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Semantic/knowledge engineer for biodiversity science

Over the last decade, the scientific community collected a considerable amount of data on trophic interactions and traits. Some of them are available on databases, others are disseminated in scientific papers, books and wiki papers. The diet is an example of trait that maps directly the consumer to all potential resources. For instance, fungivores such as some nematode genera feed on fungi while geophageous organisms such as some earthworms consume soil. The diet is a crucial information reported on most taxa-focused texts and databases. However, to our knowledge, there is no existing tool or database that maps diets to resources. Once the link between diets and resources is known, then given the diet of any consumer, we can determine the corresponding resources/preys.

Our goal is to define a set of semantic resources and tools that will allow us to automate the creation of food webs, and will provide controlled vocabularies for text mining and information retrieval pipelines. More precisely, we aim at designing, formalizing and publishing an ontology that maps diets (trophic groups) to resources so that trophic group membership can be inferred from trophic interactions, and vice versa.


  • Become familiar with the concepts of trophic groups, diets, guilds, biotic interactions, resource acquisition strategies.
  • Facilitate a collaborative and iterative ontology development process that currently involves more than twenty specialists of soil fauna and soil ecology.
  • At the end of each iteration, edit the ontology based on expert feedback and create a new release in line with OBO principles (
  • Ensure a scientific and technological watch in ontology engineering, with a particular focus on techniques for representing uncertain knowledge.


These activities will be supervised by Mickael Hedde (INRAE, Eco&Sols Montpellier) and Nicolas Le Guillarme (CNRS, LECA Grenoble). The person recruited will participate as much as necessary in the meetings of the project-team. He/she will organise and participate in meetings with international scientific network.

The position is to be filled as soon as possible and will end in February 2022. The recruited person will be based at Eco&Sols (INRAE Montpellier) and will be in regular interaction with the LECA (CNRS Grenoble). Some of the activities may be carried out remotely.

knowledge engineering; modélisation ontologique; Semantic Web
INRAe Montpellier
Date de début souhaitée
Langues obligatoires
Type de contrat
Type de poste
Ingénieur; Master; Postdoc

A semantic engineer with a background in biodiversity science, ecology or life science. Candidates without a life-science background but with extensive experience in Semantic Web technologies and ontology development are also welcome to apply.

Mastery of Semantic Web technologies (OWL, RDF, SPARQL) and ontology engineering tools (Protégé, ROBOT, ontology-development-kit).
Previous experience in ontology development would be appreciated.
Strong communication skills (fluency in English is essential) and ability to facilitate the work of a community of experts.
Programming skills : command line tools, shell scripts, Makefile, versioning using GitHub

Salaire indicatif
Depending on his/her profile and level of education, the gross monthly remuneration will be comprised between €2,000-2,400 (without a PhD degree) or €2,300-2,900 (with a PhD degree), respectively (according to INRAE salary scale).
Date limite
Informations de contact

Mickael Hedde, INRAE Montpellier,
Nicolas Le Guillarme, Laboratoire d’Écologie Alpine,