Relation Ontology II

Conceived as follow-up to recent efforts destined to supply .owl ontologies with relational tools of greater complexity, the present article focuses on four main paths, all of them consisting in providing biomedical ontologies with formal means to express (1) deviations from normality, (2) topological connectedness, (3) inherence and (4) causality and function

Ontology Based Integration of Distributed and Heterogeneous Data Sources in ACGT.

In this work, we describe the set of tools comprising the Data Access Infrastructure within Advancing Clinic-genomic Trials on Cancer (ACGT), a R&D Project funded in part by the European. This infrastructure aims at improving Post-genomic clinical trials by providing seamless access to integrated clinical, genetic, and image databases. A data access layer, based on OGSA-DAI, has been developed in order to cope with syntactic heterogeneities in databases. The semantic problems present in data sources with different nature are tackled by two core tools, namely the Semantic Mediator and the Master Ontology on Cancer. The ontology is used as a common framework for semantics, modeling the domain and acting as giving support to homogenization. SPARQL has been selected as query language for the Data Access Services and the Mediator. Two experiments have been carried out in order to test the suitability of the selected approach, integrating clinical and DICOM image databases

Scalable representations of diseases in biomedical ontologies

Abstract Background The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations — pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology. Results We describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a distinction between these three categories. An analysis of SNOMED CT revealed that numerous classes in the findings/disease hierarchy are ambiguous with respect to process vs. disposition. Here our proposed approach can easily be applied to create unambiguous classes. No ambiguities could be defined regarding the distinction of structure and non-structure classes, but here we have found problematic duplications. Conclusions We defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios.</p

Scalable representations of diseases in biomedical ontologies

Abstract Background The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations — pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology. Results We describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a distinction between these three categories. An analysis of SNOMED CT revealed that numerous classes in the findings/disease hierarchy are ambiguous with respect to process vs. disposition. Here our proposed approach can easily be applied to create unambiguous classes. No ambiguities could be defined regarding the distinction of structure and non-structure classes, but here we have found problematic duplications. Conclusions We defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios