Knowledge management for Plant Biology

I am research scientist at IRD.  I led the data integration group at the Institute of Computational Biology part of the LIRMM, in 2013-2017. I am also staff member of the South Green Platform. Formerly, i was head of the ICT Lab  2017-2020 (Vietnam)

My main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data for plant genomics. 

Short CV

- MSc in Biochemistry, 1997, Univ. Montpellier FR

- MSc in Computer Science, 2000, Univ. Montpellier FR

- Bioinformatics Engineering at CIRAD, 2001-2005

- PhD in Computer Science 2007, Univ. Montpellier FR

- Bioinformatics Engineering at CNRS, 2005-2010

- Bioinformatics Engineering at IRD, 2010 - 2018

- Researcher at IRD, 2018 - now

- HDR in computer science, 2020, Univ. Montpellier

Current projects

• DIG-AI: Deciphering plant genotype-phenotype Interactions using Knowledge Graphs and AI (ANR Funded 2023 - 2026)

• PEPR BreIF Biological Ressources Information Facility (2023 - 2028) 

• The OryzaGP : A dataset for Named Entity Recognition for rice genes.

• The AgroLD project is a knowledge system that exploits the Semantic Web technology and some of the relevant standard domain ontologies, to integrate information on plant species and in this way facilitating the formulation of new scientific hypotheses. The objective of this effort is to provide the community with a platform for domain specific knowledge, capable of answering complex biological questions. 

• PyRice a Python package  API developed to access numerous rice supported databases and produce consistent outputs. 

• 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.

Past projects

• 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.

• 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

• Bill Happi (2025) Using LLM to enhance biological information in knowledge graphs .

• 2019 Gildas Tagny - Engineer - Contribution to AgroLD project. Co-supervised with Manuel Ruiz

• 2015-2017: Nordine El Hassouni - Engineer - Contribution to AgroLD project. Co-supervised with Manuel Ruiz

• 2015-2016 : 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

• Antoine Toffano (2023 2026)  Candidate genes prioritization using knowledge graphs and AI

• Ensieyh Raouffi (2022 - 2025)  AI-driven Bottom-Up Data Linking: from Knowledge Graph Profiling to Meaningful and Interpretable Links

• Bill Happi (2021-2024) Linking complementary datasets through the augmentation of knowledge graphs and multimodal representations.

• 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, Quentin Secher,  Laurine Jaffret (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, Luyen Le Ngoc, Serge Sonfac (computer science program, IFI, Hanoi)

• Adrien Petel (computer science program, PolyTech, Grenoble)

• Ibtissam Bouzidi, Elliot Butz, Massili Kezzoul, Stella Zevio, Ahmed Saidi  (computer science program, Master, University of Montpellier)

• Huy Do, Kazim Djibrill, Khoi Le Nguyen (computer science program, Master USTH Univ. of Hanoi)

• Quan Do (computer science program, Master - University of Toulouse 1)

• Bill Happi ( University of Dschang Cameroun)

Bachelor degrees

• Vautrin Baptiste

• Jean-Christophe Ricklins

• Romane Sallio

• Quan Do (Polytechnic school of engineering of Hanoi)

Reviewer

• Nucleic Acids Research, Bioinformatics, Database, Current Plant Biology, BMC Bioinformatics, Springer Nature Scientific Report., Semantic Web Journal

Project reviewer

• ANR 

• USTH (Hanoi)

Pc member

• ISMB - The annual international conference on Intelligent Systems for Molecular Biology (ISMB)

• IC - Ingenierie des connaissances 

• INFORSID

• PFIA - RJCIA - rencontre des jeunes chercheurs en IA 

• SWAT4LS Semantic Web for Life Science

• DILS Data Integration for Life Science

• PhenoHarmonIS

• INOVIVE

Hobbies

• Guitar player and singer with the VinaBlues Revival ( 2016 - 2020)

• Ultra-marathon runner. Recently run the https://festatrail.com and previously the https://vietnamtrailseries.com/ races

• Cooking