Download Slide - The OBO Foundry

Introduction to the Plant
Ontology™
Laurel Cooper*1,
Justin Elser1, Maria A. Gandolfo3, Chris Mungall4,
Pankaj Jaiswal1, Barry Smith5, Dennis Wm.
Stevenson2, Ramona Walls2
(in alphabetical order)
1.
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
2.
The New York Botanical Garden, Bronx, NY
3.
Department of Plant Biology, Cornell University, Ithaca, NY
4.
Lawrence Berkeley National Lab, Berkeley, CA
5.
Department of Philosophy, University at Buffalo, NY
What is Plant Ontology?
• An arrangement of controlled vocabularies that describe:
– Plant Anatomy and Morphological features
– Growth and Developmental Stages
• Based on internationally published/accepted terminology and
their definitions
A tool for annotation of plant phenotypes
and gene expression patterns across all
plant species
www.plantontology.org
POC homepage: www.plantontology.org
Basic Goals of Plant Ontology:
• Encompass all plants: include terms and annotations from nonflowering plants: Gymnosperms, lycopods, ferns and mosses
• Create mappings to other ontologies such as PATO, CARO CL
and GO
• Logical (genus-differentia) definitions, follow OBO principles
• is_a completeness
• Be a tool for comparative genomics across plant taxa
Phyllogenetic Tree of Plants
Bowman et al,
Cell, 2007
Plant Genomic Resources Rapidly Expanding:
http://www.phytozome.net/
Top level terms from dev browser
POC homepage: http://dev.plantontology.org
Plant Cells terms currently in Plant
Structure:
Example- Plant Epidermal Cell
http://en.wikipedia.org/wiki/File:Leaf_anatomy.svg
part_of
Proposed new
organization of
Plant Cell terms
part_of
part_of
Mirrors organization of Plant Structure:
•Sporophytic cell- e.g. embryonic cell
•Gametophytic cell- e.g. megagametophytic cell
•Whole plant cell - can occur in a gametophyte or
sporophyte, e.g. axial cell
Plant Stem Cells in the PO:
High Resolution Analysis of Gene Expression
in Shoot and Root Stem Cells
The plant hormone,
auxin shifts from the
apical half to
concentrate at the basal
pole of the embryo
Activation of
genes during
cell
differentiation
Root meristem
(Stahl and Simon, Int. J. Dev. Biol. 2005)
Cell types of the root meristem
((Stahl and Simon, Int. J. Dev. Biol. 2005)
Gene Expression Map of the Arabidopsis
Shoot Apical Meristem
5 regions of Shoot Apical Meristems:
-Central zone narrow (CZ) (red) and broad (green)
-Rib meristem (RM) (blue)
-Peripheral zone (PZ) (cyan)
- L1 layer (black).
Hierarchical clustering
of 47 characterized
differentially expressed
genes within the SAM
Yadav et al, PNAS 2009
GO Enrichment
(E) Relative percentage of selected Gene Ontology (GO) groups identified in different DEG sectors.
Note the number above each column represents a sum of total number of genes detected for a particular
GO term in various sectors.
Yadov et al, PNAS 2009
View Annotations in PO (Gene products)
Click to view the annotation details
Shoot and Leaf Initiation from
Single Cells in the Moss
Physcomitrella patens
Three presumptive leaves (gray arrows) flank a single apical initial cell (red arrow)
Harrison et al, Current Biology, 2009
Shoot Apices of Selaginella
Kraussiania
Merophytes- apical cell derivativess
Jones and Drinnan,Int’l J. Plant Biol, 2009
PO Highlights 2010:
-Reorganization of PO terms to encompass nonflowering plants - ongoing
- Annotations of gene products and phenotypes in
a wider variety of plant species- ASPB, BSA
workshops this summer- Phenote
- Integrate data from current studies on new model
plants, for example:
- genome annotations
- microarray data sets
- high quality Next-Generation expression
datasets
Suggestions for Interaction with Cell
Type Ontology:
- Terms unique to the PO could retain the PO ID
- Annotations of those terms could be handled by the
PO curators
- Terms shared by the PO and other ontologies
represented in the CL could list the PO ID as an
alternate ID, for example: zygote, gamete, epidermal
cell
- Unique upper level terms with common lower level
children- mirroring of sites?
- Similar structures and organization?
Acknowledgements:
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