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allergene annotation

Alexander Diehl adiehl at informatics.jax.org
Tue Mar 14 06:25:30 PST 2006


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 




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