PLANT ONTOLOGY TM CONSORTIUM


  • Plant Ontology Search
  • Current Ontologies
  • Plant Ontology
  • Trait Ontology
  • Gene Ontology
  • Documentation
  • FTP archive and CVS 
  • Ontology Submission form
  • Consortium members
  • Publications 
  • Contact 
    		•
    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. anther /  cold tolerance /  chloroplast  /  TO:0000303] 

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    Current Ontologies

    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

    Gene Ontology Gene Ontology (GO) developed by the Gene Ontology Consortium to help annotate the information on gene products (and not the genes) using the three organizing principles of molecular function, biological process and cellular component as follows. Copyright © Gene Ontology Consortium.   Ontology Definition
    Molecular function The tasks performed by individual gene products; example is and Rubisco   Ontology As above
    Biological Process Broad biological goals, such as photosynthesis or ripening, that are accomplished by ordered assemblies of molecular functions  
    		 Ontology As above
    Cellular Component Subcellular structures, locations, and macromolecular complexes; examples include chloroplast, telomere, and vacuole Ontology As above

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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, 2002, Vol 3(2), April, 2002     

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

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

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

    On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998.   [HTML]

     

    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 but not limited the website contents. Documents from this server and web site are provided "AS-IS" without any warranty, expressed or implied.
     

    Site created by Pankaj Jaiswal (Gramene database).