PLANT ONTOLOGY TM CONSORTIUM
 
The  Plant OntologyTM Consortium aims to facilitate the interoperability of plant-based databases, by providing a uniform platform for queries based on controlled vocabularies for a variety of plant-specific knowledge domains such as
  • plant anatomy (includes morphology)
  • plant development 
  • plant traits (or phenotypes)
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.
Plant Ontology search
Plant Ontology Database
Type in ID or keyword to search for [e.g. cold tolerance or TO:0000303]  HELP 


 
Current Ontologies

The organizing principles of PO are anatomy, temporal and traits. Links to the most up to date versions of the ontology flat
files are provided below. Definitions of the terms within all three of the ontologies are contained in respective definitions files.
If you wish you can download the flat files and view them by using a stand alone ontology browser DAG-EDIT
 
 
Anatomy The Plant Ontology (PO) representing plant parts and their anatomy in terms of organs, tissue and cell types. 
Also available at TAIR (Link)		 Ontology Definition
Temporal The Plant Ontology (PO) representing developmental stages (growth stages) in a plant's life. 
Also available at TAIR (Link)		 Ontology Definition
Traits The Trait Ontology (TO) representing a controlled vocabulary to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature individual. 
Also available at Gramene (Link)		 Ontology Definition

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Documentation

General Documentation  Provides an overview of the PO project, definitions of key concepts, and describes ontology file formats 
Annotation Guide Describes the use of PO terms for annotating the tissue specific transcript expression or protein localization or structural modifications (as phenotypes) in a plant parts
Evidence Codes Defines the evidence codes and explains how they are used for PO annotation of genes/gene products/phenotypes
Usage Guide A guide to the general style and logic applied to the development and maintenance of the ontology content 
DBxrf_abbs Provides a list of the database abbreviations used by PO

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FTP archive and anonymous CVS repository access
 

Plant Ontology Submission/suggestion form

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 HELP
 

Consortium members

 Gramene
A Resource for Comparative Grass Genomics		 Lincoln Stein (Advisor)
Susan McCouch (Advisor)
Pankaj Jaiswal (Development and curation)
Doreen Ware (Advisor)
Kuan Chang (Web site and ontology browser)
Peter Van Buren (System administrator)
 International Rice Research Institute Richard Bruskiewich (Development and curtaion)
Victor Ulat (Development and curation)
 MaizeDB
 Maize Mapping Project		 Edward H. Coe (Advisor)
Mary Polacco (Advisor)
Leszek D. Vincent (Development and curation)
 The Arabidopsis Information Resource Sue Rhee (Advisor)
Leonore Reiser (Development and curation)
Tanya Berardini (Development and curation)

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Publication

The Plant OntologyTM Consortium and Plant Ontologies  [Abstract]  [Full Text]
Comparative and Functional Genomics, Vol 3(2), April, 2002     

Gramene: development and integration of trait and gene ontologies for rice  [Abstract]  [Full Text]
Comparative and Functional Genomics, Vol 3(2), April, 2002     

 

Contact

For suggestions and further information please write to Vincent Leszek at Leszek@missouri.edu
Department of Agronomy, University of Missouri-Columbia, Columbia, Missouri, 65211-7020, USA.
 

Acknowledgements

We kindly acknowledge Michael Ashburner (FlyBase, EBI, UK) and the Gene Ontology Consortium
This work is supported by USDA CREES grant 00-52100-9622 and USDA ARS Specific Cooperative Agreement grant 58-1907-0-041 to Gramene database.
 

Disclaimer

Copyright © 2001-2003 Plant Ontology Consortium. Permission to use the information contained in this website was given by
the researchers/institutes who contributed or published the information. Users of the Plant Ontology website contents are solely responsible for compliance with any copyright restrictions, including those applying to the website. Documents from this server and web site are provided "AS-IS" without any warranty, expressed or implied.
 

Site created by Pankaj Jaiswal (Gramene database).