Moss 2011 Meeting- PO presentation

Date and Time: Sept 12, 2011 8am EDT from NYBG

See: Moss 2011 Home Page

Link to slides: Media:PO_presentation_Moss2011.pdf

Using the Plant Ontology to Link Anatomical Structures to Gene Annotations in Physcomitrella patens

Authors:

Ramona L. Walls*1, Laurel D. Cooper2, Maria A. Gandolfo3, Dennis W. Stevenson1, Barry Smith4, Justin Elser2, Justin Preece2, Chris Mungall5 and Pankaj Jaiswal2

(*)Presenting author

1. The New York Botanical Garden, Bronx, NY

2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR

3. Department of Plant Biology, Cornell University, Ithaca, NY

4. OBO Foundry, Department of Philosophy, University at Buffalo, NY

5. Gene Ontology, Lawrence Berkeley National Lab, Berkeley, CA

Abstract

To fully explore the research possibilities created by the recent sequencing of the Physcomitrella patens genome, biological information must be linked to the genome sequence through the process of annotation. The use of ontologies ensures consistent annotations within and across species, enabling both gene prediction and cross-species comparisons of gene expression. While the Gene Ontology (GO) is an excellent tool for describing gene function and localization at the subcellular level, comprehensive annotation also requires ontology terms to describe plant anatomy and morphology, as well as growth and development stages. The Plant Ontology (PO) provides these terms through its two branches: the Plant Anatomy Ontology and the Plant Growth and Development Stage Ontology. The PO allows for uniform descriptions of the phenotypes and tissues used in gene expression studies. With the addition of over 80 new terms to describe bryophytes, the PO is well suited for the description of Physcomitrella anatomy and morphology. In this presentation, we will provide an overview of the Plant Ontology and its principles and review the new terms and changes that have been made to accommodate mosses. We will give a brief tutorial on how to access the PO and associated data, and conclude by showing examples of association files that other groups have contributed, in order to illustrate the utility of linking Physcomitrella genome data to PO terms.