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    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

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    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

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    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.

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    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.

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    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.

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    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
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    Five agronomy, agriculture, ecosystem and biodiversity driving scenarios (WP4 & WP5)

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    D2KAB develops and supports AgroPortal

    The vocabulary and ontology repository dedicated to agri-food hosts 140 semantic artefacts including some reference resources in the domain: Agrovoc, NAL thesaurus, Crop Ontology, TOP thesaurus, AnaEE thesaurus, etc.


    In Sept. 2020 D2KAB released version 2.0 of AgroPortal. Check out our release notes.

  • Consortium & Partners

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

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

    Université de Montpellier & CNRS (UMR5506)

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

    Université Côte d'Azur, Inria & CNRS

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    Delegation for Scientific and Technical Information (DipSO)


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    Information System Technologie for Agrosystems (TSCF)

    INRAE (fomer IRSTEA team)

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    Research Unit in Genomics and Bioinformatics (URGI)


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    Research Unit on Ecology of the Mediterranean Forests (URFM)


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


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    Agropolymers Engineering and Emerging Technologies (IATE)


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    Center for Functional and Evolutive Ecology (CEFE)

    Université de Montpellier & CNRS (UMR5175)

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    Agricultural Technical Coordination Association (ACTA)

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    DIversity - Adaptation - DEvelopment of plants (DIADE)

    French Research Institute for Development

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    Center for Biomedical Informatics Research (BMIR)

    Stanford University

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  • Ecosystem & Partner Projects

    D2KAB: a national component of an international ecosystem.

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    D2KAB's partner projects includes

    ANR FooSIN - French section of the GO FAIR Food Systems Implementation Network

    GO FAIR Food System Implementation Network


    OntoPortal Alliance


  • Results

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


    Some publications are also available in a Zenodo community

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    Software Developments

    Un petit slogan
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    A vocabulary and ontology repository for agronomy

    Within D2KAB, new functionalities are developed (e.g., SKOS support, FAIRness assessment, mapping interoperability, etc.), new semantic resources are regularly uploaded and the collaboration with the OntoPortal Alliance helps to mutualize efforts with BioPortal, EcoPortal, etc.

    See GitHub: https://github.com/agroportal/project-management 

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    Knowledge Graphs

    AGRO-LD, a RDF knowledge base for plant molecular networks


    WeKG-MF: A Knowledge Graph of Observational Weather Data


    Plant Health Bulletins knowledge graph


    D2KAB federated knowledge graphs endpoint

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    Ontologies, semantic resources and alignements

    We develop new or maintain pre-exisiting ontologies, thesaurus or semantic resources in-use within D2KAB scenarios

    French Crop Usage


    Catalogue des produits phytopharmaceutiques et de leurs usages, des matières fertilisantes et des supports de culture autorisés en France (E-PHY)


    Crop Planning and Production Process Ontology (C3PO)


    FCU - TAXREF-LD alignement


    WHEATPHENOTYPE - CO_321 alignement


    ANAEE Thesaurus


    ANAEE Ontology


    INRAE Thesaurus


    TOP Thesaurus

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    Other datasets and collections

    We are maintaining a D2KAB collection with other datasets, documents or collections on Zenodo.

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    Training material

    (to come)

  • Events

    List of events organized or co-organized by project partners and related to D2KAB.

    Bolzano, September 15, 2021

    Co-located with ICBO 2020, within the Bolzano Summer of Knowledge 2021


    Contact: Franck Michel

    Montpellier, Originally planned for May 26-27, 2020. New date to come.

    Free registration here.


    Contact: Clement Jonquet

    11-14 October 2021, organized by the IN-ONVIVE network. See program here.


    Contact: Patrice Buche & Pascal Neveu

    Project scientific meetings

    • Kickoff meeting, Montpellier, June 26-27, 2019.
    • 1st Mi-annual scientific meeting, Online March 3, 2020
    • 1st Annual project meeting, online. From end of September to early November 2020: 2 external keynotes by Pascal Neveu (INRAE) and Elizabeth Arnaud (Bioversity International), 5 workshops, 2 half-day plenary sessions.
    • 2nd Mi-annual scientific meeting, Online, March 11th 2021
    • 2nd Annual project  meeting, online & Paris, 22-25 June 2021. 1 external keynote by Marie-Angélique Laporte (Bioversity International)
  • Contact us

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

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    @d2kab on Twitter

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    d2kab on GitHub

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    AgroHackathon on Meetup

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    D2KAB on ResearchGate

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    D2KAB on Zenodo

  • Support & Funding

    D2KAB is mostly funded by the French National Research Agency. Additional funding is described hereafter.

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    ANR 2018 generic call

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    AGRO-NUMEV-CEMEB InterLabex 2016 call 

    Postdoc LINGUA

    Lingua Franca in Agriculture and Biodiversity

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    Labex NUMEV

    (ANR 2011-LABX-076)

    International Research Team 2019 call

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    #DigitAg Convergence Lab (ANR IA-16-CONV-0004)

    Interns & visiting scholar programs

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