CVS Access and Download Instructions

Plant Ontologies

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.

We recommend our users to use the OBO format files only. You can learn more about the OBO format by visiting this link at the Gene Ontology website.

*** Download instructions for getting the plant ontologies from Poc CVS repository and database dumps can be found here.

The ontologies are:

Plant Structure

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.

Species	Sources	Browse at source site	OBO format file Includes ontology and definitions.	Ontology flat files	Definition flat files
Flowering plants	POC	Browse	Download	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 Growth and developmental stage

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

Species	Sources	Browse at source site	OBO format file Includes ontology and definitions	Ontology flat files	Definition flat files
Flowering plants	POC	Browse	Download	Download	Download
Cereals	Gramene	Browse	Download	Download	Download

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

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Ontology Download Instructions

CVS repository access

• Anonymous access

  The CVS module name "Poc" can be checked out with the following command:
  cvs -d :pserver:anonymous@brebiou.cshl.edu:/usr/local/cvs co Poc

  There is no password for anonymous user. If your version of CVS asks for a password, use an empty password. Users can also browse the repository using Viewcvs by pointing a web browser to http://brebiou.cshl.edu/viewcvs/Poc/.

• Developer access

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