Knowledge representation for curation and analysis of crop phenotypic data underpinning nutritional security
Creators: name: Andrés Hernández, Liliana
Publisher: name: Southern Cross University
Year: 2021
Subjects: Knowledge representation
Ontologies
Crop traits
Phenotypic traits

description: Achieving global and regional nutritional security presents many challenges, including maximizing
description: dietary inputs from crop plants. Comparison of nutritional composition between crops, cultivars
description: and associated plant genetic resources requires access to datasets that provide insights into genetic
description: and environmental sources of variation. At present, the ability to access and compare crop
description: phenotypic datasets is limited, particularly for traits relating to dietary nutrition. To date, the use of
description: common trait descriptors or formal systems of knowledge representation such as controlled
description: vocabularies or ontologies has been fragmentary.
description: The primary aim of this thesis is to describe the evaluation and development of ontologies that
description: represent information about crop phenotypic traits in compliance with the Findable, Accessible,
description: Interoperable, and Reusable (FAIR) principles. This provides the opportunity to compare
description: approaches in generating a generalised trait ontology applicable to many crops. Generic efforts to
description: standardize the description and management of crop trait data are critically reviewed, and several
description: issues identified, such as inconsistencies in the syntactic and semantic crop trait descriptions that
description: currently constrain their exchange and comparison.
description: Bambara groundnut (<em>Vigna subterranea</em>) was used as an exemplar underutilised minor crop to
description: assess available formal frameworks to curate trait datasets so that they are accessible for
description: comparative analysis. The challenges in assembling and using a crop-specific Trait Dictionary (TD)
description: are outlined, and the extent to which any Crop Ontology (CO) derives knowledge from existing
description: ontological definitions and relationships quantified. Evaluation of syntactic and semantic
description: cohesiveness of trait descriptors within the Crop Ontology (CO) system helped to identify generic
description: issues limiting reuse of trait names for comparative analysis of major and minor crops. These
description: included inconsistencies in trait names assigned within the 28 published CO:TDs, a relative lack
description: of cross-referencing to other ontologies, and a flat ontological structure for classifying traits.
description: The Trait Dictionary (CO_366) was generated for bambara groundnut, and formal terms were
description: associated with trait descriptors and experimental datasets. These were curated to be compliant
description: with the Minimal Information About a Plant Phenotyping Experiment (MIAPPE) metadata
description: standard, and made available within the publicly accessible CropStoreDB database.
description: For the representation of dietary nutritional information, the Crop Dietary Nutrition Ontology
description: (CDNO) was first proposed and then developed to provide a more comprehensive vocabulary
description: compatible with terms and concepts widely used within national and international Food
description: Composition Databases (FCDBs). The CDNO represents a hierarchical structured vocabulary with
description: two major classes ‘dietary nutritional components’ and ‘nutritional component concentration’,
description: developed by reusing terms from the Chemical Entities for Biological Interest (CHEBI), the
description: Environmental Ontology (ENVO), Phenotype and Trait Ontology (PATO), Relation Ontology
description: (RO) and the Plant Ontology (PO). The reuse of terms from existing ontologies created terms
description: categorised as pre-composed (pre-coordinated), which follows the Open Biological and Biomedical
description: Ontology (OBO) principles for establishment of logically well-formed, scientifically accurate and
description: interoperable controlled vocabularies. The CDNO is open and will be releasing versions constantly
description: with new updates being track in the GitHub repository.
description: The CDNO involved collaboration and co-development of terms with the Food Ontology (FoodOn)
description: for the representation of organismal materials terms, so that they could be assigned in different
description: combinations as post-composed terms with the CDNO ‘nutritional component concentration’
description: terms. To demonstrate how the CDNO can assist in management and navigation of crop datasets
description: that quantify concentration of chemical components, specific use case implementations are
description: presented. The use case describes the association of existing trait descriptors for bambara groundnut
description: with CDNO terms incorporated into an axiom that reuses terms from FOODON, PO and NCBI
description: organismal classification ontology (NCBITaxon).
description: A more systematic and inclusive approach was proposed for a second-generation crop phenotypic
description: trait ontology system that would meet the challenges of data integration and downstream analysis,
description: by ensuring consistency in knowledge representation and implementation of machine-readable
description: axiomatic definitions. This would require establishing a universal, systematic and deeper set of
description: ontology sub-classes reusing terms from the Plant Trait Ontology (TO) and other relevant
description: ontologies.
description: In conclusion, generic systems of knowledge representation for crop plant phenotypes are expected
description: to facilitate curation of datasets according to FAIR principles. Systems such as CDNO should help
description: increase informed dialogue between crop scientists, breeders and other stakeholder in agricultural
description: production and food supply, including dieticians and nutritionists.