inquiry/wheat (fwd) (PR#7)

[Katica Ilic]

Richard, Thanks for the info, I'll get in touch with Diane.
See you next week.

Katica


On Wed, 12 May 2004, Bruskiewich, Richard (IRRI) wrote:

> Diane Mather of McGill University, Canada is interested in this. A wheat
> ontology will also be relevant to the Generation Challenge Program. CIMMYT
> will probably guide that effort.
>
> Richard
>
> -----Original Message-----
> From: Katica Ilic [mailto:jitterbug at plantontology.org]
> Sent: Thursday, May 13, 2004 3:18 AM
> To: a.garcia at imb.uq.edu.au
> Cc: po-dev at plantontology.org
> Subject: Re: inquiry/wheat (fwd) (PR#7)
>
>
> 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.
>

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Katica Ilic             		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.
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