@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 {212,
	title = {Ontologies as Integrative Tools for Plant Science},
	journal = {American Journal of Botany},
	volume = {99},
	year = {2012},
	month = {2012 Aug},
	pages = {1263-75},
	chapter = {1263},
	abstract = {PREMISE OF THE STUDY: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web.

METHODS: This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae).

KEY RESULTS: Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education.

CONCLUSIONS: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.},
	keywords = {Botany, Computational Biology, Data Interpretation, Statistical, Database Management Systems, Databases, Factual, Genome, Plant, Genomics, Molecular Sequence Annotation, Phenotype, Plants, Semantics, Terminology as Topic, Vocabulary, Controlled},
	issn = {1537-2197},
	doi = {10.3732/ajb.1200222},
	author = {Walls, Ramona L and Athreya, Balaji and Cooper, Laurel and Elser, Justin and Gandolfo, Maria A and Jaiswal, Pankaj and Mungall, Christopher J and Preece, Justin and Rensing, Stefan and Smith, Barry and Stevenson, Dennis W}
}
@conference {1617,
	title = {A plant disease extension of the Infectious Disease Ontology},
	booktitle = {International Conference on Biomedical Ontology (ICBO-2012)},
	volume = {897},
	year = {2012},
	month = {July 2012},
	publisher = {CEUR Workshop Proceedings},
	organization = {CEUR Workshop Proceedings},
	address = {Graz, Austria},
	abstract = {Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this chal{\textendash}- lenge, and methods such as high{\textendash}-throughput sequencing and automat{\textendash}- ed scoring of phenotypes can provide significant new insights. Ontolo{\textendash}- gies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease On{\textendash}- tology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geo{\textendash}- graphic location and ecology of diseases and hosts, and molecular func{\textendash}- tions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting in{\textendash}-house ontology development comple{\textendash}- mented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism.},
	url = {http://ceur-ws.org/Vol-897/},
	author = {Walls, Ramona and Smith, Barry and Elser, Justin and Goldfain, Albert}
}
@article {1615,
	title = {The genome of woodland strawberry (<i>Fragaria vesca</i>)},
	journal = {Nat Genet},
	volume = {43},
	year = {2011},
	month = {2011},
	pages = {109 - 116},
	isbn = {1061-4036},
	url = {http://dx.doi.org/10.1038/ng.740},
	author = {Shulaev, Vladimir and Sargent, Daniel J and Crowhurst, Ross N and Mockler, Todd C and Folkerts, Otto and Delcher, Arthur L and Jaiswal, Pankaj and Mockaitis, Keithanne and Liston, Aaron and Mane, Shrinivasrao P and Burns, Paul and Davis, Thomas M and Slovin, Janet P and Bassil, Nahla and Hellens, Roger P and Evans, Clive and Harkins, Tim and Kodira, Chinnappa and Desany, Brian and Crasta, Oswald R and Jensen, Roderick V and Allan, Andrew C and Michael, Todd P and Setubal, Joao Carlos and Celton, Jean-Marc and Rees, D Jasper G and Williams, Kelly P and Holt, Sarah H and Rojas, Juan Jairo Ruiz and Chatterjee, Mithu and Liu, Bo and Silva, Herman and Meisel, Lee and Adato, Avital and Filichkin, Sergei A and Troggio, Michela and Viola, Roberto and Ashman, Tia-Lynn and Wang, Hao and Dharmawardhana, Palitha and Elser, Justin and Raja, Rajani and Priest, Henry D and Bryant, Douglas W and Fox, Samuel E and Givan, Scott A and Wilhelm, Larry J and Naithani, Sushma and Christoffels, Alan and Salama, David Y and Carter, Jade and Girona, Elena Lopez and Zdepski, Anna and Wang, Wenqin and Kerstetter, Randall A and Schwab, Wilfried and Korban, Schuyler S and Davik, Jahn and Monfort, Amparo and Denoyes-Rothan, Beatrice and Arus, Pere and Mittler, Ron and Flinn, Barry and Aharoni, Asaph and Bennetzen, Jeffrey L and Salzberg, Steven L and Dickerman, Allan W and Velasco, Riccardo and Borodovsky, Mark and Veilleux, Richard E and Folta, Kevin M}
}
@conference {1618,
	title = {Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes},
	booktitle = {SWAT4LS 2011},
	series = {Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences 2011},
	year = {2011},
	month = {Dec 7-9, 2011},
	pages = {96-97},
	publisher = {ACM New York, NY},
	organization = {ACM New York, NY},
	address = {London, UK},
	isbn = {978-1-4503-1076-5},
	doi = {10.1145/2166896.2166921},
	author = {Preece, Justin},
	editor = {Elser, Justin and Jaiswal, Pankaj}
}
@conference {1616,
	title = {A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species},
	booktitle = {NETTAB 2010 conference on Biological Wikis},
	series = {Network Tools and Applications in Biology-NETTAB-BBCC 2010 Biological Wikis},
	year = {2010},
	month = {2010},
	pages = {109-112},
	publisher = {Aracne},
	organization = {Aracne},
	address = {Naples, Italy},
	url = {http://www.nettab.org/2010/},
	author = {Preece, Justin},
	editor = {Elser, Justin and Jaiswal, Pankaj}
}
