@article {10.1371/journal.pbio.1002033, title = {Finding Our Way through Phenotypes}, journal = {PLoS Biol}, volume = {13}, number = {1}, year = {2015}, month = {01}, pages = {e1002033}, publisher = {Public Library of Science}, abstract = {

Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

}, doi = {10.1371/journal.pbio.1002033}, url = {http://dx.doi.org/10.1371\%2Fjournal.pbio.1002033}, author = {Deans, Andrew R. and Lewis, Suzanna E. and Huala, Eva and Anzaldo, Salvatore S. and Ashburner, Michael and Balhoff, James P. and Blackburn, David C. and Blake, Judith A. and Burleigh, J. Gordon and Chanet, Bruno and Cooper, Laurel D. and Courtot, M{\'e}lanie and Cs{\"o}sz, S{\'a}ndor and Cui, Hong and Dahdul, Wasila and Das, Sandip and Dececchi, T. Alexander and Dettai, Agnes and Diogo, Rui and Druzinsky, Robert E. and Dumontier, Michel and Franz, Nico M. and Friedrich, Frank and Gkoutos, George V. and Haendel, Melissa and Harmon, Luke J. and Hayamizu, Terry F. and He, Yongqun and Hines, Heather M. and Ibrahim, Nizar and Jackson, Laura M. and Jaiswal, Pankaj and James-Zorn, Christina and K{\"o}hler, Sebastian and Lecointre, Guillaume and Lapp, Hilmar and Carolyn J. Lawrence and Le Nov{\`e}re, Nicolas and Lundberg, John G. and Macklin, James and Mast, Austin R. and Midford, Peter E. and Mik{\'o}, Istv{\'a}n and Mungall, Christopher J and Oellrich, Anika and Osumi-Sutherland, David and Parkinson, Helen and Ram{\'\i}rez, Mart{\'\i}n J. and Richter, Stefan and Robinson, Peter N. and Ruttenberg, Alan and Schulz, Katja S. and Segerdell, Erik and Seltmann, Katja C. and Sharkey, Michael J. and Smith, Aaron D. and Smith, Barry and Specht, Chelsea D. and Squires, R. Burke and Thacker, Robert W. and Thessen, Anne and Fernandez-Triana, Jose and Vihinen, Mauno and Vize, Peter D. and Vogt, Lars and Wall, Christine E. and Walls, Ramona L and Westerfeld, Monte and Wharton, Robert A. and Wirkner, Christian S. and Woolley, James B. and Yoder, Matthew J. and Zorn, Aaron M. and Mabee, Paula} } @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} }