Objectives:
Gramene (http://www.gramene.org) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated sequence data and associated biological information including mutants, phenotypes, polymorphisms and Quantitative Trait Loci. In order to support queries across various data sets as well as across external databases, Gramene is employing three related controlled vocabularies. First is the Trait Ontology (TO) will be implemented across the cereal crops and plants to curate and evaluate phenotype comparisons. An initial vocabulary for TO and definitions for TO terms is available at http://www.gramene.org/plant_ontology/). Second is a Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression and localization of gene and gene products. The TO and PO are both in the early stages of development in collaboration with International Rice Research Institute, TAIR, MaizeDB, International Crop Information System and CIMMYT. Finally, as part of the Gene Ontology consortium, we will classify confirmed or predicted rice gene products. The development of plant specific vocabularies is open for community discussion.
 

Ontology database search:
The ontology search page  is divided into two sections. The first section allows you to query the  various terms  and data sets contained in our ontology database. The second is in interface that displays and allows navigation of the ontology terms and their relations. Presently the data sets available for query are Trait Ontology (TO)^TM for rice and the Gene Ontology^TM terms mirrored from http://www.geneontology.org

Ontology Search Section:
In order to search for a term type in term ID or keyword [e.g. cold tolerance or 303]

Ontology Display Section:
This is the major part of QuickGO, and displays one GO term at a time, along with
various additional contextual data including

Term Name:
This is the primary name assigned to this term by either the GO consortium or the Gramene curator for the rice TO. It is intended to be
sufficient to describe the term without requiring any further reference to the structure of  the ontology.

Term ID:
This is the accession number of this term. GO accessions are in the form 'GO:'  and  TO accessions are in the form 'TO:' followed by exactly seven decimal digits e.g. (GO:0006818), (TO:0000303)

Synonyms (optional):
The synonyms are other alternate names for this term. If there are no synonyms for the term you're viewing then this box won't be present - the same applies to all the potentially optional fields in the display.

for example

%cold tolerance ; TO:0000303 ; synonym:CTol

OR

%cytoplasmic male sterility type ; TO:0000232 ; synonym:MaizeDB-64827 ; synonym:CMS

Definition:
The optional definition, if present, describes the term in more detail. GO / TO definitions are
drawn from a variety of sources.

for example

term: 100-grain weight
goid: TO:0000269
definition: measurements in grams of 100 well-developed whole grains, dried to 13% moisture content, weight on a precision balance. Determine at growth stage 9
definition_reference: IRRI:SES
definition_reference: GR:pj37 (curator)

Lineage: Derivation
This box is always present, and shows every possible path back from the selected term  to the root. Due to the 'strong path' property of the TO/GO, the implication is that if a given trait term / gene product has been assigned an ID, it is also implicitly mapped to all
the terms shown in this display. Clicking on any of the terms in the lineage will select that term as the current  displayed term and refresh the window.

Term Relationships:

Parent and Child terms:
These boxes display the immediate parents-children relationships of the currently selected term.
 

Parent-child relationships between terms are represented by indentation:

  parent_term
    child_term

Instance relationship: (marked by "%" percentage sign in the flat text files, or by [i] in the Ontology browser section)

  %term0
    %term1 % term2

To be read as term1 being an instance of term0 and also an instance of term2. Part of relationship: (marked by "<" less than sign or by [p] in the Ontology browser section)

  %term0
    %term1 < term2 < term3

<fertility or sterility trait ; TO:0000392 < whole plant related trait ; TO:0000398
  %fertility related trait ; TO:0000497
     %female fertility restoration trait ; TO:0000498
       %male fertility restoration trait ; TO:0000308 % hybrid evaluation ; TO:0000334
     %incompatibility trait ; TO:0000035
        %hybrid incompatibilty ; TO:0000036
        %self-incompatibility trait ; TO:0000310
     %sterility related trait ; TO:0000485
        %female sterility trait ; TO:0000358

Note that terms may have more than one parent, and may (obviously) have zero or more children. However, currently there are no links between the TO and the three sub-ontologies within GO. You can click on any of the terms in these lists to make the clicked term the current one for display.

Mutant/Protein Associations: Common Concurrent Assignments
This section, if present, contains a list of TO/GO terms that are, statistically speaking,  commonly assigned to the mutants or proteins along with the currently displayed term. For example, "hydrogen transport (GO:0006818)" is mapped by various methods to approximately 19 proteins from rice  but four of such proteins from rice are also mapped to the "P-type ATPase (GO:0015662)". This display allows you to investigate potential conceptual linkages between otherwise unrelated GO terms on the basis of their common assignment to sets  of proteins. This is just an example with the GO term, in future we will provide the similar examples for the mutants and phenotypes associated with the TO as well as GO terms.

Evidence codes:
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. The table of evidence codes is use by Gramene is available at http://www.gramene.org/plant_ontology/evidence_codes.html

Links to Ontology 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

Trait OntologyTM for Rice:            Trait terms                  Definitions                   Trait.zip File

Gene OntologyTM:                         Molecular function      Biological process      Cellular component       Definitions

Suggestions/Corrections:
If you would like to make any suggestion for the new term/definition/update/correction to an existing term, please use the ONLINE submission form the purpose. We appreciate your valuable feedback on our efforts. Needless to mention your contribution will be duly acknowledged.

For more details on the Gene Ontology terms please refer to www.geneontology.org