Plant Ontology Consortium

Home Search/Browse Plant Ontologies Download Ontologies Request PO terms Documentation Tutorials Mail Archives Site Map Feedback

CVS Access and Download Instructions

Plant Ontologies

Plant ontology is not an extensive collection of terms thatdescribe structure and developmental stages of a plant. However theyare arranged in a structured order/network based on the biologicalconcept describing the term's relationship in an ontology tree. Learnmore about the ontologyconcepts and how they are organized. One of our objective is tointegrate species-specific vocabulary terms into unifiedflowering-plant ontologies for rice, maize, Arabidopsis and otherAngiosperms. Species specific ontologies are also listed in thefollowing sections.

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

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

The ontologies are:

Plant Structure

A controlled vocabulary of plant's morphological and anatomicalstructures representing organs, tissues, cell types and theirbiological relationships based on spatial and developmentalorganization. Examples are stamen, gynoecium, petal, parenchyma,guard cell, etc.

Species	Sources	Browseat source site	OBOformat file Includes ontology and definitions.	Ontologyflat files	Definitionflat files
Floweringplants	POC	Browse	Download	Download	Download
Cereals	Gramene	Browse*	--	Download*	Download*
Maize	MaizeGDB	--	--	Download	Download

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

Plant Growth and developmental stage

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

Species	Sources	Browseat source site	OBOformat file Includes ontology and definitions	Ontologyflat files	Definitionflat files
Floweringplants	POC	Browse	Download	Download	Download
Cereals	Gramene	Browse	Download	Download	Download

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

---

Ontology Download Instructions

CVS repository access

• Anonymous access

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

  There is no password for anonymous user. If your version ofCVS asks for a password, use an empty password. Users can also browsethe 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 PlantOntology 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 areavailable Here.

---

Last modified: Fri Jul 23 19:41:05 2010

| Feedback/Contact Us | Copyright Statement

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.