@article {211,
	title = {The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses},
	journal = {Plant \& Cell Physiology},
	volume = {54},
	year = {2013},
	month = {2013 Feb},
	pages = {1-23},
	chapter = {1},
	abstract = {The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ({\textquoteright}ontology{\textquoteright}) 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.},
	keywords = {Alkyl and Aryl Transferases, bioinformatics, comparative genomics, genome annotation, Molecular Sequence Annotation, Multigene Family, ontology, Phenotype, plant anatomy, Plant Proteins, Software, terpene synthase},
	issn = {1471-9053},
	doi = {10.1093/pcp/pcs163},
	url = {http://pcp.oxfordjournals.org/content/54/2/e1},
	author = {Cooper, Laurel and Walls, Ramona L and Elser, Justin and Gandolfo, Maria A and Stevenson, Dennis W and Smith, Barry and Preece, Justin and Athreya, Balaji and Mungall, Christopher J and Rensing, Stefan and Hiss, Manuel and Lang, Daniel and Reski, Ralf and Berardini, Tanya Z and Li, Donghui and Huala, Eva and Schaeffer, Mary and Menda, Naama and Arnaud, Elizabeth and Shrestha, Rosemary and Yamazaki, Yukiko and Jaiswal, Pankaj}
}
@article {822,
	title = {Annotating Gene Expression in <i>Physcomitrella patens</i> using the Plant Ontology: Facilitating Cross-Taxa Comparisons},
	year = {2012},
	month = {Jan 2012},
	address = {San Diego, CA},
	abstract = {The Plant Ontology (PO: http://www.plantontology.org) is a structured vocabulary and database resource for all plant scientists that links plant anatomy, morphology and development to the rapidly expanding field of plant genomics. Recent changes in the PO include the addition of more than 80 new terms to accommodate non-seed plants, with an emphasis on those needed to annotate gene expression from the Physcomitrella patens genome. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. The use of ontologies ensures consistent annotations within and across species, enabling both prediction of gene function and cross-species comparisons of gene expression. An essential, powerful feature of the PO is the set of links from terms to associated annotations, which are structure- or development-specific genes, proteins and phenotypes sourced from numerous plant genomics datasets. Currently, the PO includes over 2 million annotations associated with over 1,300 terms. We will give a brief tutorial on how to access the PO and associated data, and demonstrate the utility of linking Physcomitrella gene expression data to PO terms. The combination of ontology terms and the annotation of diverse gene expression and phenotype data sets facilitates diverse analyses, including assessing the similarity between genes of inter- or intra-specific origin and the exploration of structural homologies among organs, tissues and cell types.},
	url = {http://pag.confex.com/pag/xx/webprogram/Paper1640.html},
	author = {Cooper, Laurel D.},
	editor = {Walls, Ramona L and Justin L. Elser and Preece, Justin and Smith, Barry and Mungall, Christopher J and Rensing, Stefan and Hiss, Manuel and Sz{\"o}v{\'e}nyi, P{\'e}ter and Lang, Daniel and Gandolfo, Maria A and Dennis Wm. Stevenson and Jaiswal, Pankaj}
}
