AgroPortal: A vocabulary and ontology repository for agronomy

Jonquet Clément, Toulet Anne, Arnaud Elizabeth, Aubin Sophie, Dzalé Yeumo Esther, Emonet Vincent, Graybeal John, Laporte Marie-Angélique, Musen Mark A., Pesce Valeria, Larmande Pierre. 2018. AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture, 144 : pp. 126-143.

Journal article ; Article de revue à facteur d'impact
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Abstract : Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications. By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain. The AgroPortal project re-uses the biomedical domain's semantic tools and insights to serve agronomy, but also food, plant, and biodiversity sciences. We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web. The AgroPortal specifically satisfies requirements of the agronomy community in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities). In this paper, we present our platform's content and features, including the additions to the original technology, as well as preliminary outputs of five driving agronomic use cases that participated in the design and orientation of the project to anchor it in the community. By building on the experience and existing technology acquired from the biomedical domain, we can present in AgroPortal a robust and feature-rich repository of great value for the agronomic domain.

Mots-clés Agrovoc : ontologie, vocabulaire, Banque de données, Modèle mathématique

Mots-clés libres : Ontologies, Controlled vocabularies, Ontology repository, Metadata, Semantic annotation

Classification Agris : C30 - Documentation and information
A50 - Agricultural research
U10 - Mathematical and statistical methods

Champ stratégique Cirad : Hors axes (2014-2018)

Agence(s) de financement européenne(s) : European Commission

Programme de financement européen : H2020

Projet(s) de financement européen(s) : Semantic Indexing of French Biomedical Data Resources - mobility

Auteurs et affiliations

  • Jonquet Clément, LIRMM (FRA) - auteur correspondant
  • Toulet Anne, LIRMM (FRA) ORCID: 0000-0003-0463-0854
  • Arnaud Elizabeth, Bioversity International (FRA)
  • Aubin Sophie, INRA (FRA)
  • Dzalé Yeumo Esther, INRA (FRA)
  • Emonet Vincent, LIRMM (FRA)
  • Graybeal John, Center for BioMedical Informatics Research (USA)
  • Laporte Marie-Angélique, Bioversity International (FRA)
  • Musen Mark A., Center for BioMedical Informatics Research (USA)
  • Pesce Valeria, FAO (ITA)
  • Larmande Pierre, IRD (FRA)

Source : Cirad-Agritrop (

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