Home

 
 
RICE Team
The Institute of Computational Biology (IBC)

Currently hosted at LMI RICE (Vietnam)

IRD - UMR DIADE

911 avenue Agropolis, BP 64501

34394 Montpellier cedex 5

pierre (dot) larmande (at) ird (dot) fr

Research Gate profile - LinkedIn profile - Google Scholar - ORCID

I am staff scientist at IRD and associate Researcher in the INRIA team Zenith.  Since 2013, I am leading the data integration group at the Institute of Computational Biology part of the LIRMM. I am also staff member of the South Green Platform.

My main research interests are (plant)-ontologies, semantic data indexing and annotation, Data integration, Semantic Web, Metadata, Knowledge management, genomics Big Data management. 


Current projects

  • The Agronomic Linked Data project (AgroLDis a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. The aim of the Agronomic Linked Data (AgroLD) project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.

  • The AgroPortal project aims at developing a reference ontology repository for the agronomic domain. By reusing the NCBO BioPortal technology, we will offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, but we will also offer services for semantically annotating data with the ontologies, as well as storing and exploiting ontology alignments and data annotations. 

  • Gigwa Genotype Investigator for Genome Wide Analyses) is a web application developed to manage genomic and genotyping data from NGS analysis. Gigwa uses of MongoDB for data storage and also provides a user-friendly web interface making such processing accessible to users with little computer expertise.

  • BIOeSAI (Biological electonic System Assistant Index) is an IRD SPIRALE funded project to developed a data integration tool in the context of studies of genetic and phenotypic diversity in Asian and African rice (Oryza sativa and Oryza glaberrima). Overview of the project here and prototype here.


Past projects

  • BioSemantic is a framework developed to automate the integration of biological databases. Data are distributed across many different biological databases, in constant evolution, dispersed across different laboratories, with different data models.
  • OryGenesDB is a database developed for rice reverse genetics. OryGenesDB contains FSTs (flanking sequence tags) of various mutagens and functional genomics data collected from both international insertion collections and the literature.

  • Oryza Tag Line consists in a searchable database integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library.


Masters, Doctoral and Post-doctoral supervision


Post-Doctoral

  • 2015- : Anne Toulet – Contribution to the Agroportal project. Co-supervised with Clement Jonquet.
  • 2014 - 2016 : Aravind Venkatesan - Data integration using metadata and ontologies to merge data coming from different sources, with different formats and semantics. The AgroLD project.
  • 2012-2013 : Julien Wollbrett - Extending the biosemantic framework to biological databases. Co-supervied with Manuel Ruiz.
Doctoral
  • Julien Wollbrett defended on Dec. 2011. His thesis was about developing a Framework Web Service automatically with additional semantic metadata annotations. Co-supervied with Manuel Ruiz.

Master degrees
  • Christine Tranchant, Gaetan Droc, Julien Wollbrett, Imene Chentli, Sara Remini, Dagmara Robakowska (Bioinformatics program, University of Montpellier)
  • Florian Philippe (Bioinformatics program, University of Marseille Lumini)
  • Nicolas Delalande (Informatics Bachelor Degree, Univ. Montpellier)
  • Sebastien Fromentin (Bioinformatics program, University of Paris Orsay)
  • Gildas Tagny and Luyen Le Ngoc (computer science program, IFI, Hanoi)
  • Adrien Petel (computer science program, PolyTech, Grenoble)
  • Stella Zevio (computer science program, Master DECOL, University of Montpellier)
Reviewer

  • Nucleic Acids Research
  • Database
  • Current Plant Biology
  • BMC Bioinformatics