Crop Ontology

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. 

Link: https://www.cropontology.org/  

Tool leaders

Funding and implementation partners

  • Generation Challenge Programme 
  • Integrated Breeding Platform 
  • National Science Foundation 
  • Planteome 

Results achieved

Through a user-friendly website Crop Ontology allow people from anywhere in the world to access and collaborate on the ontology. The system works similarly to Wikipedia. It allows anyone to sign up and create their ontologies. However, only after a moderator has validated their terms do they then become “public”. 

Crop Ontology is highly interactive and easy to use interfaces. This allows users to more easily create and edit ontologies from any computer or mobile device. 

Ontologies allows to build connections between terms and find information that we couldn’t otherwise. 

The GCP Crop Ontology currently provides validated names, definitions and relations for traits for eight crops: cassava, chickpea, groundnut, maize, musa, potato, rice, sorghum and wheat. Trait lists are being developed for common beans and cowpea. 

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 http://www.frontiersin.org/Journal/Abstract.aspx?s=907&name=plant_physiology&ART_DOI=10.3389/fphys.2012.00326    

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 - http://aobpla.oxfordjournals.org/citmgr?gca=aobpla;2010/0/plq008  

Poster: https://www.cropontology.org/posters/GRM_poster_Curation_annotation_tools.pdf  

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems 

https://www.cell.com/patterns/pdf/S2666-3899(20)30139-2.pdf