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README.md 9.48 KiB

Bio AGgressor Ontology (BAGO)

TThis ontology and associated knowledge graphs were build during the D2KAB project. The ontology goal is to model all the living organisms involved in cultivated plant disease appearance. The ontology and its documentation represent the point of view of some french researchers from differents institutions (INRAE, Elzeard, Acta, IFV).

The French ANR project "Data to Knowledge in Agronomy and Biodiversity" D2KAB (www.d2kab.org) has created 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. One of the five driving scenarii of D2KAB was to publish on the Web of Linked data an archive of French agricultural alert bulletins, called Plant Health Bulletins (Bulletins de Santé du Végétal). To annotate the bulletins using crop diseases and pests, we need a new semantic resource. Several ontologies and knowledge graphs already exist on the subject, but they do not cover all our needs. We have therefore developed a new ontology, "BioAGgressor Ontology" (BAGO), reusing elements from existing ontologies as far as possible. This new ontology was developed using the LOT methodology in partnership with 4 experts in agriculture, entomology and plant disease.

Access Description and Identifier

The licence is CC BY-NC-ND 4.0 DEED https://creativecommons.org/licenses/by-nc-nd/4.0/deed.fr due to the fact that we present some definitions proposed by Quae Books.

BAGO URI is https://opendata.inrae.fr/bag-def#

BAGO is available on :

the git repository to follow the evolution of BAGO is : https://forgemia.inra.fr/bsv/bio-agressor-ontology Do not hesitate to create an issue if you find a bug in the ontology or associated knowledge graph

Developement Process

The conceptualisation method follows the Linked Open Terms method. It is based on several version of CHOWLK diagrams discussed by experts and then some implementation tests are performed using Protege tool and cellfie plugin. The documentation was generated by Widoco tool https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html

Specification: Competency Questions (CQ).

BAGO answers those CQs:

  • What is the scientific name (kingdom rank) of the living organism O ? "Daktulosphaira vitifoliae" is an animal, "grapevine" is a plant, etc.
  • What is the scientific name (species rank) of the living organism O ? cultivated grapevine species is "Vitis vinifera", grape phylloxera species is "Daktulosphaira vitifoliae", etc.
  • What is the vernacular name of the living organism O ? "Vitis vinifera" vernacular name is "cultivated grapevine", "Daktulosphaira vitifoliae" vernacular name is "grape phylloxera", etc.
  • What is the role of living organism O involved in the bioagressor attack A ? "Vitis vinifera" is the host, "Daktulosphaira vitifoliae" is the agressor, etc.
  • What is the type of bioaggressors B ? "Daktulosphaira vitifoliae" is a pest animal, etc.
  • Which cultivated plant C is attacked by the bioaggressor B ? "cultivated grapevine" is attacked by "grape phylloxera", etc.
  • What are the diseases related to the cultivated plant C ? diseases related to "cultivated grapevine" are phylloxera disease, mildew disease, etc.
  • Which pathogen causes the disease D ? The phylloxera disease is caused by the "Daktulosphaira vitifoliae", etc.
  • Which parts of the cultivated plant C present some symptoms of the bioaggressor attack? "Daktulosphaira vitifoliae" attacks the leaves and the roots, etc.
  • What is the disease class organised by organs attacked? phylloxera disease is a root disease and an leave disease, etc.
  • What is the disease class organised by pathogen types ? phylloxera disease is a Non Parasitic Biotic Plant Disease, etc.

Sources of information

The reference sources of information used during the conceptualisation of BAGO and grapevine disease KG are:

Authors and contributors

Catherine ROUSSEY: MISTEA INRAE Occitanie Center Montpellier (https://orcid.org/0000-0002-3076-5499): She is a researcher in Semantic Web technologies and ontology design. She is in charged of the CHOWLK conceptualiaation, the formalisation using Protégé Tool and the documentation.

A pool of experts was interviewed during the conceptualization of BAGO and grapewine disease KG :

The grapevine disease KG was build thanks to NLP process designed by :

The grapevine disease KG is aligned with INRAE thesaurus.

  • Sophie AUBIN, DIPSO, INRAE (https://orcid.org/0000-0003-4805-8220): she manages the discussions between INRAE thesaurus managers and BAGO creator and contributors in order to propose some alignements between those semantic resources.

Some engineers published the RDF graphs on the web:

  • Stephan BERNARD, LISC INRAE Center ARA Clermont-Ferrand (https://orcid.org/0000-0001-9694-1443): He is a Semantic Web expert in charge of the grapevine disease KG publication in SPARQL Endpoint.

Productor:

Funding:

  • ANR-18-CE23-0017 D2KAB (Data to Knowledge in Agronomy and Biodiversity) http://www.d2kab.org . WP T4.3 BSV Reader

Documentation

  • F. AMARDEILH, S. BERNARD, R. BOSSY, M. COURTIN, M. HIRSCHY, P. LARIGNON, C. ROUSSEY, N. SAUVION. Une ontologie pour modéliser les bioagresseurs des plantes. Dans les actes des 35es Journées francophones d'Ingénierie des Connaissances (IC 2024) associée à la Plate-Forme Intelligence Artificielle (PFIA 2024), 3-5 Juillet 2024, La Rochelle, France. pp.8-13, ⟨https://hal.science/hal-04638343⟩