final PAMGO proposal submitted to GO
Jane Lomax
jane at ebi.ac.uk
Thu Jan 27 06:59:04 PST 2005
Hi Alex - I see your point - we have all these active evasion and passive
evasion terms under evasion of host defenses don't we? I seem to remember
Evelyn and I creating those terms some time ago. I guess the whole
node needs sorting out and standardising a bit. But I agree it should
probably wait until the PAMGO terms are all in,
thanks,
Jane
On Wed, 26 Jan 2005, Alexander Diehl wrote:
> 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
>
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