[PhD’s Corner] Luis Felipe Vargas Rojas: Combining Semantic Web and modelling approaches for organizing phenotyping data collected at different scales of plant organization

Luis Felipe Vargas Rojas is one of the #DigitAg co-funded  PhDs

Combining Semantic Web and modelling approaches for organizing phenotyping data collected at different scales of plant organization

 

  • Start Date:  1st April 2020
  • University:  MUSE University of Montpellier
  • PhD School: GAIA
  • Field(s): Informatics, Data science
  • Doctoral Thesis Advisor: François Tardieu, LEPSE, Inra
  • Co-supervisors : Llorenç Cabrera-Bosque, LEPSE, Inra  & Danai Symeonidou, MISTEA, Inra
  • Funding: INRA  / #Digitag
  • #DigitAg:  Axis 4, 6 – Challenge 2

Keywords: ontologies, plant phenomics, modelling

Abstract: In recent years, plant phenomics has generated massive datasets obtained in the field or in phenotyping platforms, at organ, plant or canopy levels. Such multi-origin, multi-scale datasets generate a massive problem for designing ontology-based information systems. The thesis consists in combining Semantic Web and modelling approaches to facilitate the mapping of concepts and ontologies at different levels of organization, thereby developing a framework for organising phenomic datasets. (i) He/she will adapt Semantic Web methods for expressing relationships between traits in field and greenhouse in such a way that software agents can query and integrate data originating from different contexts (e.g. greenhouse and field) and sources (e.g. databases and Web APIs). This will involve exploring existing ontologies, using existing tools for ontology alignment and adapting querying mechanisms to the sources mentioned above. (ii) He/she will then develop ontology extensions from sets of equations that link variables at plant by expressing the operations as semantic properties able to link concepts at plant and canopy levels. In this way the “field” and “greenhouse” concepts will be automatically translated one to the other via the existing knowledge expressed as equations. Proof of concepts will be carried out at each step by using existing datasets, for testing to what extent the conceptual framework developed in the thesis allows assembling datasets from different phenomic platforms in greenhouse and fields. This will allow mapping concepts able to cross scales of organisation and to create dynamic links between traits, with the final aim to re-use knowledge acquired in different contexts. The thesis will focus on traits associated with canopy development.

 

Contact:  luis-felipe.vargas-rojas [AT] inrae.fr​, Cell: 07 66 84 74 35

Social Networks: LinkedIn