allergene annotation

[Jane Lomax]

I concede that the argument doesn't hold up as well for allergens as it 
does for pathogenic organisms.

But aren't you making a value judgement about what constitutes a 'normal' 
interaction? How do we know that the fact that the plant protein induces a 
hypersensitive response in another organism doesn't confer some advantage 
to the plant? Perhaps hay-fever promotes the spreading of pollen?!

jane


On Tue, 14 Mar 2006, Alexander Diehl wrote:

> Sorry to be a few minutes late on this.
> 
> The function of a protein, any protein, is not to be an allergen, or 
> antigen, for another organism's immune system.  This is not appropriate 
> annotation at all.  Indeed, nearly any protein can be made antigenic 
> when given in the right context.  The plant proteins in question may be 
> known allergens, but that is not their natural role in the plant or for 
> the plant.  Annotation of allergenic potential would be appropriate with 
> an ontology focused on disease and pathology, but not for the GO.
> 
> We can discuss at the meeting, but I am quite firm in my conviction here,
> 
> Alex
> 
> 
> Jane Lomax wrote:
> > 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
> >
> >   
> 
> -- 
> Alexander Diehl, Ph.D.
> Scientific Curator
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
> 
> email:  adiehl at informatics.jax.org
> work:  +1 (207) 288-6427
> fax:  +1 (207) 288-6131 
> 
> 

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