From Mary.Schaeffer at ars.usda.gov Mon Mar 10 13:56:13 2008 From: Mary.Schaeffer at ars.usda.gov (Mary Schaeffer) Date: Mon, 10 Mar 2008 12:56:13 -0500 Subject: [Po-dev] Re: Question concerning MaizeGBB term ontologies In-Reply-To: Message-ID: 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" wrote: > Mary, > > Can you help Raymond with his inquiries on ontologies? > > Thanks, > Carolyn > > > On 3/6/08 11:49 AM, "Raymond DiDonato" > 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 > From pj37 at cornell.edu Mon Mar 10 16:49:34 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 10 Mar 2008 16:49:34 -0400 Subject: [Po-dev] Re: Question concerning MaizeGBB term ontologies In-Reply-To: References: Message-ID: <47D59EDE.4070507@cornell.edu> 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