Titre en anglais non fourni ; Intéropérabilité sémantique dans le domaine du diagnostic in vitro : Représentation des Connaissances et Alignement

The centralization of patient data in different digital repositories raises issues of interoperability with the different medical information systems, such as those used in clinics, pharmacies or in medical laboratories. The public health authorities, charged with developing and implementing these repositories, recommend the use of standards to structure (syntax) and encode (semantic) health information. For data from in vitro diagnostics (IVD) two standards are recommended: - the LOINC® terminology (Logical Observation Identifier Names and Codes) to represent laboratory tests;- the SNOMED CT® ontology (Systematized Nomenclature Of MEDicine Clinical Terms) to express the observed results.This thesis focuses on the semantic interoperability problems in clinical microbiology with two major axes: How can an IVD Knowledge Organization System be aligned with SNOMED CT®? To answer this, I opted for the development of alignment methodologies adapted to the in vitro diagnostic data rather than proposing a specific method for the SNOMED CT®. The common alignment methods are evaluated on a gold standard alignment between LOINC® and SNOMED CT®. Themost appropriate are implemented in an R library which serves as a starting point to create new alignments at bioMérieux.What are the advantages and limits of a formal representation of DIV knowledge? To answer this, I looked into the formalization of the couple ‘test-result’ (observation) in a laboratory report. I proposed a logical formalization to represent the LOINC® terminology and I demonstrated the advantages of an ontological representation to sort and query laboratory tests. As a second step, I formalized an observation pattern compatible with the SNOMED CT® ontology and aligned onthe concept of the top-ontology BioTopLite2. Finally, the observation pattern was evaluated in order to be used within clinical microbiology expert systems. To resume, my thesis addresses some issues on IVD patient data share and reuse. At present, the problems of semantic interoperability and ...