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Ontology Database
Type ID or keyword to search    
select ontology (optional)   Gene (GO)  Plant structure (PO)  Growth stage (GRO)
Trait (TO)    Environment (EO) Taxonomy(GR_tax) 		[e.g. flower or TO:0000303]
 
You can search the ontology database by using either of the following queries:

Searches can be limited by checking any one or more of the ontology types (GO/PO/GRO/TO/EO/GR_tax) below the text search box.

For more information on each ontology type please visit the current ontologies section. You may like to browse the tutorial to learn more about the ontologies and how to use the database or may like to seek the help document.

The ontology database aims to provide a collective resource for structured controlled vocabularies (Ontologies) for the following knowledge domains and their associations to various objects such as QTL, phenotype gene, proteins and Ensembl rice genes.
  • Plant Ontology (PO)
    • Plant Structure (morphology, organs, tissue and cell types)*
    • Growth stages (plant growth and developmental stages) 
  • Trait Ontology (TO)
    • Plant traits and phenotypes 
  • Gene Ontology (GO)** 
    • Molecular function
    • Biological process
    • Cellular component
  • Environment Ontology (EO)
  • Gramene's taxonomy ontology (GR_tax)
The vocabularies are derived from internationally published sources and the terms are accompanied by appropriate definitions. Through this effort, the database as member of Gene Ontology Consortium, aims to foster consistency and encourages international usage of these ontologies in the annotation of data objects.

[ * Developed by the Plant Ontology Consortium / ** Developed by the Gene Ontology Consortium]
Links to the most up to date versions of ontology flat files are provided below. Definitions of the terms in all three ontologies are contained in respective definition files.  You may wish to download the flat files and view them by using a stand alone ontology browser DAG-EDIT
Current Ontologies
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(in OBO format)
Trait OntologyTM (TO)

It is a controlled vocabulary to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature individual. Examples are glutinous endosperm, disease resistance, plant height, photosensitivity, male sterility, etc.

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Ontology + Definitions
Gene OntologyTM (GO)

Developed by the Gene Ontology Consortium to help annotate information on gene products (not the genes) using the following three organizing principles of molecular function, biological process and cellular component. Copyright © Gene Ontology Consortium.
  
All ontologies + Definitions
Molecular Function: The tasks performed by individual gene products; example is Rubisco
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Biological Process: Broad biological goals, such as photosynthesis or ripening, that are accomplished by ordered assemblies of molecular functions.
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Cellular Component: Subcellular structures, locations, and macromolecular complexes; examples include chloroplast, telomere, vacuole, nucleus, etc. .
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Plant OntologyTM (PO)

Gramene is collaborating with The Plant Ontology Consortium (POC) to develop a controlled vocabulary for plant structure (anatomy) and growth stages.

    

   
Plant Structure (PO): The controlled vocabulary of plant structures representing organs, tissue and cell types. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.
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 Ontology + Definitions
Cereal Plant Growth Stages (GRO):   The controlled vocabulary of growth and developmental stages in various cereal plants. Examples are germination, seedling, booting, flowering, etc. Available only for rice, maize, sorghum, wheat, wheat, oat and barley.
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 Ontology + Definitions
Environment Ontology  (EO)

It represents a controlled vocabulary to describe different types of supplemental environments that have been reported in the experimental profiles of gene expression and phenotype (mutant and QTL) studies on cereal plants.
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Ontology + Definitions
Taxonomy Ontology  (GR_tax)

It is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxonomy, the revisions were made as and when/where required in the rankings. The rank of genome types was added by this project. This taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.
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Ontology + Definitions
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Documentation
 More information on ontology,  their structure,  concepts and  help on how to search [VIEW]
Release Notes
Evidence codes
 Defines the evidence codes and explains how they are used for PO annotation of genes/gene products/phenotypes
FTP archive
 Anonymous user access to Plant Ontology archive is at ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/ontology/ .
The ontology files are organized by ontology type(s).
Ontology
submission 		Any suggestions for the addition, replacement or modification of the controlled vocabulary can be made via a web based SUBMISSION FORM or by using a PDF of the form. If you have problems look for Submission help document.
Associations
 Gene ontology associations based on Gramene curation and Interpro assignments.
Results available at:
Publications

Gramene: development and integration of trait and gene ontologies for rice
Comparative and Functional Genomics, Vol 3(2), April, 2002
[ see Abstract] or [search for full text (search for "91016047")] .

The Plant OntologyTM Consortium and Plant Ontologies  
Comparative and Functional Genomics, 2002, Vol 3(2), April, 2002
[see Abstract] or [search for full text (search for "91016119")]

Creating the gene ontology resource: design and implementation.   
Genome Research, 2001, Vol 11(8), 1425-1433 [Abstract]  [Full Text]

Gene Ontology: tool for the unification of biology.   
Nature Genetics, 2000, 25: 25-29 [Abstract]  [Full Text]