final PAMGO proposal submitted to GO

[Alexander Diehl]

Jane,

Sorry for the confusion.  I don't mean to introduce superfluous terms 
in the GO, but I was trying to make a distinction between evasion and 
suppression.  I guess there are really three levels here.

Evasion of pre-existing host defenses -- The PAMGO "evasion of host 
defenses" term and its child term "viral host defense evasion" 
(GO:0019049).

Evasion of host defense responses -- "viral evasion of host immune 
response" (GO:0030683) falls here.

Suppression of host defense responses -- my suggested (and slightly 
revised) "viral suppression of host immune response" falls here,

It's not clear to me that my suggested term is an is-a of GO:0030683 
or GO:0019049, since it denotes a more active process.  One would 
have to consider carefully how the definitions are written.

Another problem related to the whole defense response/immune response 
distinction in the GO, which I think is poorly thought out in 
general, and needs a reexamination.  I can cite a number of papers 
which refer to plant defenses as being immune responses, and which 
point out the many similarities between plant mechanisms and innate 
immunity in animals such as flies or mammals.  As we have been 
discussing today, there are clearly defenses which are not defense 
responses, and defense responses themselves are probably best divided 
between non-immune responses, such as behavioral responses to danger, 
and immune responses, which include most responses occurring on a 
cellular or molecular scale in multicellular organisms, and which can 
be divided between innate and adaptive responses.

Anyway, since I can't solve that problem today, and since a "viral 
suppression of host immune response" falls here will never be of any 
use to me in my work at MGI, I will simply drop the suggestion for 
the moment and let you get on with entering the PAMGO terms.

-- Alex


At 5:16 PM +0000 1/26/05, Jane Lomax wrote:
>Alex - I got a little bit lost with your comments (the whole
>evasion/invasion thing) - could you draw out as a tree for me do you
>think? cheers,
>
>Jane
>
>On Wed, 26 Jan 2005, ccollmer wrote:
>
>>  Hi All -
>>    The suggestions by Alex seem very good to me -- I agree that 
>>suppression and
>>  evasion (not invasion) can often be separated and it seems both of these
>>  terms, vis a vis a virus, are useful and necessary.  -Candace
>>
>>   >===== Original Message From Alexander Diehl <adiehl at informatics.jax.org>
>>  =====
>>  >Jane,
>>  >
>>  >My comments are interspersed:
>>  >
>>  >At 12:50 PM +0000 1/26/05, Jane Lomax wrote:
>>  >>Hi guys,
>>  >>
>>  >>I'm just finishing making the pathogenesis changes at the moment - I'll
>>  >>send the file for you to look at as soon as I'm finished. I've just got a
>>  >>couple of questions and suggestions...
>>  >>
>>  >>The following terms will be made obsolete:
>>  >>
>>  >>host-pathogen interaction ; GO:0030383
>>  >>invasive growth ; GO:0001404
>>  >>necrosis
>>  >
>>  >I agree with these obsoletions.
>>  >
>>  >>but not pathogenesis which is just being moved - is that right? Have I
>>  >>missed any others?
>>  >
>>  >I don't know of others right now.
>>  >
>>  >>Some suggested name changes:
>>  >>
>>  >>Name change: cell invasion -> host cell invasion
>>  >
>>  >Works for me.
>>  >
>>  >>
>>  >>Name change: viral host defense evasion -> evasion of host defense
>>  >>response by virus
>>  >
>>  >I agree with Candace about the fact that some host defenses are
>>  >pre-existing (evolutionary responses, really), but I wonder if a
>>  >child term such as "suppression of host defense response by virus"
>>  >would be useful to cover the many ways, for instance, viruses mess up
>>  >the immune system to evade host defense responses.
>>  >
>>  >>
>>  >>Name change: competition with another, non-host, organism -> competition
>>  >>with other, non-host, organism
>>  >>
>>  >>Name change: interaction between host and another organism -> interaction
>>  >>between host and other organism
>  > >
>>  >I am fine with these.
>>  >
>>  >
>>  >>I think this is a bit wrongly laid out:
>>  >>
>  > >>-----evasion of host defenses
>  > >>------viral host defense evasion (GO:0019049) (and its children terms)
>  > >>-------viral evasion of host immune response (GO:0030683)
>>  >>------evasion of host defense response (GO:0030682)
>>  >>-------evasion of host immune response
>>  >>
>>  >>GO:0019049 is currently a child, rather than a sibling of GO:0030682,
>>  >>which I think is correct. This is how I've done it - let me know if this
>>  >>is wrong:
>>  >>
>>  >>evasion of host defenses
>>  >>---[i] evasion of host defense response (GO:0030682)
>>  >>------[i] evasion of host immune response
>>  >>---------[i] viral evasion of host immune response (GO:0030683)
>>  >>------[i] viral host defense evasion (GO:0019049) (and its children terms)
>>  >>---------[i] viral evasion of host immune response (GO:0030683)
>>  >
>>  >I basically agree with Candace's reasoning here, but would argue that
>>  >viral invasion of host defenses would come under "viral host defense
>>  >invasion" whereas viral suppression of host defenses would fall under
>>  >my suggested "suppression of host defense response by virus" term.
>>  >
>>  >A real world example to illustrate the difference.  The HIV protease
>>  >has a non-proofreading reverse transcriptase which leads to a fairly
>>  >high rate of change in the sequence of the virus's surface
>>  >glycoprotein within a few viral generations.  Because of these
>>  >changes, the antibody response stimulated by the earlier generations
>>  >of the virus are in effect evaded by the later generations, and one
>>  >can fairly annotate the reverse transcriptase to "viral invasion of
>>  >host immune response."
>>  >
>>  >However, another mechanism HIV uses to promote its survival is
>>  >through the direct induction of apoptosis in uninfected CD4 T-cells
>>  >(which are central to driving an immune response) by binding of the
>>  >HIV Env glycoproteins to the CD4 and CCR5 or CXCR4 conreceptors.  In
>  > >this case I would annotate to my suggested "suppression of host
>  > >defense response by virus" term for the HIV Env gene product.
>>  >
>>  >
>>  >>
>>  >>Possible missing term: 'interaction with other, non-host organism' as
>>  >>child of 'symbiosis' and parent of 'competition with another, non-host,
>>  >>organism', like this:
>>  >>
>>  >>interaction between organisms
>>  >>---[i] symbiosis
>>  >>------[i] interaction between host and another organism
>>  >>------[i] interaction with other, non-host organism *NEW*
>>  >>---------[i] competition with another, non-host, organism
>>  >
>>  >I think that your suggested term is a good idea for annotating the
>>  >genes involved in a variety of situations where a 'host' is hard to
>>  >define that are not exactly competition between species.  Please add
>>  >it.
>>  >
>>  >I agree with Candace's comment about "competition with another,
>>  >non-host, organism," however.
>>  >
>>  >
>>  >>let me know what you think,
>>  >>
>>  >>thanks,
>>  >>
>>  >>Jane
>>  >
>>  >-- Alex
>>  >
>>  >--
>>  >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
>>
>>  ----------------------------
>>  Candace W. Collmer, Ph.D.
>>  Professor of Biology
>>  Wells College
>>  Aurora, NY 13026
>>    phone: 315-364-3271
>>    email: ccollmer at wells.edu
>>
>>


-- 
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