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

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.

Plant phenotyping relevance

作物表現型データの標準化、Trait Dictionary、Crop Ontology、データキュレーションおよびFAIR準拠評価が研究の中心であり、再利用可能な表現型データ記述手法を扱うため。

Code and data availability

The paper's bambara groundnut phenotype datasets and Trait Dictionary are publicly available: the curated bambara trait datasets are hosted in CropStoreDB, and the authors' Trait Dictionary (134 terms, crop code CO_366) is published on the Crop Ontology portal. Supplementary tables (S1–S7) contain the multi-species TD,