Logical comparison over RDF resources in bio-informatics

Simona Colucci, Francesco M. Donini, Eugenio Di Sciascio

Abstract: Highlights • A logical approach to the comparison of RDF resources describing drugs is proposed. • The approach returns an explicit description of features shared by compared drugs. • The returned explanation is an RDF graph. • The approach overcomes purely numerical methods, that only measure similarity. Abstract Comparison of resources is a frequent task in different bio-informatics applications, including drug-target interaction, drug repositioning and mechanism of action understanding, among others. This paper proposes a general method for the logical comparison of resources modeled in Resource Description Framework and shows its distinguishing features with reference to the comparison of drugs. In particular, the method returns a description of the commonalities between resources, rather than a numerical value estimating their similarity and/or relatedness. The approach is domain-independent and may be flexibly adapted to heterogeneous use cases, according to a process for setting parameters which is completely explicit. The paper also presents an experiment using the dataset Bioportal as knowledge source; the experiment is fully reproducible, thanks to the elicitation of criteria and values for parameter customization.