TO/PO for annotating Citrus mutant collection

[Pankaj Jaiswal]

Dear Ana,

Thank you for your interest in using the PO/TO for describing your 
phenotypes. Please see my comments below.

Best
Pankaj

Ana Conesa wrote:

> Dear sirs, 
> 
> We are developing a Citrus mutant tree database and we would like to use a
> controlled vocabulary to describe phenotypes and phenotype values. We think
> that the Trait and Plant Ontology could provide a good framework to do so.
> However, there are a number of issues that are still not clear for us. I would
> appreciate if you could provide us with some additional information. Our main
> questions are:
> As we are aiming to describe tree phenotypes, rather than annotating genes, we
> would like to assign a numeric value to a given TO/PO term . For example, to
> describe sugar content of the fruit , we would like to provide for each mutant
> tree a representative value(ie., Sugar content=4.5). Can the TO/PO support
> this type of annotations, are there examples of such a use?

The which is a trait ontology is simply a vocabulary of traits. The way 
you are suggesting, by adding a value to the trait (TO) term i.e. 4.5, 
we are making it a phenotype term
Another example would be "Leaf color yellow"

In this example Leaf color is a trait (TO term) and yellow is the value 
you are providing. Together this term is representing a phenotype.
You can also decompose the phenotype text "leaf color yellow" into the 
following EAV model.
E=Anatomy/Entity=Leaf
A=Property/attribute=color
V=Value/score=yellow

A score could be an absolute value (4.5 in your example) or a relative 
one (high/low/more/less/normal/optimal/absent/present etc.)

So you have a choice to use the anatomy+property combination and let the 
annotations make combination or you predefine the concept in the form of 
a trait and provide a value for it.

In Gramene we understand that this being a comparative database, it will 
be rather less effective to bring the absolute values, because these 
phenotypes depend largely on GxE parameters. Instead we are striving for 
  bringing the "relative values" in the TO in a very near future.

Similar efforts are being carried out in the PATO discusssion group. 
This is addressing the EAV model for phenotype and trait ontology. For 
more information please visit 
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/phenotype/meetings/


> As we work on Citrus, we expect there will be specific terms which will be
> missing in the current Ontologies. Is there an easy, direct way for the user
> to add new terms to the Ontology?. We are thinking now for our own use, not
> for directly contribuiting to the Ontology development, although this could
> be, of course, a interesting possibility.
> 
You can download the Trait ontologies from the anonymous CVS 
http://brebiou.cshl.org/viewcvs/*checkout*/Poc/traits/
I suggest you work with trait.obo files in future.

We will be glad to work with you for new term suggestions as required by 
you. This will help us maintain a synchrony with your requirements and 
possibly with other, that may require the same trait terms.

As far as plant anatomy related requirements are there, you can download 
the files by following instructions  at 
http://www.plantontology.org/download/download.html
If you are requesting a anatomy/plant structure term then please e mail 
the request to po-dev at plantontology.org

> Looking forward for your reply
> 
> We remain, 
> 
> Ana Conesa
> Oscar Sánchez
> 
> ------------------------------------------------------------
> Ana Conesa, PhD.
> Instituto Valenciano de Investigaciones Agrarias (IVIA)
> Carretera Moncada - Náquera, Km. 4,5
> Apartado Oficial 46113- Moncada (Valencia)
> SPAIN
> email aconesa at ivia.es
> ------------------------------------------------------------
> IVIA (http://www.ivia.es)
> Open WebMail Project (http://openwebmail.org)
> Debian Project (http://www.debian.org)
> 
> 

-- 
************************
Pankaj Jaiswal, PhD
G15-Bradfield Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
************************