The Plant Ontology ConsortiumLincoln Stein1, Susan McCouch2, Elizabeth Kellogg3, Seung Rhee4,

Pankaj Jaiswal2, Doreen Ware1, Peter Stevens5

1Cold Spring Harbor Laboratory, Cold Spring harbor, NY; 2Cornell University, Ithaca, NY; 3University of Missouri, St. Lois, MO; 4Carnegie Institution of Washington, Stanford University, San Francisco, CA; 5Missouri Botanical Garden, University of Missouri, St. Lois, MO

website: http://www.plantontology.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

• 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.

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.

The PO Consortium adopted a simple data structure called the Directed Acyclic Graph

(DAG), keeping it consistent with its use by the Gene Ontology Consortium

(www.geneontology.org) . This structure is a type of hierarchy where the biological

concepts are organized as a network tree structure in which the nodes at the top (“root”)

of the tree are more general cases of specific terms at the bottom (“leaves”) of the

structure. Like a simple hierarchy, children are not allowed to be their own ancestors;

hence cycles are forbidden. The different term-term relationships described are:

instance-of:

This relationship is used in both the developmental and anatomy ontologies to indicate the relationship between a specific term to a more general one. For example achenium is an instance-of a dry indeshiscent fruit, which in turn is an instance-of fruit.

part-of:

This relationship is used in the anatomy ontology to indicate a subpart/part relationship within a tissue or organ. Ectocarp is part-of pericarp, which in turn is part-of fruit

derived-from:

This relationship is used in the anatomy and developmental stage ontologies to indicate the temporal relationship between a tissue or organ and its developmental predecessor. Ectocarp is derived-from ovary outer.

Unlike a simple hierarchy, child nodes are allowed to have more than one parent node, thus allowing multiple child to parent relationships.

The broader impact of this project is that it will provide a framework of plant development to allow researchers to make meaningful cross-database queries across the various species-specific resources in order to discover patterns of similarities and dissimilarities involved in plant development. For example, researchers will be able to obtain a definitive list of genes whose action affects plant stem development. The interaction between research communities will be facilitated by a “rosetta stone” that bridges their historical differences in terminology. This will allow the fruits of research in one plant species to be more easily used in the study of other species, leading to a greater understanding of plant biology.

Medicago truncatula functional genomics

Last Name First Name Institution Role E-Mail

Stein Lincoln Cold Spring Harbor Laboratory PI lstein@cshl.org

McCouch Susan Cornell Univ. co-PI srm4@cornell.edu

Kellogg Elizabeth University of Missouri co-PI kellogge@msx.umsl.edu

Rhee Sue Carnegie Institution of Washington co-PI rhee@acoma.stanford.edu

Jaiswal Pankaj Cornell University co-PI pj37@cornell.edu

Ware Doreen Cold Spring Harbor Laboratory co-PI ware@cshl.org

Reiser Leonore Carnegie Institution of Washington Key person lreiser@acoma.stanford.edu

Stevens Peter Missouri Botanical Garden, University of Missouri

Key person peter.stevens@mobot.org

Vincent Leszek University of Missouri Key person Leszek@missouri.edu

Douglas Cook University of California Davis Key person drcook@ucdavis.edu

Tanksley Steve Cornell University Key person sdt4@cornell.edu

• Plant anatomy ontology: Anatomic terms and relationships.• Plant development ontology: Developmental terms and relationships.• Plant Ontology definitions: Definitions of anatomy and developmental terms• The Plant Ontology Consortium website.• A CVS repository and FTP site for distribution of the consortium’s resources

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

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

NSF Award - #0321666

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 the

one to one relationships.An example displaying how “endosperm” will be defined in the anatomy tree. An example displaying the organization of growth

and developmental stages in rice plant.

An example displaying the organization of fruits in an anatomy ontology tree and their relationship to each other.

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

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

Example Data Sets

Project Objectives

Information/Materials to be Generated:

Broader Impact