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.

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*
Arabidopsis	TAIR	Browse*	--	Download*	Download*
Maize	MaizeGDB	--	--	Download	Download

* Both Gramene and TAIR database projects have started using the plant structure ontology developed by POC for flowering plants. They 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
Arabidopsis	TAIR	Browse	--	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.