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

Permanent URL:
http://handle.nal.usda.gov/10113/57978
Abstract:
The Plant Ontology (PO; http://www.plantontology.org/) is a publically-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy and morphology, and the stages of plant development. The goals of the PO are to link (annotate)gene expression and phenotype data to different plant structures and stages of plant development, using the 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 entity branch 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 the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
Author(s):
Laurel Cooper , Ramona L. Walls , Justin Elser , Maria A. Gandolfo , Dennis W. Stevenson , Barry Smith , Balaji Athreya , Christopher J. Mungall , Stefan Rensing , Manuel Hiss , Daniel Lang , Ralf Reski , Tanya Z. Berardini , Dongjui Li , Eva Huala , Mary Schaeffer , Naama Menda , Elizabeth Arnaud , Rosemary Shrestha , Yukiko Yamazaki , Pankaj Jaiswal
Subject(s):
Arabidopsis , Internet , Oryza sativa , RNA , Zea mays , corn , databases , gene expression , genes , genomics , germplasm , languages , models , phenotype , plant anatomy , plant development , proteins , quantitative trait loci , rice
Source:
Plant Cell Physiology 2013 2 1 v.54 no.2
Language:
English
Year:
2013
Collection:
Journal Articles, USDA Authors, Peer-Reviewed
File:
Download [PDF File]
Rights:
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.