inquiry/wheat (fwd) (PR#7)

[Katica Ilic]

Dear Garcia,

I am not aware of any ongoing effort in the public sector with respect to
developing anatomy and developmental stages ontologies specifically for wheat.

However, Gramene has a Cereal Plant Anatomy ontology (the controlled vocabulary
of plant anatomy representing organs, tissues and cell types), and Cereal Plant
Growth Stages ontology (the controlled vocabulary of growth and developmental
stages; examples are germination, seedling, booting, flowering, etc.), available
for rice, maize, sorghum, wheat, oat and barley. You can download and browse
these two ontologies on our POC web site or at Gramene.

Currently, we are in the process of integrating Arabidopsis and cereal
ontologies into generic plant anatomy ontology. The first version of the
ontology will be released in the summer. We hope to make it applicable to most
of the flowering plants. Furthermore, over the next two years, POC project will
expand its plant-ontology-development effort to include other crops such as
wheat, barley, tomato legumes and cotton. 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.

The short answer to your question about the ontology editing tool, Protégé is
no, we don’t use it for our Plant anatomy ontology, and I am not sure how widely
this tool is used for biological ontologies. Instead, we use the DAG-edit, which
is also a standard editor for GO  (http://www.geneontology.org). Arabidopsis,
Gramene and maize ontologies that you have seen on the POC web site, are all
edited using DAG editor.

I have recently communicated with Shenghui Wang from UK (wangs at cs.man.ac.uk),
who was telling me that he uses Protégé for building the ontology for
Ranunculus, so my suggestion to you is to contact him. He might be able to give
you some specific information about the Protege. Unfortunately, I don’t have any
experience with this tool, but from what I understood, this ontology editor has
only IS_A relationship type, which can be seen as a kind_of relationship type.
The DAG edit has three relationship types describing the component/location
(PART_OF), class (INSTANCE OF) and lineage (DERIVED_FROM). You can see example
for each relationship type on our web site
(http://www.plantontology.org/docs/otherdocs/poc_file.html).

Thank you for your interest in POC and plant ontologies. For additional
questions about our project, plant ontologies and editing tools, please feel
free to contact me directly or send us an email at po at plantontology.org.

Best regards,

Katica Ilic, POC curator

>Date: Tue, 11 May 2004 23:39:06 +1000
> From: a.garcia at imb.uq.edu.au
> Reply-To: po-dev at plantontology.org
> To: po at plantontology.org
> Subject: inquiry/wheat
> 
> I would like to know if there is an ontology for wheat; I
> would also like to know if someone has ported the plant
> ontology to protege. cheers
> 
> 
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.