important -- question for PAMGO

[Alexander Diehl]

Brett,

I agree that we should carefully review the types of organisms that 
warrant response to terms.  My omission of oomycetes and others was 
not meant to exclude them, but rather to avoid complexity while we 
were deciding on the basic DAG structure.  I think in particular we 
need input on which organisms need "response to symbiotic [organism]" 
terms, as well as "defense response to [organism]" terms.

The existence of the yeast terms is due to me, unfortunately 
("response to yeast" and "detection of yeast").  I'll accept any 
proper advice about whether the terms valid or not.  I guess the 
question is really whether there are additional or different pathways 
for responses to yeast versus multicellular fungi.

Thanks,

Alex

At 1:58 PM -0500 3/30/05, Brett Tyler 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
>
>
>--
>*****************
>Brett Tyler
>Professor
>Virginia Bioinformatics Institute
>Virginia Polytechnic Institute and State University
>Washington Street
>Blacksburg, VA 24061-0447
>


-- 
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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