@article {235, title = {Development of a Unified Phenotype Dataset for Plants}, year = {2013}, month = {Jan. 11-16, 2013}, type = {Poster presentationPoster presentation}, address = {San Diego, CA}, abstract = {Plant phenotype datasets can be found in a range of formats including free text and species-specific or knowledge domain-specific controlled vocabularies. While this enables some limited comparison of phenotype data across a single species or within a knowledge domain such as crop breeding, queries or analyses that span a broader set of species are not possible in the absence of a common vocabulary for describing phenotypes. To enable cross-species and cross-domain phenotype comparisons and analyses in plants, we have launched an effort to convert existing phenotype datasets for 8 plant species, encompassing both model species and crops, into a common format using taxonomically broad ontologies representing plant anatomical parts and developmental stages (Plant Ontology), biological processes (Gene Ontology), chemicals (ChEBI), and phenotypic qualities (PATO). Our effort focuses on mutant and overexpression phenotypes associated with genes of known sequence in Arabidopsis, tomato, potato, pepper, maize, rice, soybean and Medicago. Shared use of ontologies, annotation standards, formats and best practices across these eight plant species ensures that the resulting dataset will produce valid results for cross-species querying and semantic similarity analyses. Additionally, the dataset will enable us to explore the relationship between sequence similarity and phenotypic similarity across a range of plant species.}, url = {https://pag.confex.com/pag/xxi/webprogram/Paper5616.html}, author = {Huala, Eva}, editor = {Steven B. Cannon and Cooper, Laurel and George Gkoutos and Lisa C Harper and Jaiswal, Pankaj and Carolyn J. Lawrence and Johnny Lloyd and David Meinke and Menda, Naama and Laura Moore and Mueller, Lukas and Nelson, Rex T and Walls, Ramona L} } @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 {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} }