The volume of agriculture-related information and terminology related to phenotype, breeding, germplasm, pedigree, traits, among others, is increasing exponentially. In order to facilitate access to the data held within and/or across databases, Trait Dictionaries were developed for breeders' fieldbooks and a Crop Ontology to facilitate the harmonization of the data capture and powerful manipulations of the data through ontology-driven queries.
The Crop Ontology compiles validated concepts along with their inter-relationships on anatomy, structure, and phenotype of crops, on trait measurement and methods as well as on germplasm with the multi-crop passport terms. The concepts of the CO are used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.
Developed originally by the Generation Challenge Programme, the GCP Crop Ontology is a global public good, available to be used freely by all.
In what context is this tool useful?
The Crop Ontology, in combination with the crop trait dictionaries, provides a tool to foster phenotypic and genotypic data curation and annotation by the communities of practice (CoP) of several crops using validated common trait names, particularly breeders' traits, protocols, and scales.
This facilitates direct annotation of breeders' data captured in the field and enables the integration of phenotypic and genetic data sets. It helps breeders, when evaluating traits in the field, to access the correct trait information they need, including detailed standard protocols and scales. Thanks to the online curation and annotation tool, the curators of crop specific ontologies can interactively modify existing trait names or add new ones along with images, methods and scales.
Crop Ontology boasts trait descriptions for 17 crops: cassava, banana, barley, chickpea, common bean, cowpea, groundnut, lentil, maize, pearl millet, pigeon pea, potato, rice, soybean, sorghum, wheat and yam. A large number of breeders, students and professors have been trained in the use of the field book to record field evaluation data in 27 countries using the Crop Ontology traits.
The Crop Ontology has been used for data annotation by the International Cassava Database, Wageningen University and Research Centre, and the CGIAR Research Program on Climate Change, Agriculture and Food Security’s repository of evaluation trials.
As of 2021, GCP Crop Ontology was providing 4,784 validated trait names with their definitions and relations and 6,297 variables for eight crops: cassava, chickpea, groundnut, maize, Musa, potato, rice, sorghum and wheat. Trait lists were being developed for common beans and cowpea of 32 plant species.
The list of the 32 ontology curators in CGIAR and in contributing institutions is available in the Crop Ontology site.
Variations on this method
The information below is just about improvements to the Crop Ontology itself. However, the most exciting adaption of the method was the development of the Agronomy Ontology https://bigdata.cgiar.org/resources/agronomy-ontology/
- Guidelines for creating crop-specific ontologies to annotate phenotypic data: version 2.1
- Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice
- The ontologies community of practice: a CGIAR initiative for big data in agrifood systems
- Requesting new terms in ontologies: the example of Crop Ontology and the Agronomy Ontology
- The Crop Ontology: a source of standard traits and variables for breeding and agronomy
Elizabeth Arnaud – firstname.lastname@example.org
Marie-Angélique Laporte - email@example.com
Carlos Quiros - C.F.Quiros@cgiar.org