Missouri Botanical Garden Open Conference Systems, TDWG 2014 ANNUAL CONFERENCE

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Crop Ontology: A web tool for managing plant breeders’ traits
Luca Matteis, Marie-Angélique LAPORTE, Harold Duruflé, Léo Valette, Elizabeth Arnaud

Building: Elmia Congress Centre, Jönköping
Room: Rydbergsalen
Date: 2014-10-28 11:15 AM – 11:30 AM
Last modified: 2014-10-04

Abstract


The Crop Ontology project was launched in 2008 and consists in a system for managing plant breeder traits with their methods and their scales of measurement, as well as environment and experimental design variables. The Crop Ontology adopted the RDF (Resource Description Framework) language that is a standard model for data interchange on the Web facilitating data merging even if the underlying schemas differ. It allows structured and semi-structured data to be exposed and shared across different applications. With this addition, Crop Ontology is capable of storing various formats of controlled vocabularies ranging from semantically-rich ontologies to simpler tabular based structures such as Comma-Separated Values (CSV). In order to link gene expression data and phenotype data from diverse plant databases, latest developments focused on the integration of routines to automatically convert at the download, the Excel Trait Dictionaries into an OBO file (Open Biomedical Ontologies), which is the format required by the Chado phenotypic databases of the Integrated Breeding Platform (IBP). Furthermore, the Trait Dictionaries published on the Crop Ontology website are used as the basis for the creation of the breeders’ fieldbooks of the Breeding Management System. Ensuing from the need to characterize crops using farmers’ opinions, as in participatory plant breeding or pre-breeding programs, the Crop Ontology is developing further by looking at how to integrate citizen science.