title: The plant ontology as a tool for comparative plant anatomy and genomic analyses.
abstract: The Plant Ontology (PO; http://www.plantontology.org/) 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 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.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA.
authors.forename: Laurel
authors.initials: L
authors.lastname: Cooper
authors.forename: Ramona L
authors.initials: RL
authors.lastname: Walls
authors.forename: Justin
authors.initials: J
authors.lastname: Elser
authors.forename: Maria A
authors.initials: MA
authors.lastname: Gandolfo
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.forename: Justin
authors.initials: J
authors.lastname: Preece
authors.forename: Balaji
authors.initials: B
authors.lastname: Athreya
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.forename: Stefan
authors.initials: S
authors.lastname: Rensing
authors.forename: Manuel
authors.initials: M
authors.lastname: Hiss
authors.forename: Daniel
authors.initials: D
authors.lastname: Lang
authors.forename: Ralf
authors.initials: R
authors.lastname: Reski
authors.forename: Tanya Z
authors.initials: TZ
authors.lastname: Berardini
authors.forename: Donghui
authors.initials: D
authors.lastname: Li
authors.forename: Eva
authors.initials: E
authors.lastname: Huala
authors.forename: Mary
authors.initials: M
authors.lastname: Schaeffer
authors.forename: Naama
authors.initials: N
authors.lastname: Menda
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Arnaud
authors.forename: Rosemary
authors.initials: R
authors.lastname: Shrestha
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Yamazaki
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000235:genetics; D030541:Databases, Genetic; D035264:Flowers / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020407:Internet; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010641:Phenotype; D018515:Plant Leaves / Q000033:anatomy & histology; D010940:Plant Proteins / Q000235:genetics; D010944:Plants / Q000033:anatomy & histology* / Q000235:genetics*; D012984:Software
chemical_list: D010940:Plant Proteins; D019883:Alkyl and Aryl Transferases; C108877:terpene synthase