The plant ontology as a tool for comparative plant anatomy and genomic analyses

Published in Plant and Cell Physiology 54 (2) : 1-23, 2013

Laurel Cooper, Ramona L. Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith, Justin Preece, Balaji Athreya, Christopher J. Mungall, Stefan Rensing, Manuel Hiss, Daniel Lang, Ralf Reski, Tanya Z. Berardini, Donghui Li, Eva Huala, Mary Schaeffer, Naama Menda, Elizabeth Arnaud, Rosemary Shrestha, Yukiko Yamazaki and Pankaj Jaiswal

The Plant Ontology (PO; is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entitybranch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of theLEAFY (LFY) and terpene synthase (TPS) gene homologs.

Bioinformatics, Comparative genomics, Genome annotation, Ontology, Plant anatomy, Terpene synthase

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