The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

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

doi:10.1093/pcp/pcs163

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Journal Article · Thu Dec 06 00:00:00 EST 2012 · Plant and Cell Physiology

DOI:https://doi.org/10.1093/pcp/pcs163· OSTI ID:1625581

Cooper, Laurel ^[1]; Walls, Ramona L. ^[2]; Elser, Justin ^[3]; Gandolfo, Maria A. ^[4]; Stevenson, Dennis W. ^[2]; Smith, Barry ^[5]; Preece, Justin ^[3]; Athreya, Balaji ^[3]; Mungall, Christopher J. ^[6]; Rensing, Stefan ^[7]; Hiss, Manuel ^[7]; Lang, Daniel ^[8]; Reski, Ralf ^[9]; Berardini, Tanya Z. ^[10]; Li, Donghui ^[10]; Huala, Eva ^[10]; Schaeffer, Mary ^[11]; Menda, Naama ^[12]; Arnaud, Elizabeth ^[13]; Shrestha, Rosemary ^[14] more »

Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology; DOE/OSTI
New York Botanical Garden, Bronx, NY (United States)
Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
Cornell Univ., Ithaca, NY (United States). Dept. of Plant Biology. L.H. Bailey Hortorium
Univ. at Buffalo, NY (United States). Dept. of Philosophy
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Berkeley Bioinformatics Open-Source Projects
Univ. of Freiburg (Germany). Faculty of Biology. BIOSS Centre for Biological Signalling Studies
Univ. of Freiburg (Germany). Faculty of Biology. Plant Biotechnology
Univ. of Freiburg (Germany). Faculty of Biology. Plant Biotechnology; Univ. of Freiburg (Germany). FRIAS, Freiburg Inst. for Advanced Studies
Carnegie Inst. of Science, Stanford, CA (United States). Dept. of Plant Biology
US Dept. of Agriculture (USDA), Columbia, MO (United States). Agriculture Research Services (ARS); Univ. of Missouri, Columbia, MO (United States). Dept. of Agronomy. Division of Plant Sciences
Boyce Thompson Inst. for Plant Research, Ithaca, NY (United States)
Bioversity International, Rome (Italy)
Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT) (Mexico). Genetic Resources Program
National Inst. of Genetics, Mishima, Shizuoka (Japan)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625581

Journal Information:: Plant and Cell Physiology, Journal Name: Plant and Cell Physiology Journal Issue: 2 Vol. 54; ISSN 0032-0781

Publisher:: Japanese Society of Plant PhysiologistsCopyright Statement

Country of Publication:: United States

Language:: English

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