The amount of available data in information systems is constantly increasing and more and more efforts have been made in trying to interconnect this data in order to gain knowledge or meaning. Yet, these attempts at interconnecting such data have never been satisfactory enough when it comes to using the information at a wider scale. The origins of such difficulties are manifold. First, information is represented in many different structures. Second, the vocabulary used to express data is heterogeneous. Finally, the quality of the information is often too poor to be used and to withdraw any knowledge from it. Such observation applies specifically to the biomedical area where it is still difficult to agree on a common and shared representation (structures and vocabulary) concerning a particular sub-domain of the medical field. It would appear difficult in such a context to solve the problem of information sharing by imposing standard coding and standard information models. More recently, the introduction of semantics in the process of information sharing enables us to setup pivots representations which are independent from the structure or from the naming of the data. This thesis deals with the problematics of biomedical information sharing in the study of antibiotics resistance evolution to bacteries in Europe. Our general working hypothesis is : how can we share biomedical information in Europe in a non ambiguous way, in a fast way, and on demand ? Many issues are raised by this working hypothesis. We will deal with the issue of the quality of the data, the issue of the representation of data through their structure, their vocabulary, their semantics. We will also address the problems of alignment of data with domain ontologies. And the problem of data mediation helped with domain ontologies. We will then present a system of semantic interoperability based on rules which addresses the problem of semantic alignment of heterogeneous systems applied to our domain. Finally we will discuss how semantics can contribute to the improvement of information sharing and we will also discuss the limits of the current tools and methods.
Sharing biomedical information : models, semantics and quality