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allergene annotation

Alexander Diehl adiehl at informatics.jax.org
Tue Mar 14 07:10:04 PST 2006


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 




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