important -- question for PAMGO

[Brett Tyler]

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
*****************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://fafner.stanford.edu/pipermail/pathogenesis/attachments/20050330/1a7bfd69/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: digraph_Responses_S-#181E_2.pdf
Type: application/pdf
Size: 18725 bytes
Desc: not available
Url : http://fafner.stanford.edu/pipermail/pathogenesis/attachments/20050330/1a7bfd69/attachment.pdf