The Plant Ontology: Linking Phenotypes and Genomics Across

Plant Taxa

Laurel D. Cooper*1, Ramona L. Walls2, Justin Elser1, Justin Preece1, Dennis W. Stevenson2, Barry Smith3, Chris Mungall4, Maria A. Gandolfo5, Pankaj Jaiswal1

*Presenting Author

• Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR• The New York Botanical Garden, Bronx, NY• Department of Philosophy, University at Buffalo, NY• Lawrence Berkeley National Lab, Berkeley, CA• Department of Plant Biology, Cornell University, Ithaca, NY

What is Plant Ontology?

• A structured vocabulary for plants that covers:– Plant anatomy and morphology– Plant growth and developmental stages

• A source for:– standard definitions reviewed by experts– links to annotations from multiple genome databases

www.plantontology.org

The PO is expanding to covers all plants:

Seed plants(Angiosperms and Gymnosperms)

Pteridophytes*(Ferns and Lycopods)

Bryophytes(Mosses, Hornworts and

Liverworts)

Algae*

* Not in the PO, yet, but will come

Bowman et al, Cell, 2007

Vision for Plant Ontology:• Encompass all plants• Facilitate consistency in:

• Annotation of comparative genomics data• Cross-database queries

• Develop PO as a reference ontology for plants:• Provide mappings to other ontologies in use by

plant databases• Create cross-products to other ontologies such as

PATO, to describe phenotypic characters

The PO facilitates phenotype descriptions through cross-product definitions

TO: leaf size(precomposed)

PO: leaf

TO: shoot anatomy and morphology

traitis_a

PATO: sizeinheres_in

needle = frond = vascular leaf

Consistent use of vocabulary

Explicit, logical definitions and relationships among concepts

inheres_in

Allows both pre- (biologist) and post -composition (tech savy)

Tools:

• Developing the ontology using OBO-Edit

• Ontology is displayed on our website using AmiGO

• OWL version of the ontology

• Protégé

• Semantic web via SSWAP (Simple Semantic Web Architecture and Protocol )

• Phenote annotation tool being developed for use by plant scientists

Phenote Annotation toolWith Two Configurations : Advanced and ‘Smart’

Custom Phenote tool allows inputs by authors. Advanced configuration allows savy people to build cross-products for

phenotype annotations.

Challenges and/or Roadblocks• Other species-specific vocabularies should use cross

references to PO terms

• Need to encourage more groups to send annotations to PO

• Shortage of plant-specific phenotypic descriptors in PATO

• Need to expand development of bridge and /or mapping files

Acknowledgements: