EO annotations + plants in space

[Ware, Doreen]

Hi Chris,

I had a colleague that sent arabidopsis on a shuttle trip, a few years
back do you want me to see if they will do some annotations?

dor

-----Original Message-----
From: owner-po-dev at plantontology.org
[mailto:owner-po-dev at plantontology.org] On Behalf Of Chris Mungall
Sent: Friday, May 04, 2007 9:42 PM
To: gramene at gramene.org; Pankaj Jaiswal; po-dev at plantontology.org;
Georgios V. Gkoutos (Genetics)
Subject: EO annotations + plants in space

Hi all

Where can I download EO annotations? They don't seem to be available  
from the downloads page without resorting to SQL dumps. Have you  
considered making these available using the GO annotation format  
(perhaps a generalized form of)?

How should I interpret annotations such as this:
http://www.gramene.org/db/genes/search_gene?acc=GR:0101182

 From the report it doesn't look as if the environments and the  
traits are explicitly linked. Is this the case?

This is one of my favourite OBO terms:
http://www.gramene.org/db/ontology/search_term?id=EO:0007315

"The treatment involving use of gravity factor to study various types  
of responses in the absence of gravity or space like conditions."

Unfortunately there are no annotations to it :-(

Now I read more closely I see that this term can also be used to  
annotated space-like conditions on earth. But there are experiments  
on plants in space aren't there?

http://arjournals.annualreviews.org/doi/citedby/10.1146/annurev.pp. 
38.060187.001533?cookieSet=1
http://exploration.nasa.gov/programs/station/PESTO_lite.html

It's probably not high in your priority queue but I think it would be  
kind of cool if there was at least one annotation here.. I'll buy a  
drink for whoever creates the first non-Earthbound OBO annotation!

George, are there mouse in space experiments?

Not being a plant scientists I can't claim this would help in my  
research in any way - however, I do have a genuine ontological use  
case. At the moment, PATO and the Units ontology exhibit a bit of  
confusion over the weight-mass distinction. As the majority of  
biology so far discovered happens on earth which has a reasonably  
constant enough gravity, it may seem overly fussy to insist on a  
clear distinction. However, I think that there may be practical cases  
where the confusion could cause problems, such as in interpreting  
PATO annotations in the context of EO:0007315.

Also when mapping TO terms to PATO+PO logical definitions, I had been  
using PATO:0000128 (weight) for terms like TO:0000181 (seed weight),  
but I think the actual quality is seed mass is it not? So we should  
be using PATO:0000125 (mass).

If I was really fussy I'd insist on a distinction between apparent  
weight and weight.. but I'm not.

Cheers
Chris