Agronomy and biodiversity shall address several major societal, economical, and environmental challenges. However, data are being produced in such big volume and at such high pace, it questions our ability to transform them into knowledge and enable, for instance, translational agriculture i.e., rapidly and efficiently transferring results from agronomy research into the farms (“bench to farmside”). Semantic interoperability enables data integration and fosters new scientific discoveries by exploiting various data acquired from different perspectives and domains.
D2KAB’s primary objective is to create a framework to turn agronomy and biodiversity data into –semantically described, interoperable, actionable, open– knowledge, along with investigating scientific methods and tools to exploit this knowledge for applications in science and agriculture. We will adopt an interdisciplinary semantic data science approach that will provide the means –ontologies and linked open data– to produce and exploit FAIR (Findable, Accessible, Interoperable, and Re-usable) data. To do so, we will develop original approaches and algorithms to address the specificities of our domain of interests, but also rely on existing tools and methods.
D2KAB involves a multidisciplinary (and international) research consortium of three computer science labs (UM-LIRMM, CNRS-I3S, STANFORD-BMIR), four bioinformatics, biology, agronomy and agriculture labs (INRA-URGI, INRA-MaIAGE, INRA-IATE, IRSTEA-TSCF), two ecology and ecosystems labs (CNRS-CEFE, INRA-URFM), one scientific & technical information unit (INRA-DIST), and one association of agriculture stakeholders (ACTA). The consortium’s expertise ranges from ontologies and metadata, semantic Web, linked data, ontology alignment, knowledge reasoning and extraction, natural language processing to bioinformatics, agronomy, food science, ecosystems, biodiversity and agriculture.
The project is structured with three work-packages of research and development in informatics and two work-packages of driving scenarios. WP1 will focus on ontologies/ vocabularies and turn the AgroPortal prototype into a reference platform that addresses the community needs and reaches a high level of quality regarding both content and services offered e.g., SKOS compliance, semantic search over linked data, text annotation, interoperability with other repositories. WP2 will focus on the critical issue of ontology alignment and develop new functionalities and state-of-the-art algorithms in AgroPortal using background knowledge methods validated in ag & biodiv. WP3 will design the methods and tools to reconcile the scenarios' heterogeneous ag & biodiv data sources and turn them into linked data within D2KAB distributed knowledge graph. It will also investigate exploitation of this graph through novel visualization, navigation and search methods.
WP4 includes four interdisciplinary research driving scenarios implementing translational agriculture. For instances, an ontology-driven decision support system to select the most appropriate food packaging or an augmented semantic reader for Plant Health Bulletins. We will provide a unique scientific knowledge base for wheat phenotypes and offer the first agricultural data resource empowered by linked open data. WP5 will develop semantic resources for the annotation of ecosystem experiments data and functional biogeography observations. A plant trait-environment-relationships study will be conducted to understand the impacts of climatic changes on vegetation of the Mediterranean Basin.
Within a dedicated work-package, we will focus on maximizing the impact of our research. Each of the project driving scenarios will produce concrete outcomes for ag & biodiv scientific communities and stakeholders in agriculture. We have planned multiple dissemination actions and events where we will use our driving scenarios as demonstrators of the potential of semantic technologies in agronomy and biodiversity.
Monsieur Jonquet Clement (Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier)
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
INRA-URFM Ecologie des Forêts Méditerranéennes
UM-LIRMM Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier
STANFORD-BMIR Stanford University / Stanford Center for Biomedical Informatics Research
CNRS-I3S Laboratoire informatique, signaux systèmes de Sophia Antipolis
IRSTEA-TSCF Technologies et Systèmes d'Information pour les Agrosystèmes
CNRS-CEFE Centre d'Ecologie Fonctionnelle et Evolutive
ACTA ASSOCIATION COORDINATION TECHNIQUE AGRICOLE
INRA-DIST Délégation Information Scientifique et Technique
INRA-MaIAGE Mathématiques et Informatique Appliquée du Génome à l'Environnement Unité de recherche
INRA-URGI Unité de Recherche Génomique-Info
INRA-IATE Ingénierie des Agropolymères et Technologies Emergentes
Help of the ANR 951,180 euros
Beginning and duration of the scientific project: May 2019 - 48 Months