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• W2188329981 abstract "OWL 21 is commonly used to represent objects with complex structure, such as complex assemblies in engineering applications [5], human anatomy [13], or the structure of chemical molecules [7]. In order to ground our discussion, we next present a concrete application of the latter kind; however, the problems and the solution that we identify apply to numerous similar scenarios. The European Bioinformatics Institute (EBI) has developed the ChEBI2 ontology— a public dictionary of molecular entities used to enhance interoperability of applications supporting tasks such as drug discovery. In order to automate the classification of molecular entities, ChEBI descriptions were translated into OWL and then classified using automated reasoning. However, this approach was hindered by the fundamental inability of OWL to precisely represent the structure of complex molecular entities, as the tree-model property of OWL prevents one from describing non-tree-like relationships using schema axioms. For example, OWL axioms can state that butane molecules have four carbon atoms, but they cannot state that the four atoms in a cyclobutane molecule are arranged in a ring. Please note that this applies to schema descriptions only: the structure of a particular cyclobutane molecule can be represented using class and property assertions, but the general definition of all cyclobutane molecules—a problem that terminologies such as ChEBI aim to solve—cannot be fully described in OWL. As we show in Section 3, an ontology may therefore fail to entail certain desired consequences. A common solution to this problem is to extend OWL 2 with a rule-based formalism such as SWRL;3 however, this either results in undecidability [9] or requires restrictions in the shape of the rules [8], which typically prevent the rules from axiomatising the required structures. An alternative approach suggests a combination of OWL 2, rules, and description graphs (DGs) [12]—a graphical notation for describing non-tree-like structures. Decidability of reasoning is ensured via a property separation condition and by requiring DGs to be acyclic. Intuitively, the latter means that DGs can describe structures of arbitrary shape, but bounded in size, while the former limits the interaction between the OWL and DG parts, thus preventing multiple DG structures from merging into one structure of (potentially) unbounded size. As reported in [7], DGs solved" @default.
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• W2188329981 date "2012-01-01" @default.
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• W2188329981 title "Classifying Chemicals Using Description Graphs and Logic Programming" @default.
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