Plant OntologyTM
Gramene is collaborating with The Maize Mapping Project (MaizeDB), The Arabidopsis Information Resource (TAIR), and the International Rice Research Institute (IRRI) as part of the Plant OntologyTM Consortium (POC) to develop a controlled vocabulary for plant-based databases. We aim to facilitate the interoperability of plant-based databases, providing a uniform platform for queries based on controlled vocabularies for a variety of plant-specific knowledge domains, including plant anatomy, plant morphology and plant development. The terms used in the controlled vocabularies will be derived from internationally published sources and will be accompanied by appropriate definitions. Through this effort, the POC aims to foster consistency in the annotation of data by database curators and to encourage international usage of the ontologies.
Trait OntologyTM for
Rice 
Gramene is also a repository for rice functional mutations
and quantitative trait loci (QTL) curated from the literature. To facilitate
the curation of phenotypic trait data, we have developed a
Trait OntologyTM (TO) for Rice. This represents a controlled vocabulary that can be used to describe each trait as a distinguishable
feature, characteristic, quality or phenotypic feature of a developing or mature individual.
The TO for Rice provides a set of terms that are widely used to describe rice phenotypes and
was originally based on IRRI's Standard
Evaluation System for Rice (1996). As it evolves, the TO for Rice will provide the
basis for distributed curation of phenotypic data associated with mutants and QTL. In the future,
the TO for Rice will be expanded to be descriptive of traits across the grasses, thereby
encouraging interoperability across plant databases. In order to realize the full potential
of the rich source of phenotypic information in the cereals, Gramene curators, in collaboration with
IRRI (rice), ICIS (representing several
crops), MaizeDB
(maize) and CIMMYT (maize and wheat), are putting
intensive effort into the development of a Trait OntologyTM
for the Grasses.
Gene OntologyTM 
Developed by the Gene
Ontology Consortium, the goal is to produce a dynamic controlled vocabulary
that has been widely applied in the annotation of the genomes from model
organisms viz. fly, mouse, worm, yeast and
Arabidopsis.
Goals
-
Develop a "Trait OntologyTM" (TO) for Grasses that can be
used to facilitate phenotypic comparisons both within
and between grass genera.
-
Develop the tools and expertise necessary to classify 4000
rice genes according to the "Gene OntologyTM" (GO) classification
system
Support each assertion of phenotypic or the protein information from
rice by Evidence
Codes, that describes the basis for the assertion of either the trait
or the GO components.
Links to flat files
The flat files for the TO / GO terms and definitions
can be downloaded from the following sites and can be browsed by using
the stand-alone browser
Any suggestions for the addition, replacement or modification
of the controlled vocabulary can be made via a web submission
form or by a PDF.
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