The Crop Ontology project is the creation of the Generation Challenge Programme (GCP), which understood from its inception the importance of controlled vocabularies and ontologies for the digital annotation of data. In ontologies, terms bear a particular, logically defined relationship to each other, allowing computational reasoning on data annotated with a structured vocabulary. 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 the databases, GCP initiated the development of Trait Dictionaries for breeders' fieldbooks and a Crop Ontology (CO) to facilitate the harmonization of the data capture and powerful manipulations of the data through ontology-driven queries.
The Crop Ontology (CO) current objective is to compile 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 being 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. Development of crop-specific trait ontologies and the germplasm ontologies began in 2008 for chickpea, maize, Musa, potato, rice and wheat, and in 2010 for cassava. The GCP Crop Ontology is a global public good, available to be used freely by all.
In what context is this tool useful?
This curation and annotation web site is a participatory tool that enables you to browse the Crop Ontology, search for specific terms and access the definition, as well as additional information. It is possible to post a suggestion at the level of a term and provide feedback on your experience using the site. Please, consult the video tutorials to get a visual explanation of the web site use.
The Ontology curators are able to upload a full ontology in OBO format, create it online, add attribute information, and submit or delete terms from the Crop Ontology. Researchers can also submit/deposit trait names using the curation/annotation tool ‘add an ontology’ to increment the tool’s capacity.
All lists can be downloaded and a web service API is available. The site is hosted on Google App Engine and the versioned code is hosted on GitHub.
The tool is still under development, so your feedback will help to improve it. Please provide any comments or suggestions using the ‘Feedback’ button.
This work was greatly inspired by the Crop Ontology Look-up service developed by Martin Senger, consultant in Bioinformatics, and by Terminizer, online annotation tool developed by David Hancock, from the University of Manchester.
Funding and implementation partners
- Generation Challenge Programme
- Integrated Breeding Platform
- National Science Foundation
CGIAR Platform for Big Data in Agriculture
AgriFood Systems CRPs
In 2021, GCP Crop Ontology currently provides 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 are 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.
Links to related publications and stories
- 2012 - Shrestha Rosemary, Matteis Luca, Skofic Milko, Portugal Arlett, McLaren Graham, Hyman Glenn, Arnaud Elizabeth - 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 , in Frontiers in Physiology , vol.3, no.0326
- 2012 - Elizabeth Arnaud, Laurel Cooper, Rosemary Shrestha, Naama Menda, Rex T. Nelson, Luca Matteis, Milko Skofic, Ruth Bastow, Pankaj Jaiswal, Lukas Mueller, Graham McLaren: Towards a Reference Plant Trait Ontology For Modeling Knowledge of Plant Traits and Phenotypes in: proceedings of the 4th Conference on Knowledge Engineering and Ontology Development, 4-7 October 2012 , Spain.
- 2010 - Rosemary Shrestha, Elizabeth Arnaud, Ramil Mauleon, Martin Senger, Guy F. Davenport, David Hancock, Norman Morrison, Richard Bruskiewich, and Graham McLaren - Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature, AoB PLANTS (2010) Vol. 2010 first published online May 27, 2010 doi:10.1093/aobpla/plq008
- The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems
- AgTrials variables measured
Elizabeth Arnaud – email@example.com
Tool team: Marie-Angélique Laporte, Carlos Quiros