important -- question for PAMGO

[Matthew Berriman]

I haven¹t followed the previous discussions but should you not have response
to <any taxon>? Some granularity amongst protozoa might be required to
differentiate amoebae, Apicomplexa (e.g. Toxoplasma), trypanosomatidae (e.g.
Leishmania), giardia, etc.  You also have response to nematodes but do not
have response to trematodes or cestodes.  (The latter two could perhaps be
groups as platyhelminths).

cheers
Matt


Matthew Berriman, PhD
Project Manager
Pathogen Sequencing Unit

Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton CB10 1SA, UK

http://www.sanger.ac.uk/Projects/Pathogens










On 30/3/05 8:01 pm, "Brett Tyler   (by way of Alexander Diehl)"
<bmtyler at vt.edu> wrote:

> Alex,
> 
> Looks good. I agree that this is ready to put out for further discussion by
> the wider community.
> 
> Here is some further discussion right away :-)
> 
> There should be terms for oomycete (organisms that we work on that look like
> fungi but are in a different kingdom), apicomplexans (malaria, Toxoplasma
> etc), which belong to different kingdoms than those listed in your diagram,
> plus something like protist or protozoa (Leishmania, trypanosomes, Giardia etc
> etc)
> 
> At some point GO will have to decide how deeply into the tree of life to
> specify terms like "response to <some organism>" - it's similar to the sensu
> issue.  Perhaps it should be left at the kingdom level (easy for crown
> eukaryotes, but tough for "protists"), which would eliminate yeast, until
> evidence is obtained that a host organism really has a response that is more
> specific than that.
> 
> A related issue is whether common names like "yeast" are appropriate in this
> context - and maybe that issue has already been decided in the context of
> "sensu" terms.
> 
> Cheers
> 
> Brett
> 
> 
> At 1:33 PM -0500 3/30/05, Alexander Diehl wrote:
>> Brett,
>> 
>> Thanks for your correction.  Here is an updated DAG based on Chris's
>> suggestion and your correction:
>> 
>> 
>> 
>> At this point I'm going to send out an email digest of these discussions to
>> the pathogenesis (pathogenesis at geneontology.org) mailing list to engage a
>> larger group of people in these discussions.
>> 
>> -- Alex
>> 
>>> Chris' proposal is fine with me (with one trivial correction - see below).
>>> 
>>> As I think about it, the term "Response to symbiont" already is agnostic of
>>> the outcome of the interaction because "symbiont" spans many possible
>>> outcomes of the association.
>>> 
>>> Also a clarification: I did not intend to propose that  "response to
>>> potential symbiont" would be used to annotate genes known ONLY for their
>>> role in susceptibility responses, without other evidence as to their role in
>>> mutualistic responses - I had in mind that annotation would be applied AFTER
>>> their role in a mutualistic response was discovered.
>>> 
>>> Finally a trivial correction: Chris' diagram shows yeast as a distinct
>>> organism from fungi.  All yeasts re of course fungi, so any terms specific
>>> to yeast should first be a child of the relevant fungi term.
>>> 
>>> Cheers
>>> 
>>> Brett
>>> 
>>> --
>>> *****************
>>> Brett Tyler
>>> Professor
>>> Virginia Bioinformatics Institute
>>> Virginia Polytechnic Institute and State University
>>> Washington Street
>>> Blacksburg, VA 24061-0447
>>> Telephone: (540) 231-7318
>>> Fax: (540) 231-2606
>>> Email: bmtyler at vt.edu
>>> Web: https://www.vbi.vt.edu/article/articleview/141
>>> *****************
>> 
>> 
>> --
>> 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
> 
> 
> --
> *****************
> Brett Tyler
> Professor
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Washington Street
> Blacksburg, VA 24061-0447
> Telephone: (540) 231-7318
> Fax: (540) 231-2606
> Email: bmtyler at vt.edu
> Web: https://www.vbi.vt.edu/article/articleview/141
> *****************
> 


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