EO annotations + plants in space

[Pankaj Jaiswal]

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
> 

On this page it is just the summary of all the ontologies that can be 
associated. For more details you need to go to the respective protein 
pages e.g.
http://www.gramene.org/db/protein/protein_search?acc=Q8H5T6


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

You are right. They should be and it is on our to dod list. Its not a 
simple case because the number of EO associations can be one to many for 
a single TO association.

> 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!
> 

I will see if its possible. I haven't come acros any gene/protein 
annotations as most of these experiments are on whole plant wide responses.

In any case we have some reports from plants. analysed for 
seedling/plant development in zero gravity environment. this can be 
performed by physically taking the plants in space or by simulating the 
conditions of a free fall. Many such experiments were done on cell 
suspensions but here is a good one
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15538652&query_hl=3&itool=pubmed_docsum

Also there is a recent interesting report of induction of mutation of 
paddy rice under space conditions
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=11541262&query_hl=3&itool=pubmed_docsum



> 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).
> 

I haven't seen PATO def. but won't use mass here because it was  wt=m.g
Though we do have other terms with mass in it 
http://www.gramene.org/db/ontology/search?query=mass&btn=Search&ontology_type=TO

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

> Cheers
> Chris
> 
>