1. The Plant Ontology: Linking Phenotypes and Genomics Across Plant Taxa Laurel D. Cooper* 1, Ramona L. Walls 2, Justin Elser 1, Justin Preece 1, Dennis W. Stevenson 2, Barry Smith 3, Chris Mungall 4, Maria A. Gandolfo 5, Pankaj Jaiswal 1 *Presenting Author 1. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 2. The New York Botanical Garden, Bronx, NY 3. Department of Philosophy, University at Buffalo, NY 4. Lawrence Berkeley National Lab, Berkeley, CA 5. Department of Plant Biology, Cornell University, Ithaca, NY

2. 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

3. 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

4. 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

5. The PO facilitates phenotype descriptions through cross-product definitions TO: leaf size (precomposed) PO: leaf TO: shoot anatomy and morphology trait is_a PATO: size inheres_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)

6. 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

7. Phenote Annotation tool With Two Configurations : Advanced and ‘Smart’ Custom Phenote tool allows inputs by authors. Advanced configuration allows savy people to build cross-products for phenotype annotations.

8. 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

9. Acknowledgements: