[Po-dev] Re: Question concerning MaizeGBB term ontologies

[Mary Schaeffer]

Hi  Raymond,

RE PO anatomy terms.
The Zea terms you refer to --  are anatomy terms developed prior to the
Plant Ontology project, with very detailed descriptions of the terms as
applied to maize. All of these have, in MaizeGDB, a Plant Ontology
counterpart, but we do retain the maize-specific definitions, with links to
PO central for more general view.  These are posted at the Plant Ontology
site in the format of the time. If you require the OBO format, someone in
the Plant Ontology project needs to make the conversion as they are
responsible for maintaining any of these formats. I can provide to you the
terms and definitions we have with the PO accession attached if that would
help. Just let me know.

Note,  the associations provided by us to the Plant Onotology site are to
GENES which have a phenotype in any of the alleles or mutants for that gene.
All our phenotypes are linked to terms of the Plant Ontology, although we
may use a synonym - eg for kernel, we use the  maize term, but have the
Plant Ontology term clearly identified in the database, along with the PO
identifier.

Let me know if I can do something else here,

 mary


-- 
Mary Schaeffer (Polacco), PhD Geneticist/Curator MaizeGDB USDA/ARS Plant
Genetics Research Unit; Adj Assoc Professor, Division of Plant Sciences; 203
Curtis Hall, University of Missouri, Columbia, MO 65211
Phone: 573 884 7873 FAX: 573 884 7850



On 3/6/08 1:17 PM, "Carolyn Lawrence" <Carolyn.Lawrence at ars.usda.gov> wrote:

> Mary,
> 
> Can you help Raymond with his inquiries on ontologies?
> 
> Thanks,
> Carolyn
> 
> 
> On 3/6/08 11:49 AM, "Raymond DiDonato"
> <raymond.didonato at biobase-international.com> wrote:
> 
>> Dear Dr. Lawrence,
>> 
>> I am the product manager for Plant Databases at BIOBASE Corporation, a
>> company that develops and markets curated protein database products.
>> 
>> We are interested in possibly utilizing the MaizeGDB structure and
>> phenotype ontologies in order to increase the level of curated detail in
>> our database.
>> 
>> I noticed that while MaizeGDB uses the PO, it also uses a supplemental
>> ontology (with the term designation ZEA) to annotate proteins.  I also
>> found this ontology at CSHL, however it is not available in OBO format.
>> 
>> I was also unable to find a downloadable version of the MaizeGDB
>> phenotype hierarchy on your webpages.
>> 
>> I am wondering whether theses two hierarchies, the ZEA structure
>> hierarchy and the phenotype hierarchy are available in OBO format- I am
>> also wondering whether these would be available for use by BIOBASE, of
>> course crediting MaizeGDB as the source of the hierarchies.
>> 
>> Your comments and suggestions are appreciated.
>> 
>> Kind regards,
>> Raymond DiDonato
>> Product Manager, Plant Databases
>> BIOBASE Corporation
>