Crop Ontology: A web tool for managing plant breeders’ traits

Marie-Angélique Laporte
Bioversity international, Montpellier, France
Tuesday, November 4 2014, 2.30 pm, Génopolys (How to come)


Plant breeders are producing a large amount of trait data in different environmental conditions to allow crop characterization and evaluation. In order to facilitate the data integration and sharing for such data in multi-crop platforms, controlled vocabularies and ontologies should be used to annotate not only genetic data but also phenotypic data.

The Crop Ontology (CO) is a resource of the Integrated Breeding Platform, which publishes plant breeder traits along with their methods and scales of measurement, as well as environment and experimental design variables. It also offers a forum to discuss the traits, methods and scales of measurement among breeders and geneticists. 18 Breeder Trait Dictionaries (TD) were produced with the Crop Lead Centers and breeders from different regions. The Crop Ontology adopted the RDF language that is a standard model for data interchange on the Web facilitating data merging even if the underlying schemas differ. 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 the Comma-Separated Values (CSV). CO aims also to support a common integration framework of genetic and phenotypic data. 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, 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. An API has been developed to enhance the reuse of the CO concepts by third party database or web site (like Agtrials, Phenotyping platforms, etc). 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.


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