Soybean ontology (PR#24)

[Katica Ilic]

Hi Rex, 

Thanks again for your interest in plant ontologies. It's great that you have
plans to create a comprehensive ontology for soybean and other legumes that will
be freely available to the public. I am sure that both, developmental stages and
anatomy/morphology ontologies for soybean will be used by a large number of
researchers. 

Regarding  a help with DAG-edit, I agree with you, it's not very intuitive tool,
but after solving few initial problems, it's relatively easy to edit ontology
using this tool. Of course, I'll be happy to help you with tips and suggestions
(I had generous help from my colleagues at TAIR). Please feel free to contact me
any time. To report bugs that you may sometimes discover, especially with new
released versions of Dag-edit, please contact John Day-Richter
(john.richter at aya.yale.edu).

I look forward to hearing from you and Dr. Randy Schoemaker about possibility
for collaboration and joining our efforts at POC.

Best Regards,

Katica

On Tuesday, Aug 31, Rex Nelson wrote:
> >Hi Rex,
>>
>>The short answer to your question would be: us 
>>at Plant Ontology Consortium. You
>>have definitively contacted the right people.
> 
> Yes, I knew it was the right place :>
> 
>>At present time, I am not
>>aware of any ongoing effort in the public sector with respect to developing
>>anatomy and developmental stages ontologies for soybean.
> 
> Good, I did not think that there was an organized 
> effort yet.  That is why I wanted to contact you 
> (PO).
> 
>>However, there is a
>>growing interestin the plant research community and we have often had people
>>asking us about such project. It would help (to give you more specific
>>suggestions and tips) if you could tell me a bit 
>>more about the ontology project
>>you have in mind, for instance, a scope of the 
>>project. Is it going to be a tool
>>to facilitate ëin-houseí projects (for instance, large-scale gene expression
>>profiling), or do you have in mind a comprehensive species-specific ontology
>>that would be freely available for a large number of researches working with
>>soybean (and others as well).
> 
> I work with Dr. Randy Shoemaker (Research 
> Geneticist USDA-ARS CICGR Ames, IA) we are 
> interested in starting an effort to put together 
> a comprehensive ontology for soybean and then 
> perhaps extend it to other legumes.  As you may 
> know there are microarray chips currently 
> available for soybean and an Affy array will be 
> released soon, thus we are very interested in 
> getting a controlled vocabulary set to ensure 
> meaningful annotations to future microarray 
> experiments can be made.  There are also Tilling 
> mutants for soybean and thus there will be a need 
> for a vocabulary to describe phenotypic variants. 
> Any efforts in this direction will of course be 
> in the public domain.
> 
>>In either case, I can offer you help, and since we
>>at POC are open to collaboration and welcome everyone who is genuinely
>>interested in collaborating, we can certainly initiate a dialog by discussing
>>our mutual interests in soybean ontology project.
>>
>>Since the first version of the Plant Structure 
>>Ontology was released last month,
>>the current task of the POC is work on the growth and developmental stages
>>ontology, primarily having in mind an integration of Arabidopsis and cereal
>>ontologies for the first release. Starting at 
>>the beginning of 2005, we hope to
>>make our two plant ontologies applicable to most of the flowering plants by
>>including other plant species, among others, tomato and legumes (such as
>>Medicago and soybean).
> 
> The first part of our effort would be aimed at 
> getting a growth and developmental stage ontology 
> for soybean established.  I think that this 
> should be the place to start because it will be 
> needed for the microarray experiments to come. 
> At the same time we will look at the published 
> anatomical vocabularies and make a list of terms 
> specific to soybean/legumes that may be needed.
> 
>>Furthermore, over the next two years, POC project will
>>expand its plant-ontology-development effort to include other angiosperms
>>(tomato, barley, cotton and others). At the end, the controlled vocabularies
>>developed by the POC will be generic enough to encompass/cover all the plant
>>model systems; this includes cereals/brassicas/solanaceae/gossypium/legumes.
>>
>>Since I donít know if you need any specific information about ontology
editing
>>tools or ontology structure at this point, I decided to leave it out for now.
> 
> I have DAG-Edit and will use that for the 
> project.  DAG-Edit does not seem intuitive to me 
> so I may have to ask for help from time to time. 
> It seems that I will also need at some point a 
> block of PO numbers for soybean/legumes.  I also 
> have some questions regarding style and correct 
> procedures for the nomenclature.
> 
>>  If
>>you need suggestions and help with the software for editing your ontology,
>>please let me know and don't hesitate to contact us for any other ontology
>>related issues. I would be happy to provide you with information and perhaps
>>give you some suggestions how to build your ontology. If you are interested
in
>>collaboration with POC, I would like to discuss such a possibility with you.
> 
> I will pass this note on to Randy for his 
> consideration and get back in touch with you.
> 
> Regards,
> 
> Rex Nelson
> 
> -- 
> Rex Nelson Ph. D.
> Postdoctoral Fellow
> nelsonrt at iastate.edu

Katica Ilic, TAIR Curator,	     E-mail: katica at acoma.stanford.edu	
The Arabidopsis Information Resource	Tel: (650) 325-1521 ext. 253	
Carnegie Institution of Washington	Fax: (650) 325-6857	
Department of Plant Biology	        URL: http://arabidopsis.org/		
260 Panama St.
Stanford, CA 94305, U.S.A.