EO annotations + plants in space

[Chris Mungall]

Hi Doreen - good to see you the other day albeit briefly - I'm back  
in berkeley now, not staying for the conference like everyone else

weed on a space shuttle - sounds like a good experiment

seriously - I think it would be kind of cool for OBO to have those  
annotations

On May 7, 2007, at 6:08 AM, Ware, Doreen wrote:

> 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
>
>