Section: Application Domains

Biomedical Knowledge Discovery

Participants : Marie-Dominique Devignes [contact person] , Malika Smaïl-Tabbone, Sabeur Aridhi, David Ritchie, Gabin Personeni, Seyed Ziaeddin Alborzi, Kévin Dalleau, Bishnu Sarker, Emmanuel Bresso, Claire Lacomblez.

This projects in this domain are carried out in collaboration with the Orpailleur Team.

Huge and ever increasing amounts of biomedical data (“Big Data”) are bringing new challenges and novel opportunities for knowledge discovery in biomedicine. We are actively collaborating with biologists and clinicians to design and implement approaches for selecting, integrating, and mining biomedical data in various areas. In particular, we are focusing on leveraging bio-ontologies at all steps of this process (the main thesis topic of Gabin Personeni, co-supervised by Marie-Dominique Devignes and Adrien Coulet from the Orpailleur team). One specific application concerns exploiting Linked Open Data (LOD) to characterise the genes responsible for intellectual deficiency. This work is in collaboration with Pr. P. Jonveaux of the Laboratoire de Génétique Humaine at CHRU Nancy [71], [72]. This involves using inductive logic programming as a machine learning method and at least three different ontologies (Gene Ontology, Human Phenotype Ontology, and Disease Ontology). This approach has also been applied using pattern structure mining (an extension of formal concept analysis) of drug and disease ontologies to discover frequently associated adverse drug events in patients [70]. This work was performed in collaboration with the Centre for BioMedical Informatics Research (BMIR) at Stanford University.

Recently, a new application for biomedical knowledge discovery has emerged from the ANR “FIGHT-HF” (fight heart failure) project, which is in collaboration with several INSERM teams at CHRU Nancy. In this case, the molecular mechanisms that underly HF at the cellular and tissue levels will be considered against a background of all available data and ontologies, and represented in a single integrated complex network. A network platform is under construction with the help of a young start-up company called Edgeleap. Together with this company, we are developing query and analysis facilities to help biologists and clinicians to identify relevant biomarkers for patient phenotyping [48]. Docking of small molecules on candidate receptors, as well as protein-protein docking will also be used to clarify a certain number of relations in the complex HF network.