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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
    • 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 180 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.

    Since then, multiple features and additons where implemented. Check out our release notes.

  • Consortium & Partners

    ANR D2KAB is a formal consortium of 10 research 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

    We mention some of our results hereafter. For a complete overview and informaiton about our results, checkout D2KAB Data Managnement Plan.

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

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    Software Development

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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.


    Check out AgroPortal Release Notes since 2020 to see the amoiunt of work relaised within D2KAB!

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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

    All semantic resources (22 in total and 32 if we include views) developped within D2KAB are gathered within a group and slice in AgroPortal.


    D2KAB has especially produced:

    • BBCH-based Plant Phenological Description Ontology (PPDO), an ontology framework (1 ontology, 9 views) to represent multiples phenological scales.
    • Catalogue des produits phytopharmaceutiques et de leurs usages, des matières fertilisantes et des supports de culture autorisés en France (E-PHY), a prototype ontological representation of ANSES's E-Phy database.
    • Crop Planning and Production Process Ontology (C3PO) , an ontology, developped with Elzeard, to represent general information about agroecological production.
    • Ontology for Observational Weather Data (WeKG).
    • THESOLIVE, a thesaurus of phenotypic traits specifically to olive tree, currently developped on OpenTheso.


    As well as extensions, or new version of:

    We have also produced alignements betweem semantic resources

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    Knowledge Graphs

    D2KAB is very much about producing multiples or fererated knowledge graphs. Here we list the KGs not explicilty listed above as semantic resources.

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


    D2KAB federated knowledge graphs endpoint (based on Corese)


    KartoGraphI: Knowledge graph cartography and index (done in collaboration with ANR DEKALOG)

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    Collections and other datasets (on Zenodo)

    We are maintaining a D2KAB community with other datasets, documents or collections on Zenodo. It oculd also be used to assign DOI to resources mostly served elsewhere (e.g., ontologies).

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    Collections and other datasets (on ResearchDataGouv)


    We do not have a collection or community on RDG, but D2KAB results can be found with this query. It contains other datasets, documents or collections. It oculd also be used to assign DOI to resources mostly served elsewhere (e.g., ontologies).

  • Events

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

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




    10-13 October 2023, organized by CATIs DIISCICO et CODEX. See program here.


    Contact: Patrice Buche & Pascal Neveu

    PhenoHarmoIS 2024

    D2KAB followed and support the 2024 edition of PhenoHarmonIS workshop: Data & Dialogue: Agrifood semantics in the Age of Artificial Intelligence


    Contact: Elizabeth Arnaud & Pascal Neveu

    Observable Properties workshop 2022

    D2KAB organized, 27-28 October 2022, a restricted workshop to work on the different models of scientific variables or observable properties.


    We had representative of the following models:

    • I-ADOPT framework (G. Moncoiffé)
    • OBOE (C. Pichot & D. Maurice)
    • COSWOT (C. Roussey & D. Charpenay)
    • RDF Data Cube (G. Atemezing)
    • SSN/SOSA (C. Roussey)
    • PO2 (L. Ibanescu & S. Dervaux)
    • OpenSILEX (P. Neveu)

    Contact: Clement Jonquet & Christian Pichot

    Taxonomies in ecology/biodiversity workshop 2022

    D2KAB organized, 24 May 2022, a restricted workshop to work on taxonomies in ecology/biodiversity.


    We had representative of the following institutions: MNHN, sDiv, etc.


    Contact: Clement Jonquet & Eric Garnier

    Bolzano, September 15, 2021

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


    Contact: Franck Michel

    The 3rd AgroHackathon "FAIRness assessment" 2022 took place over a little more than 24 hours on August 29 and 30, 2022, on the SupAgro Montpellier campus.


    It was preceded by the final meeting of the ANR FooSIN project and followed by a public presentation of the project's outcomes.


    Contact: Clement Jonquet & Sophie Aubin

    Project scientific meetings

    • Kickoff meeting, Montpellier, June 26-27, 2019.
    • 1st Annual project meeting, online. From end of September to early November 2020. With 5 workshops, 2 half-day plenary sessions and 2 external keynotes by:
      • Pascal Neveu (INRAE)
      • Elizabeth Arnaud (Bioversity International)
    • 2nd Annual project meeting, online & Paris, 22-25 June 2021. With external keynote by:
      • Marie-Angélique Laporte (Bioversity International)  
    • 3rd Annual project meeting, online & Sophia-Antipolis, 22-24 June 2022. With 2 external keynotes by:
      • Raphael Troncy (EURECOM)
      • Yvan LeBras (MNHN)
    • 4th Annual project meeting, online & Avignon, 21-23 June 2023. With 2 external keynote by:
      • Dominique Vachez (INIST)
      • Daniel Martini (KTBL, FAIRagro)
    • Final project meeting in Montpellier, 17--20 June 2024. With external keynotes by:
    • Christelle Pierkot (CNRS/Data Terra)
    • Gaelle Cheruy Pottiau (AgDataHub)
  • 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 Zenodo

    161Rue Ada
    34090 Montpellier
  • 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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