EO annotations + plants in space

[Georgios V. Gkoutos (Genetics)]

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On Fri, 4 May 2007, Chris Mungall wrote:

> 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?

I bet there are - I haven't come accross such data but .....

> 
> 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
> 
>