the plant ontology consortium website: contact information for deliverables lincoln stein,...
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The Plant Ontology Consortium
website: http://www.plantontology.org
Contact Information for deliverables Lincoln Stein, [email protected]
• 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
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