Transcript nsf_awardees_09_2003

The Plant Ontology Consortium
1
Stein ,
Lincoln
NSF Award - #0321666
2
McCouch ,
3
Kellogg ,
Susan
Elizabeth
Seung
2
1
5
Pankaj Jaiswal , Doreen Ware , Peter Stevens
4
Rhee ,
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
Project Objectives
• 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
An example displaying the organization
of fruits in an anatomy ontology tree
and their relationship to each other.
genes and phenotypes of mutants in experimental and agronomically
Classically various models of plant
important plants, such as Arabidopsis, rice and maize
glossaries were established over a period
of time, by numerous researchers,
• Develop an infrastructure to support plant comparative genomics to discover
patterns of similarities and dissimilarities involved in plant development.
namely, Katherine Esau, A. Fahn,
Elizabeth Cutter and those who defined
• Impart training to collaborators from other model organism databases.
• Community outreach to involve plant researchers, breeders, and systematists
the growth stages in different plants.
These glossaries were primarily organized
by simple hierarchy addressing only the
one to one relationships.
Example Data Sets
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:
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.
In order to help in annotation, the project will develop the
standardized, controlled vocabulary (ontology) for following
aspects of plants.
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 derivedfrom ovary outer.
Unlike a simple hierarchy, child nodes are allowed to have more
than one parent node, thus allowing multiple child to parent
relationships.
Anatomy
Broader Impact
Term-1
Term-7
instance_of
Term-2
Term-6
instance_of
Term-3
part_of
Term-4
Plant growth stage
Describes the developmental stage at which the gene and /or phenotype
expression is observed and assayed
derived_from
Term-5
Contact Information for deliverables
Lincoln Stein, [email protected]
Medicago truncatula
functional genomics
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
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
instance_of
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
An example displaying annotation of Arabidopsis gene PHR1 using the
Ontology term.
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•
•
•
•
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:
•
An example displaying the organization of growth
and developmental stages in rice plant.
Information/Materials to be Generated:
instance-of:
Suggested, application of plant ontology helping plant biologist
to make useful queries.
An example displaying how “endosperm”
will be defined in the anatomy tree.
Instance_of
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.
Last Name
First Name
Institution
Role
E-Mail
Stein
Lincoln
Cold Spring Harbor Laboratory
PI
[email protected]
McCouch
Susan
Cornell Univ.
co-PI
[email protected]
Kellogg
Elizabeth
University of Missouri
co-PI
[email protected]
Rhee
Sue
Carnegie Institution of Washington
co-PI
[email protected]
Jaiswal
Pankaj
Cornell University
co-PI
[email protected]
Ware
Doreen
Cold Spring Harbor Laboratory
co-PI
[email protected]
Reiser
Leonore
Carnegie Institution of Washington
Key person
[email protected]
Stevens
Peter
Key person
[email protected]
Vincent
Leszek
Missouri Botanical Garden,
University of Missouri
University of Missouri
Key person
[email protected]
Douglas
Cook
University of California Davis
Key person
[email protected]
Tanksley
Steve
Cornell University
Key person
[email protected]