Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies

Andrés-Hernández, Liliana; Halimi, Razlin Azman; Mauleon, Ramil; Mayes, Sean; Baten, Abdul; King, Graham J.

Abstract

Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops. We used bambara groundnut (Vigna subterranea) as an exemplar underutilized crop to assess the ability of the Crop Ontology system to facilitate curation of trait datasets, so that they are accessible for comparative analysis. This involved generating a controlled vocabulary Trait Dictionary of 134 terms. Systematic quantification of syntactic and semantic cohesiveness of the full set of 28 crop-specific COs identified inconsistencies between trait descriptor names, a relative lack of cross-referencing to other ontologies and a flat ontological structure for classifying traits. We also evaluated the Minimal Information About a Phenotyping Experiment and FAIR compliance of bambara trait datasets curated within the CropStoreDB schema. We discuss specifications for a more systematic and generic approach to trait controlled vocabularies, which would benefit from representation of terms that adhere to Open Biological and Biomedical Ontologies principles. In particular, we focus on the benefits of reuse of existing definitions within pre- and post-composed axioms from other domains in order to facilitate the curation and comparison of datasets from a wider range of crops. Database URL: https://www.cropstoredb.org/cs_bambara.html.

Citation

Andrés-Hernández, L., Halimi, R. A., Mauleon, R., Mayes, S., Baten, A., & King, G. J. (2021). Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. Database, 2021, Article baab028. https://doi.org/10.1093/database/baab028

• Journal Article Type: Article
• Acceptance Date: Apr 30, 2021
• Online Publication Date: May 14, 2021
• Publication Date: May 15, 2021
• Deposit Date: May 19, 2021
• Publicly Available Date: May 25, 2021
• Journal: Database : the journal of biological databases and curation
• Electronic ISSN: 1758-0463
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 2021
• Article Number: baab028
• DOI: https://doi.org/10.1093/database/baab028
• Public URL: https://nottingham-repository.worktribe.com/output/5560797
• Publisher URL: https://academic.oup.com/database/article/doi/10.1093/database/baab028/6276174