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allergene annotation
Jane Lomax
jane at ebi.ac.uk
Tue Mar 14 06:45:08 PST 2006
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
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