allergene annotation

[Jane Lomax]

LOL!

Okay, okay - I take your point - the hay-fever example wasn't entirely 
serious. Although I do remain to be convinced that there are _no_ cases 
where inducing a hypersensitive response in another organism doesn't 
confer some selective advantage, but I don't know enough about this 
field and will bow to your superior knowledge ;)

Out of interest (and I remember having this discussion with you before 
Alex, I just can't remember the conclusion) what's the rationale behind 
having GO:0016068 (type I hypersensitivity) in the ontology if all 
hypersensitivities are disregulations?

thanks,

jane



On Tue, 14 Mar 2006, Alexander Diehl wrote:

> No,
> 
> Allergen and antigens are simply the substrates of the immune system.  
> What makes something an allergen or an antigen is  dependent on the 
> responding immune system, and varies by both individual and species.  A 
> response to a particular allergen or antigen is a phenotypic quality of 
> the responding organism.  Furthermore, allergies are far more prevalent 
> in "western" human populations than in societies with less 
> well-developed systems of sanitation and medicine, and thus reflect 
> largely an inappropriate refocusing of the immune system in the absence 
> of the threats humans faced in evolution, primarily parasites.  The 
> suggestion that an allergen confers an advantage to plant reproduction 
> also seems amazingly far fetched, given that the vast majority of plant 
> pollen ends up somewhere else than up a person's nose.  Even in sneezing 
> (if I am to pursue what may be intended facetiously here), the pollen 
> would be primarily expelled covered in mucus and probably inactivated.
> 
> Allergies are pathogenic disregulations of the normal "hypersensitivity" 
> responses.  We should not be stretching the GO to become a disease 
> ontology unless that is what we want to do with it.  If we want to make 
> the GO into a disease ontology then let's do it officially and not on 
> the sly.
> 
> -- Alex
> 
> 
> Jane Lomax wrote:
> > 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
> >
> >   
> 
> -- 
> 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