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Gramene Ontologies Database

Ontology Search Find: Ontology Type: Gene (GO) Plant Structure (PO) Growth Stage (GRO) Trait (TO) Environment (EO) Taxonomy (GR_tax) All Ontology Types Options: Exact Match Include Obsolete Terms E.g., flower or TO:0000303.

Annotation Search Find: Annotation Type: Ensembl arabidopsis gene Ensembl rice gene Ensembl sorghum gene Gene Germplasm Map set Marker library Marker species Protein QTL All Object Types Options: Exact Match E.g., d1 or waxy.

The Ontologies database provides a collective information 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 anatomy and the stages of plant development
• 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)
[ * Developed by the Plant Ontology Consortium / ** Developed by the Gene Ontology Consortium]

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.

Search or Browse Options

Home Page	Search the Ontologies database by keyword, and optionally filter by ontology. Get an introduction to ontologies.
Browse	Browse by a specific ontology, get a general introduction to the ontologies in Gramene, or download the ontologies and definitions.

Help

Help	Presents an overview on how to use the Ontologies database and lists explanations of field names.
Tutorial	More in-depth than the help pages, use the tutorial for an exaple of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ	Frequently Asked Questions - see what questions users have asked, and get the developers answers.
Release Notes	For more information about the most recent release.
Evidence codes	Defines the evidence codes and explains how they are used for PO annotation of genes/gene products/phenotypes

Ontology Submission

Any suggestions for the addition, replacement or modification of the controlled vocabulary can be made via the Plant Ontology Consortium's PO Term Requests Tracker or the Trait Ontology Consortium's TO Term Requests Tracker.

Download

The data can be downloaded in bulk from our FTP Plant Ontology archive at ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/ontology/. The ontology files are organized by ontology type(s).

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 Ontology™ 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]

Acknowledgements

• Plant Ontology has been developed and contributed by the Plant Ontology Consortium. Gramene is collaborating with The Plant Ontology Consortium (POC) to develop the controlled vocabulary for plant anatomy and the stages of plant development.
• Gene Ontology has been developed and contributed by the Gene Ontology Consortium. Gene ontology associations are based on Gramene curation and Interpro assignments. Results are available at:
  • Gramene [view]
  • Gene Ontology Consortium [view] - [download]
  • Help on Gene Ontology associations [view]
• For a list of data contributors, please see Collaborators and Contributors.

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