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

[Pankaj Jaiswal]

Dear Mary and Carolyn,

Is there a way MaizeGDB can allow the search of their datasets using the 
Trait Ontology (TO) and Plant Ontology (PO) to find the associated 
(mapped terms) phenotype/trait/anatomy/growth_stage terms assigned 
internally by the MaizeGDB in the allele and/or gene annotations.

If I can get a list of trait/phenotype/anatomy terms, their definitions 
and STABLE_IDs along with some hierarchy used by you, I will make sure 
that those terms get integrated in the PO and TO. We will not 
particularly create a ZEA version but integrate them in the reference 
ontologies PO and TO. I am sure many of the Zea terms are already 
integrated. Both Gramene and Plant Ontology projects would like to 
collaborate with you and see that the TO and PO can be used by 
integration and by creating mapping/Xrefs to the existing 
terminology/concepts in MaizeGDB.

Best
Pankaj

Mary Schaeffer wrote:
> 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
> 
> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683