Plant Ontology Consortium

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SVN Access and Download Instructions

Plant Ontology

Plant ontology is not an extensive collection of terms that describe structure and developmental stages of a plant. However they are arranged in a structured order/network based on the biological concept describing the term's relationship in an ontology tree. Learn more about the ontology concepts and how they are organized. One of our objective is to integrate species-specific vocabulary terms into unified flowering-plant ontologies for rice, maize, Arabidopsis and other Angiosperms. Species specific ontologies are also listed in the following sections.

Click here to download the most recent versions of the Plant Ontology in OBO format.

Click here to download the most recent versions of the Plant Ontology in OWL format .

Beginning with Version #14 (January 2011), the Plant Ontology has been merged from two separate files (po_anatomy.obo and po_temporal.obo) into a single file called plant_ontology.obo. We recommend that all users switch to the single, merged file. If you need current versions of the po_anatomy.obo and po_temporal.obo, please contact us.

The plant ontologies, which includes both the plant structure and growth and devlopment stages can be downloaded as a single file in TBL format.

Previously used ontology files from the POC and collaborators

The ontologies are:

Plant Anatomy

A controlled vocabulary of plant's morphological and anatomical structures representing organs, tissues, cell types and their biological relationships based on spatial and developmental organization. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.

	Sources	Browse at source site	OBO format file Includes ontology and definitions.	Ontology flat files	Definition flat files	Term List files
Plant Anatomy	POC	Browse	Download	--	--	Download
Cereals	Gramene	Browse*	--	Download*	Download*	--
Maize	MaizeGDB	--	--	Download	Download	--

* Gramene, TAIR and MaizeGDB database projects have started using the plant structure ontology developed by POC for flowering plants. Both Gramene and TAIR have retired the cereal and Arabidopsis specific anatomy ontologies previously developed by them. You can still download the species specific ontologies by visiting the download links.

Plant Structure Development Stage

A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.

	Sources	Browse at source site	OBO format file Includes ontology and definitions	Ontology flat files	Definition flat files	Term List files
Plant Structure Development Stage	POC	Browse	Download	Download	Download	Download
Cereals	Gramene	Browse	Download	Download	Download	--

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Ontology Download Instructions

SVN repository access

• Anonymous access

  The SVN repository "Poc" can be checked out with the following command:
  svn co http://palea.cgrb.oregonstate.edu:/svn/Poc

  There is no password for anonymous user. If your version of SVN asks for a password, use an empty password. Users can also browse the repository using Viewvc by pointing a web browser to http://palea.cgrb.oregosntate.edu/viewsvn/Poc/.

• Developer access

  If you are an ontology developer recognized by the Plant Ontology Consortium, please follow the instructions on developers guide to SVN access.

Browsing ontologies

If you are interested in browsing the Ontology please visit the browser links

Database dumps

The latest MySQL dump files, as well as previous versions are available Here.

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Last modified: Fri Dec 16 16:52:22 2011

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Plant Ontology by Plantontology.org is licensed under a Creative Commons Attribution-NoDerivs 3.0 United States License. Based on a work at www.plantontology.org.