@article {230,
	title = {Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics},
	year = {2014},
	month = {Jan. 11-15, 2014},
	address = {San Diego, CA},
	abstract = {Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvement may be combined with next-generation methods such as automated scoring of traits and phenotypes to develop improved varieties. Linking these analyses to the growing corpus of genomics data generated by high-throughput sequencing, transcriptomics, proteomics, phenomics and genome annotation projects requires common, interoperable, reference vocabularies (ontologies) for the description of the data. The {\textquoteleft}Common Reference Ontologies for Plant Biology{\textquoteright} (cROP) initiative is building the needed suite of reference ontologies, together with enhanced data storage and visualization technologies. The cROP will assume the further development of the existing Plant Ontology (PO), Plant Trait Ontology (TO), and Plant Environment Ontology (EO) and will develop the Plant Stress Ontology (PSO) for abiotic and biotic stresses. It will also include relevant aspects of ontologies such as Gene Ontology (GO), Cell Type (CL), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PRO) and the Phenotypic Qualities Ontology (PATO). It will include a centralized platform where reference ontologies for plants will be used to access cutting-edge data resources for plant traits, phenotypes, diseases, genomes and semantically-queried gene expression and genetic diversity data across a wide range of plant species. cROP will unify and streamline a fragmented semantic framework and will support allele discovery, advance the understanding of crop evolution, and facilitate crop development.},
	url = {https://pag.confex.com/pag/xxii/webprogram/Paper9799.html},
	author = {Cooper, Laurel},
	editor = {Justin L. Elser and Preece, Justin and Arnaud, Elizabeth and Sinisa Todorovic and Eugene Zhang and Christopher Mungall and Smith, Barry and Dennis Wm. Stevenson and Jaiswal, Pankaj}
}
@article {238,
	title = {Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics},
	year = {2013},
	month = {Jan. 11-16, 2013},
	type = {PosterPoster},
	address = {San Diego, CA},
	abstract = {One of the central principles of biology is the concept that an organism{\textquoteright}s genotype interacts with the environment to produce the observable characteristics, or phenotype. Understanding this interaction is a core goal of modern biology, and enables development of organisms with commercially useful characteristics through modern breeding programs. A number of crop- or clade-specific plant trait ontologies have been developed to describe plant traits important for agriculture in order to address major scientific challenges such as food security. Traditionally, phenotype information has been captured in a free text manner, which cannot be easily indexed and presents an obstacle to data sharing. Recent advances in next generation sequencing and phenotyping technologies have allowed researchers to access a growing mountain of data, resulting in an emerging gap between the genomics information and the quantitative information describing phenotypes and traits. One approach to overcome this obstacle is through the annotation of data using a common controlled vocabulary or {\textquotedblleft}ontology". We present our vision of a species-neutral Reference Plant Trait Ontology (Ref-TO) which would be the basis for linking the disparate knowledge domains and that will support data integration and data mining across species. The Ref-TO is one of the modules for the Common Reference Ontology for Plant Science (cROP) which is being developed.},
	url = {https://pag.confex.com/pag/xxi/webprogram/Paper7640.html},
	author = {Cooper, Laurel},
	editor = {Laura Moore and Arnaud, Elizabeth and Nelson, Rex T and Menda, Naama and Shrestha, Rosemary and Grant, David and L. Matteis and Mungall, Christopher J and Bastow, Ruth and McLaren, Graham and Jaiswal, Pankaj}
}
@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 {231,
	title = {A Resource for a Common Reference Ontology for Plants},
	year = {2013},
	month = {Jan. 11-16, 2013},
	address = {San Diego, CA},
	abstract = {In the new age of comparative plant biology, we are looking at datasets from numerous inter and intra-specific comparative analysis experiments on transcriptome, proteomics, phenomics and genome annotation projects. These experiments may describe, for example, a set of genes from one or more plant species that are differentially expressed in response to some type of treatment. These genes may have associations to phenotypes and molecular functions, in addition to various gene and protein features. For a researcher looking at this data, the value comes from the analysis of this data. Unfortunately, the data is present in many locations in online data repositories and is also annotated using different vocabularies and keywords that often do not match descriptions between different resources. The problem can be solved in two ways: (1) keep the data in different locations, but annotate it with common reference vocabularies that can be queried in real time using common query words and/or (2) keep the data in a centralized location, and resolve the conflicting descriptions by adopting a single standard. Considering the limited resources and enormous amount of data distributed at many sites, an integrated approach of adopting common annotation standards and a set of reference ontologies is desired. We will present a vision of an international resource for a Common Reference Ontology for Plants (cROP), in order to develop common standards for annotating plant gene function, expression and phenotypes, in addition to describing the anatomy and responses such as diseases, reported in various experiments and resources.},
	url = {https://pag.confex.com/pag/xxi/webprogram/Paper5587.html},
	author = {Jaiswal, Pankaj},
	editor = {Smith, Barry and R. Bastow and Paul J. Kersey and Arnaud, Elizabeth and Cooper, Laurel and Christopher Rawlings}
}
@article {236,
	title = {The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes},
	year = {2013},
	month = {Jan. 11-16, 2013},
	type = {Ontology Workshop TalkOntology Workshop Talk},
	address = {San Diego, CA},
	abstract = {The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) currently contains eleven crop-specific ontologies and has been developed for the Integrated Breeding Platform (IBP) (https://www.integratedbreeding.net/) by several CGIAR centers. The CO provides validated trait names used by crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for automatic annotation of the phenotypic data measured in the field. The CO acts as a trait name server for various sites and databases: the Genotyping Data Management System (GDMS); the cassava database at Cornell University (http://cassavadb.org); Agtrials, the Global Repository for Evaluation Trials of Climate Change, Agriculture and Food Security (CCAFS), a CGIAR Research Program (http://agtrials.org ); and the EU-Sol BreedDB website (https://www.eu-sol.wur.nl/). The vision will be presented of a species-neutral and overarching Reference Plant Trait Ontology to support data annotation, integration and data mining across species, which has resulted from the successful collaboration between the CO project, the Plant Ontology (PO; http://www.plantontology.org/), the Trait Ontology (TO;http://www.gramene.org/plant_ontology/) the USDA-ARS SoyBase Database (http://www.soybase.org/), the Solanaceae Genomic Network (http://solgenomics.net/), and GarNet (http://www.garnetcommunity.org.uk/).},
	url = {https://pag.confex.com/pag/xxi/webprogram/Paper5002.html},
	author = {Arnaud, Elizabeth},
	editor = {Shrestha, Rosemary and Kulakow, Peter and Bakare, Moshood and Antonio Lopez-Montes and Ofodile, Sam and T., Praveen Reddy and Prasad, Peteti and Shah, Trushar and Hash, Charles Thomas and Weltzien-Rattunde, Eva and Sissoko, Ibrahima and Guerrero, Alberto Fabio and Simon, Reinhard and Borja-Borja, Nikki Frances and Ramil, Mauleon and L. Matteis and Skofic, Milko and Hazekamp, Tom and McLaren, Graham and Cooper, Laurel and Jaiswal, Pankaj and Menda, Naama and Nelson, Rex and Grant, David and Bastow, Ruth and Rami, Jean-Francois}
}
@conference {223,
	title = {Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotype},
	booktitle = {International Conference on Knowledge Discovery and Information Retrieval (IC3K2012)},
	year = {2012},
	month = {10/2012},
	address = {Barcelona, Spain},
	author = {Arnaud, Elizabeth and Cooper, Laurel and Shrestha, Rosemary and Menda, Naama and Nelson, Rex T and L. Matteis and M. Skofic and R. Bastow and Jaiswal, Pankaj and Mueller, Lukas and McLaren, Graham}
}
