Soybean ontology (Feedback Submission from Plant Ontology Live Site) (PR#23)

[Katica Ilic]

Hi Rex,

The short answer to your question would be: us at Plant Ontology Consortium. You
have definitively contacted the right people. I am happy to hear that you are
interested in working on the ontology for soybean. 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. 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 ‘in-house’ 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). 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). 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 don’t 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. 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.


Best regards,

Katica Ilic

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.