The Crop Ontology: a source of standard traits and variables for breeding and agronomy

Abstract

The Crop Ontology is a service of the Integrated Breeding Platform (www.integratedbreeding.net) in collaboration with the CGIAR and partners and under the leadership of Bioversity international. The Crop Ontology (www.cropontology.org) provides harmonized and validated breeders’ trait names, measurement methods, scales for currently 18 crops that are used by the Breeding Management System (BMS). The NextGeneration Breeding Databases developed by Boyce Thompson Institute also embed the Crop Ontology traits. The Crop Ontology contributes to the content of the reference ontologies of the Planteome project (http://www.planteome.org/). A new Trait Dictionary Template was released that now includes the ‘standard variable’. A standard variable is equal to 'one trait+one method+one variable' and a trait can be measured through different variables, according to the method or the scale used. These variables will accurately annotate the measurements stored in the BMS databases and also will support the creation of standard manual or electronic fieldbooks. Ten crop trait dictionaries have already been migrated into this new template and uploaded on the Crop ontology site. Using similar methodology, an Agronomy Ontology is being developed to support combining results of field management practices with crop traits which is important to fully understand the dynamic of varying factors within any cropping system. Curation is currently performed to secure the compliance between the Agronomy ontology and the variables of the International Consortium for Agricultural Systems Applications (ICASA)