Building the Core Vocabulary of Crop Names to Integrate the Vocabularies by Multiple Government Agencies

Joo, Su-Chong; Takeda, Hideaki; Takezaki, Akane; Yoshida, Tomokazu

doi:10.1007/978-3-030-04284-4_22

Cited by 2 publications

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“…The Crop Ontology (CO 17 ; Shrestha et al, 2011) is not actually an individual ontology, but a collection of approximately 40 species-specific vocabularies with very limited semantics, covering germplasm, phenotype or trait, and location and environment. The Common Agricultural Vocabulary (CAVOC; Joo et al, 2018) is a Japanese vocabulary system of agricultural crop names developed for the purpose of data cooperation between agricultural systems, presented in Japanese. The Agronomy Ontology (Devare et al, 2016) describes agronomic practices, techniques, and variables used in agronomic experiments.…”

Section: Discussionmentioning

confidence: 99%

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

et al. 2019

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The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database ( http://www.planteome.org ) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.

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Section: Discussionmentioning

confidence: 99%

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

et al. 2019

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“…. 2-2, "Cucumber (leaves)," "Cucumber (flowers)," and "Cucumber (fruits)"](Joo et al 2018), because the acceptable limits of agricultural chemical use and residues differ among the different edible parts of a crop. Although the item names in the "Agricultural Chemical Use Reference"[Fig.…”

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Common Agriculture Vocabulary for Enhancing Semantic-level Interoperability in Japan

Takezaki

Joo

Takeda

et al. 2020

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We introduce the features of Common Agriculture Vocabulary (CAVOC) and CAVOC-based services, review other resources for standards in the domains of agriculture and food, and briefly discuss the future direction of agricultural semantics standards in Japan based on reviews. CAVOC has been developed as a core vocabulary for enhancing semantics-level interoperability. It specifies concepts that are frequently used to annotate agricultural data on agricultural activities and crops in Japan. The CAVOC website provides uniform resource identifiers by which the concepts in CAVOC are given. The data in CAVOC can be downloaded from the website. The extension of CAVOC coverage is important to unambiguously define objects and their relationships in the domains of agriculture and food. International collaborative efforts to create standards in agricultural semantics are underway through mapping among semantic resources within international projects and by holding meetings among stakeholders. We need to join the international community in creating agricultural semantics standards so as to extend CAVOC coverage through the utilization of foreign resources.

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Building the Core Vocabulary of Crop Names to Integrate the Vocabularies by Multiple Government Agencies

Cited by 2 publications

References 1 publication

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

Common Agriculture Vocabulary for Enhancing Semantic-level Interoperability in Japan

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