Project D2KAB
Data to Knowledge in Agronomy and Biodiversity
2019-2024
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
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
- WP3: Building and harnessing an ag & biodiv distributed knowledge graph
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.
Laboratory of Informatics, Robotics and Microelectronics of Montpellier (LIRMM)
Université de Montpellier & CNRS (UMR5506)
Web-instrumented man-machine interactions, communities and semantics (Wimmics)
Université Côte d'Azur, Inria & CNRS
Information System Technologie for Agrosystems (TSCF)
INRAE (fomer IRSTEA team)
Research Unit in Genomics and Bioinformatics (URGI)
INRAE
Research Unit on Ecology of the Mediterranean Forests (URFM)
INRAE
Applied Mathematics and Informatics, from Genomes to the Environment (MaIAGE)
INRAE
Agropolymers Engineering and Emerging Technologies (IATE)
INRAE
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
API AGRO
Elzeard
Ecosystem & Partner Projects
D2KAB: a national component of an international ecosystem.
D2KAB's partner projects includes
ANR FooSIN - French section of the GO FAIR Food Systems Implementation Network
GO FAIR Food System Implementation NetworkResults
We mention some of our results hereafter. For a complete overview and informaiton about our results, checkout D2KAB Data Managnement Plan.
Software Development
Our software is open source and available on multiple Git repositories:
https://gitlab.irstea.fr/copain
https://github.com/ontoportal-lirmm
AgroPortal
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!
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:
- French Crop Usage thesaurus (FCU)
- INRAE Thesaurus
- ANAEE Thesaurus and soon coming the ANAEE ontology.
- TOP Thesaurus (with extension to plant roots)
- WTO (a new version now in OWL)
We have also produced alignements betweem semantic resources
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)
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).
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).
Final project meeting materials
(to come)
Contact us
We also have a public mailing list open for project-related discussions: d2kab-public@lirmm.fr
Support & Funding
D2KAB is mostly funded by the French National Research Agency. Additional funding is described hereafter.
AGRO-NUMEV-CEMEB InterLabex 2016 call
Postdoc LINGUA
Lingua Franca in Agriculture and Biodiversity
Labex NUMEV
(ANR 2011-LABX-076)
International Research Team 2019 call
#DigitAg Convergence Lab (ANR IA-16-CONV-0004)
Interns & visiting scholar programs
