replicate, etc.).  Many people are 
> allergic to gluten, but is that a normal function/process of  gluten? 
> 
> 
> Jane Lomax wrote:
> > Unfortunately that term only works where one organism is living in 
> > symbiosis with another organism (e.g. host/pathogen) which is why I 
> > suggested that new term...
> >
> >
> > On Tue, 14 Mar 2006, Harold Drabkin wrote:
> >
> >   
> >> But, I did find this term, and related?
> >>
> >> GO term: 	*induction of host defense response*
> >> GO id: 	*GO:0044416*
> >> Definition: 	*The elicitation by an organism of the defense response of 
> >> the host. The host is defined as the larger of the organisms involved in 
> >> a symbiotic interaction. *
> >>
> >>
> >> which I think might be more in line with a direct annotation to 
> >> something like this???
> >>
> >>
> >> Harold Drabkin wrote:
> >>     
> >>> I would not; they are the a cause, but they are not involved in the 
> >>> process (which is not occurring in the plant).
> >>> The GO is used to indicate the normal function and process of a gene 
> >>> product. You need to look at it from the point of view of the organism 
> >>> that produces the gene product. If these perform some function for the 
> >>> plant, that is what you would annotate them to. Perhaps there are 
> >>> terms associated with defense in a plant (ie, along the lines of 
> >>> something that is released to deter the plant from being eaten???__?
> >>>
> >>>
> >>>
> >>> adepto at cribi.unipd.it wrote:
> >>>       
> >>>> Hi All
> >>>> I have to annotate plant genes described as "allergenic peptides" in 
> >>>> pFam these
> >>>> genes are described as:
> >>>> "Allergies are hypersensitivity reactions of the immune system to 
> >>>> specific
> >>>> substances called allergens (such as pollen, stings, drugs, or food) 
> >>>> that, in
> >>>> most people, result in no symptoms. A nomenclature system has been 
> >>>> established
> >>>> for antigens (allergens) that cause IgE-mediated atopic allergies in 
> >>>> humans..."
> >>>>
> >>>> So, where may I annotate these allergenes? It is GO:0016068 (type I
> >>>> hypersensitivity) the right term? Thanks in advance.
> >>>> Alessandro
> >>>>   
> >>>>         
> >>     
> >
> > Dr Jane Lomax
> > GO Editorial Office
> > EMBL-EBI
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridgeshire, UK
> > CB10 1SD
> >
> > p: +44 1223 492516
> > f: +44 1223 494468
> >
> >   
> 
> 

Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468




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