• Project D2KAB

    Data to Knowledge in Agronomy and Biodiversity


  • We want to create a framework to turn agronomy and biodiversity data into knowledge –semantically described, interoperable, actionable, open– and investigate scientific methods and tools to exploit this knowledge for applications in science & agriculture

  • Where are agronomy and biodiversity in the famous Linked Open Data cloud diagram?

    We want D2KAB to accomplish a similar role in agronomy, agriculture and biodiversity

  • News

  • Our project

    What we (will) do?

    D2KAB’s primary objective is to create a framework to turn agronomy and biodiversity data into knowledge –semantically described, interoperable, actionable, open– and investigate scientific methods and tools to exploit this knowledge for applications in science & agriculture. Agronomy/agriculture and biodiversity (ag & biodiv) face several major societal, economical, and environmental challenges, a semantic data science approach will help to address. We shall provide the means –ontologies and linked open data– for ag & biodiv to embrace the semantic Web to produce and exploit FAIR data. To do so, we will develop new original methods and algorithms in the following areas: data integration, text mining, semantic annotation, ontology alignment and linked data exploitation.

    Who are we?

    D2KAB project brings together a unique multidisciplinary consortium of 12 partners to achieve this objective: 2 informatics research units (LIRMM, I3S); 6 INRA/IRSTEA/IRD applied informatics research units (URGI, MaIAGE, IATE, DIST, TSCF, DIADE) specialized in agronomy or agriculture; 2 labs in biodiversity and ecosystem research (CEFE, URFM); 1 association of agriculture stakeholders (ACTA); and 1 partnership with Stanford BMIR department. Each of the project driving scenarios (food packaging, agro-agri linked data, wheat phenotype, ecosystems & plant biogeography) will have a significant impact and produce concrete outcomes for ag & biodiv scientific communities and socio-economic actors in agriculture.

    What are our objectives?

    Objective 1: To develop state-of-the-art methods and technologies for ontology lifecycle and alignment.


    Objective 2: To build the agronomy, agriculture and biodiversity Linked Open Data cloud.


    Objective 3: To enable new semantically driven agronomy and biodiversity science.

    How we will do?

    • WP1: Ontology-based services
    • WP2: Ontology alignment and the Global Agricultural Concept Scheme (GACS)
    • WP3: Building and harnessing an ag & biodiv distributed knowledge graph

    Five agronomy, agriculture, ecosystem and biodiversity driving scenarios

    • T4.1 Ontology driven food packaging solutions [INRA-IATE/CNRS-I3S]
    • T4.2-3 Plant Health Bulletins augmented semantic reader with lifting of API-AGRO data [IRSTEA-TSCF/ACTA/INRA-DIST/CNRS-I3S]
    • T4.4 Wheat phenotype data integration [INRA-MaIAGE/INRA-URGI/INRA-IATE/UM-LIRMM]
    • T5.1 New ontologies and thesaurus in biodiversity and ecosystem research [INRA-URFM/CEFE]
    • T5.2 Plant functional biogeography data integration in the Mediterranean Basin [CEFE/INRA-URFM]
  • D2KAB develops and supports AgroPortal

    We have already designed and implemented an advanced prototype that hosts 108 ontologies or vocabularies including some reference resources in the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc.


    During D2KAB, we will transform the AgroPortal prototype into a widely adopted, long-term supported, robust and curated ontology repository.

  • Partners

    ANR D2KAB is a formal consortium of 10 units and 2 external collaborators, which cover 7 important research organisations.

    Laboratory of Informatics, Robotics and Microelectronics of Montpellier (LIRMM)

    Université de Montpellier & CNRS (UMR5506)

    Web-instrumented man-machine interactions, communities and semantics (Wimmics)

    Université de Nice, Inria & CNRS

    Scientific and Technical Information Department (DIST)


    Research Unit in Genomics and Bioinformatics (URGI)


    Applied Mathematics and Informatics, from Genomes to the Environment (MaIAGE)


    Agropolymers Engineering and Emerging Technologies (IATE)


    Research Unit on Ecology of the Mediterranean Forests (URFM)


    Information System Technologie for Agrosystems (TCSF)

    National Research Institute of Science and Technology for Environment and Agriculture

    Center for Functional and Evolutive Ecology (CEFE)

    Université de Montpellier & CNRS (UMR5175)

    Agricultural Technical Coordination Association (ACTA)

    DIversity - Adaptation - DEvelopment of plants (DIADE)

    French Research Institute for Development

    Center for Biomedical Informatics Research (BMIR)

    Stanford University

  • Ecosystem

    D2KAB: a national component of an international ecosystem.

  • Results


    Publications associated with the project are referenced on the HAL platform.


    Some publications are also available in a Zenodo community


    A vocabulary and ontology repository for agronomy

    Software Developments

    Un petit slogan

    Our software is open source and available on GitHub: https://github.com/d2kab

  • Events

    Kick off meeting

    Project kickoff meeting is organized in Montpellier June 26-27, 2019.

  • Open Positions

    We offer several positions including PhDs, postdocs, researcher and research engineer. Please contact us for more information.

    PhD – Data linking and enrichment

    LIRMM (Montpellier)

    Contact K. Todorov & C. Jonquet




    Not open for application yet. Please contact for info.

    Master Interns – Ontology & knowledge engineering

    LIRMM (Montpellier)

    Contact C. Jonquet


    Description (in French)


    Application by email

    Master Intern – Conception and implementation of a termino-ontological resource editor

    INRA-IATE (Montpellier)

    Contact P. Buche


    Description (in French)


    Application by email

    Master Intern – Text mining for extraction of agricultural terminologies

    IRSTEA-TSCF (Clermont-Ferrand)

    Contact C. Roussey & R. Bossy


    Description (in French)


    Application by email

  • Closed positions

    Semantic Web Postdoc / Researcher – Ontology management and alignment -LIRMM (Montpellier)

    Contact C. Jonquet – Description


    CIFRE PhD LIRMM-Elzeard – Mixing machine learning and semantic web methods for the optimization and planning of market gardening in agro-ecology

    LIRMM & Elzeard (Montpellier, Bordeaux)

    Contact K. Todorov & C. Jonquet & F. Amardeilh – Description (in French)


    PhD – Ontology alignement & property graphs

    LIRMM (Montpellier)

    Contact C. Jonquet & A. Castelltort – Description & Slides


    Full stack Developer (Web application, Ruby/Rails, Java, Semantic web)

    LIRMM (Montpellier)

    Contact C. Jonquet – DescriptionDescription (english)

  • Contact us

    We also have a public mailing list open for project-related discussions: d2kab-public@lirmm.fr

    @d2kab on Twitter

    d2kab on GitHub

    AgroHackathon on Meetup

    D2KAB on ResearchGate

    D2KAB on Zenodo

    161Rue Ada
    34090 Montpellier
  • Support & Funding

    ANR 2018 generic call