Connecting GOMMA with STROMA: An Approach for Semantic Ontology Mapping in the Biomedical Domain

Möller, Maximilian
Abstract in English: 
This thesis establishes a connection between GOMMA and STROMA – both are tools of ontology processing. Consequently, a new workflow of denoting a set of correspondences with five semantic relation types has been implemented. Such a rich denotation is scarcely discussed within the literature. The evaluation of the denotation shows that trivial correspondences are easy to recognize (tF > 90). The challenge is the denotation of non-trivial types ( 30 < ntF < 70). A prerequisite of the implemented workflow is the extraction of semantic relations between concepts. These relations represent additional background knowledge for the enrichment tool STROMA and are integrated to the repository SemRep which is accessed by this tool. Thus, STROMA is able to calculate a semantic type more precisely. UMLS was chosen as a biomedical knowledge source because it subsumes many different ontologies of this domain and thus, it represents a rich resource. Nevertheless, only a small set of relations met the requirements which are imposed to SemRep relations. Further studies may analyze whether there is an appropriate way to integrate the missing relations as well. The connection of GOMMA with STROMA allows the semantic enrichment of a biomedical mapping. As a consequence, this thesis enlightens two subjects of research. First, STROMA had been tested with general ontologies, which models common sense knowledge. Within this thesis, STROMA was applied to domain ontologies. Studies have shown that overall, STROMA was able to treat such ontologies as well. However, some strategies for the enrichment process are based on assumption which are misleading in the biomedical domain. Consequently, further strategies are suggested in this thesis which might improve the type denotation. These strategies may lead to an optimization of STROMA for biomedical data sets. A more thorough analysis will review their scope, also beyond the biomedical domain. Second, the established connection may lead to deeper investigations about advantages of semantic enrichment in the biomedical domain as an enriched mapping is returned. Despite heterogeneity of source and target ontology, such a mapping results in an improved interoperability at a finer level of granularity. The utilization of semantically rich correspondences in the biomedical domain is a worthwhile focus for future research.
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