The Crop Ontology system – next steps

May 19, 2022

Since its inception 14 years ago, the Crop Ontology has become an essential source of controlled vocabularies to define traits and variables that support the standardisation of crop breeding databases.

Crop Ontology has successfully worked with breeder and pre-breeder communities to establish 32 ontology sets. Notably, the conceptual model that guides their ontology defines a phenotypic variable as a combination of a trait, a method, and a scale.

Their crop ontologies are free to access – regularly synchronised with the Ontology Lookup Service of the European Bioinformatics Institute, as well as Agroportal.

The most recent crop to be included in their system was bambara groundnut (CO_366) – proposed by an earlier DivSeek working group, to be developed as a representative of an under-utilised crop. Some of the issues arising from this process were described by Andres-Hernandez et al (2021).

Crop Ontology has significantly increased in scope and use, such that a Governance and Stewardship Framework has very recently been established. Their community of practice is organised around a Project PI (Elizabeth Arnaud, Alliance Bioversity International-CIAT), a Technical Coordinator (Marie-Angélique Laporte, Alliance Bioversity International-CIAT) and three Advisory Committees – Curators, Strategy and a Scientific Advisory Committee.

DivSeek is keen to promote the development of the Crop Ontology and other relevant ontologies that adhere to the principles of the Open Biological and Biomedical Ontology (OBO) Foundry. A major challenge for our community is to embrace vocabularies that address different domains within the spectrum of production to consumption (like agronomy, crop protection, food and nutrition, and renewable raw materials) and to resolve these to crop-specific nomenclature.