Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa

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Poster presented at the 2011 CGRB Fall Conference, Oregon State University, September 18th-19th, 2011.

Laurel Cooper a, Ramona Walls b, Justin Elser a, Justin Preece a , Barry Smith c, Chris Mungall d, Stefan A. Rensing e, Manuel Hiss e, Péter Szöevényi e, Daniel Lang e, Maria A. Gandolfo f, Dennis Wm. Stevenson b , Pankaj Jaiswal a

a. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR b. The New York Botanical Garden, Bronx, NY c. Department of Philosophy, University at Buffalo, NY d. Lawrence Berkeley National Lab, Berkeley, CA e. Faculty of Biology, University of Freiburg, Germany f. Department of Plant Biology, Cornell University, Ithaca, NY

The Plant Ontology (PO: http://www.plantontology.org) is a structured vocabulary and database resource for all plant scientists that links plant anatomy, morphology and development to the rapidly expanding field of plant genomics. Originally designed to span the monocot-dicot divide in flowering plants, the PO has been redesigned to encompass a wider variety of angiosperm species, as well as gymnosperms, pteridophytes (ferns), lycophytes (lycopods) and bryophytes (liverworts, mosses and hornworts). Recent changes in the PO include the addition of more than 80 new terms to accommodate non-vascular plants, with an emphasis on terms needed to annotate the Physcomitrella patens genome. In addition, many existing terms and definitions have been modified to make them applicable to all plants. An essential, powerful feature of the PO is the set of links from terms to associated annotations, which are structure- or development-specific genes, proteins and phenotypes sourced from numerous genomics datasets. Currently, the PO includes over 500,000 annotations associated with over 1,100 terms. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. To this end, the PO consortium is working to develop annotation tools for the plant science community. Outreach activities include workshops, conference presentations and outreach booths. Also, image libraries are being created through PlantSystematics.org and linked to PO terms to provide reference images for plant structure terms. The PO is a valuable resource for both research and teaching that can be used as a guide to plant structures and growth and developmental landmarks in life cycles of plants across many taxa.