title: A framework for unifying ontology-based semantic similarity measures: a study in the biomedical domain.
abstract: Ontologies are widely adopted in the biomedical domain to characterize various resources (e.g. diseases, drugs, scientific publications) with non-ambiguous meanings. By exploiting the structured knowledge that ontologies provide, a plethora of ad hoc and domain-specific semantic similarity measures have been defined over the last years. Nevertheless, some critical questions remain: which measure should be defined/chosen for a concrete application? Are some of the, a priori different, measures indeed equivalent? In order to bring some light to these questions, we perform an in-depth analysis of existing ontology-based measures to identify the core elements of semantic similarity assessment. As a result, this paper presents a unifying framework that aims to improve the understanding of semantic measures, to highlight their equivalences and to propose bridges between their theoretical bases. By demonstrating that groups of measures are just particular instantiations of parameterized functions, we unify a large number of state-of-the-art semantic similarity measures through common expressions. The application of the proposed framework and its practical usefulness is underlined by an empirical analysis of hundreds of semantic measures in a biomedical context.
authors.affiliation: LGI2P/EMA Research Centre, Site de Nîmes, Parc scientifique G. Besse, 30035 Nîmes cedex 1, France. Electronic address: sebastien.harispe@mines-ales.fr.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Harispe
authors.affiliation: Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, Av. Països Catalans, 26, 43007 Tarragona, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Sánchez
authors.affiliation: LGI2P/EMA Research Centre, Site de Nîmes, Parc scientifique G. Besse, 30035 Nîmes cedex 1, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Ranwez
authors.affiliation: LGI2P/EMA Research Centre, Site de Nîmes, Parc scientifique G. Besse, 30035 Nîmes cedex 1, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Janaqi
authors.affiliation: LGI2P/EMA Research Centre, Site de Nîmes, Parc scientifique G. Besse, 30035 Nîmes cedex 1, France.
authors.forename: Jacky
authors.initials: J
authors.lastname: Montmain
mesh_terms: D000465:Algorithms; D006801:Humans; D008490:Medical Informatics / Q000379:methods*; D008962:Models, Theoretical; D009323:Natural Language Processing; D015203:Reproducibility of Results; D012660:Semantics; D012984:Software; D039061:Systematized Nomenclature of Medicine; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
keywords: Biomedical ontologies; Ontologies; SNOMED-CT; Semantic similarity measures; Unifying framework