Release: Crop Ontology Guidelines for Annotation of Phenotypic Data version 2.0

The Crop Ontology (CO) compiles concepts related to crops (traits, methods and scales), validated by community members. To better structure the integration of new traits and ontologies, and ease the participation of members in this effort, a Trait Dictionary Template has been designed. The guidelines to use this template have just been revised and released.

Why use the Guidelines?

The Guidelines version 2.0 supports the use of the Crop Ontology (CO) Trait Dictionary Template (TD) v.5.1 for developing a new species-specific ontology. The TD Template is a structured format that can be used to compile, curate, and harmonize the phenotypic variables for the crop and produce an ontology.

We strongly recommend reading and applying the Guidelines to develop a high-quality Trait Dictionary. This is the condition to enable the use of Crop Ontology by a wide community, including industries, and robust mapping with other ontologies. CO’s traits that are properly described following the guidelines are progressively mapped to the Planteome species-neutral Trait Ontology (TO) maintained by Oregon State University, thus enabling users to search for a trait without consideration of the species for e.g. studies in comparative genomics or for grouping traits for a family or a clade. Once the TD is finalised and is considered stable, it can be uploaded and published on the Crop Ontology Curation Tool website with a CC BY 4.0 license. It will then be synchronized with the Ontology Lookup Service of the European Bioinformatics Institute (EMBL-EBI) and Agroportal, a registry of ontologies in agriculture and related domains.

To further support the standardization of the breeding data sets, the CO format was adopted by the metadata schema called the Minimum Information About a Plant Phenotype Experiment (MIAPPE2020) and also by the Breeding Application Programming Interface (BrAPI).

What is new in Version 2?

The Crop Ontology evolves to address the feedback of curators and contributors, as well as the new types of trait measurement methods and modelling. Therefore, the Guidelines need regular revision. In Version 2, some sections and tables have been revised to improve their clarity. New sections were added, such as ‘The boundaries of the CO Model’ about the metadata that describes the trait but is not part of the CO model, like time series, timestamp, subsamples, and experiment factors. Frequently Asked Questions and a bibliography for further reading were added as well as guidance in defining the abiotic and biotic stress variables in Annex 1.

The list of method types has been augmented with the prediction type to include trait predictive tools like Near-Infrared Spectroscopy (NIRS) which are not calculations with a formula. A new method class was added to include trait classification methods using Machine Learning algorithms. According to Table 5, we have also added a Description class.

Crop Ontology is an open collaborative product

We acknowledge the valuable contribution of the curators (see list below) to the maintenance of quality content addressing the guidelines recommendations, and partners’ active collaboration. The development of a crop-specific ontology is a community-driven effort that is usually coordinated by a curator (or curators) nominated within the community itself. The curator(s) are responsible for coordinating discussions with domain experts and developing a quality Trait Dictionary (TD) using the template.

Guidelines Authors and Reviewers

The first version of the Guidelines was written by Julian Pietragalla, Integrated Breeding Platform, and Léo Valette, formerly Research assistant at Bioversity international. The revised version 2.0 was written by Julian Pietragalla (IBP), Rosemary Shrestha (CIMMYT), Marie-Angélique Laporte (Alliance Bioversity-CIAT) and Elizabeth Arnaud (Alliance Bioversity-CIAT) and Tom Hazekamp (Consultant for the Alliance), and submitted for feedback to Célia Michotey (INRAe, URGI),Cyril Pommier (INRAe, URGI), Françoise Potier (CIRAD) David Waring (Cornell University)

Citation

Pietragalla J., Valette L., Shrestha R., Laporte M.-A., Hazekamp T., Arnaud E. Guidelines for creating crop-specific ontologies to annotate phenotypic data, version 2.0, Alliance Bioversity International-CIAT, 2020

Grants

The Crop Ontology was created with the financial support of Bioversity International and the Integrated Breeding Platform and is maintained thanks to the CGIAR Research Programmes’ support, the CGIAR Platform for Big Data in Agriculture, all funded by the CGIAR Fund Council and, from 2014 to 2019, with the award of the US National Science Foundation (NSF) to the cROP-Planteome Project (IOS:1340112 award).

Ontology principal curators in 2020 and 2021

Bambara Groundnut Liliana Andres, South King Cross University
Banana Marie-Angélique Laporte, Alliance Bioversity-CIAT
Barley Ramesh Verna, ICARDA

Fawzy Nawar, ICARDA

Beet Daphne Verdelet, INRAE

Cyril Pommier, INRAE

Bracharia Valheria Castiblanco, CIAT

Luis Miguel Hernandez, CIAT

Brassica Wiktor Jurkowski, Earlham Institute
Cassava Afolabi Agbona, IITA

Naama Menda, Boyce Thompson Institute

Castor Bean Salihu, B. Z., NCRI, Nigeria
Chickpea Roma Das, ICRISAT

Abhishek Rathore, ICRISAT

Common Bean Guerrero Alberto Fabio, CIAT
Cotton Jing Yu, Washington State University
Cowpea Sam Ofodile, IITA

Tunde Agbaje, IITA

Faba Bean Fouad Maalouf, ICARDA
Groundnut Abhishek Rathore, ICRISAT
Lentil Harindra William, IBP
Maize Rosemary Shrestha, CIMMYT

Kate Dreher, CIMMYT

Julian Pietragalla, IBP

Mungbean Julian Pietragalla, IBP
Oats David Waring, Cornell University
Pearl Millet Roma Das, ICRISAT

Abhishek Rathore, ICRISAT

Pigeon Pea Roma Das, ICRISAT

Abhishek Rathore, ICRISAT

Potato Vilma Hualla, CIP until 2020

Elisa Salas, CIP

Thiago Mendes, CIP

Rice Jeffrey Detras, IRRI until 2020

Julia Mae Pasuquin, IRRI

Sorghum Abhishek Rathore, ICRISAT
Soybean Rex T. Nelson, USDA
Sugar Kelp Joshua Mao, Cornell University
Sunflower Evan Staton, University of British Columbia
Sweet Potato Jolien Swanckaert, CIP

Godwill Makunde, CIP

Vitis Eric Duchêne, INRA
Wheat Rosemary Shrestha, CIMMYT

Julian Pietragalla, IBP

Woody Species Celia Michotey, INRAE

Ines Chaves, IBET

April 21, 2021

Elizabeth Arnaud, the Alliance Bioversity International - CIAT



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