The Plant Ontology Consortium

website: http://www.plantontology.org

Contact Information for deliverables Lincoln Stein, lstein@cshl.org

• Pilot project to develop a common set of standardized and controlled vocabulary (Ontology) terms to describe anatomy and developmental stages for rice, maize and Arabidopsis.

• Apply the vocabulary to the task of describing the localized expression of the genes and phenotypes of mutants in experimental and agronomically important plants, such as Arabidopsis, rice and maize

• Develop an infrastructure to support plant comparative genomics to discover patterns of similarities and dissimilarities involved in plant development.

• Impart training to collaborators from other model organism databases.

• Community outreach to involve plant researchers, breeders, and systematists

Project Objectives

Some example datasets displaying transcript or protein expression, localization and Mutant phenotypes in cereals and Arabidopsis which needs annotation with a standardized anatomy and growth stage vocabulary terms.

Example Data Sets

• Find all rice mutants associated with dwarfism (Trait-Plant Height/culm or stem length).

• What genes are predicted to be involved in association to a particular phenotype ?

• Find orthologs between rice / maize / Arabidopsis that may lead to similar phenotypes.

• Show all the genes that are induced by growth hormone which are also expressed in the plant’s internode.

Suggested, application of plant ontology helping plant biologist to make useful queries.

Plant Ontology (PO)

Plant anatomy

Describes the location in a plant where the gene is expressed, a gene product is localized and its associated phenotype is observed

Plant growth stage

Describes the developmental stage at which the gene and /or phenotype expression is observed and assayed

In order to help in annotation, the project will develop the standardized, controlled vocabulary (ontology) for following aspects of plants.

Classically various models of

plant glossaries were established

over a period of time, by

numerous researchers, namely,

Katherine Esau, A. Fahn,

Elizabeth Cutter and those who

defined the growth stages in

different plants. These glossaries

were primarily organized by

simple hierarchy addressing only

one to one relationships.

Term-1

Term-4

Term-2 Term-3

instance_of

part_of

Term-5

derived_from

Term-6

instance_of

Instance_of

Term-7

Anatomy

instance_of

An example displaying annotation of Arabidopsis gene PHR1 using the Ontology term.

Year-1Q1-Preview and rel 0.1 of Arabidopsis and cereal ontology

Q2-Preview rel. 0.2, 1st POC meeting

Q3-Preview rel. 0.3, 2nd POC meeting

Q4-Dicot–monocot integration complete. Rel 1.0. 3rd POC and 1st users meeting at Botany 2004.

Year-2Q1-Preview and rel 2.0. legume and solanaceae groups join. Maize associations

begin. 4th POC meeting

Q2-Preview rel. 3.0, 5th POC meeting, 2nd users meeting

Q3-Preview rel. 4.0, with preliminary legume and solanaceae ontology

Q4-Preview rel. 5.0 with legume and solanaceae integration complete and begin association activities. 6th POC and 3rd users meeting

Year-3Q1-Rel 6.0. Agronomically important crops join. 7th POC meeting

Q2-Rel. 7.0, 8th POC meeting, 4th users meeting

Q3-Rel 8.0, with prelim. Ontology contains prelim term from new members

Q4-Rel 9.0 new members integrated. 8rd POC and 5st users

Data Release timetable:

Discussion points

• What mechanisms should be introduced so that all the groups annotating rice gene products share the same annotation tools, guidelines/standards and Ontology association files.

Last Name

First Name Institution Role

Stein Lincoln Cold Spring Harbor Laboratory

PI

McCouch Susan Cornell Univ. co-PI

Kellogg Elizabeth University of Missouri co-PI

Rhee Sue Carnegie Institution of Washington

co-PI

Jaiswal Pankaj Cornell University co-PI

Ware Doreen Cold Spring Harbor Laboratory

co-PI

Reiser Leonore Carnegie Institution of Washington

Key person

Stevens Peter Missouri Botanical Garden, University of Missouri

Co-PI

Vincent Leszek University of Missouri Key person

Douglas Cook University of California Davis

Key person

Tanksley Steve Cornell University Key person

Medicago truncatula functional genomics

Core participants

Supporting members