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This article is part of the supplement: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011)

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Open biomedical pluralism: formalising knowledge about breast cancer phenotypes

Aleksandra Sojic1* and Oliver Kutz2

Author Affiliations

1 European School of Molecular Medicine; European Institute of Oncology; University of Milan; Milan, Italy

2 Research Center on Spatial Cognition (SFB/TR 8), University of Bremen, Germany

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Journal of Biomedical Semantics 2012, 3(Suppl 2):S3  doi:10.1186/2041-1480-3-S2-S3

Published: 21 September 2012


We demonstrate a heterogeneity of representation types for breast cancer phenotypes and stress that the characterisation of a tumour phenotype often includes parameters that go beyond the representation of a corresponding empirically observed tumour, thus reflecting significant functional features of the phenotypes as well as epistemic interests that drive the modes of representation. Accordingly, the represented features of cancer phenotypes function as epistemic vehicles aiding various classifications, explanations, and predictions. In order to clarify how the plurality of epistemic motivations can be integrated on a formal level, we give a distinction between six categories of human agents as individuals and groups focused around particular epistemic interests. We analyse the corresponding impact of these groups and individuals on representation types, mapping and reasoning scenarios. Respecting the plurality of representations, related formalisms, expressivities and aims, as they are found across diverse scientific communities, we argue for a pluralistic ontology integration. Moreover, we discuss and illustrate to what extent such a pluralistic integration is supported by the distributed ontology language DOL, a meta-language for heterogeneous ontology representation that is currently under standardisation as ISO WD 17347 within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. We particularly illustrate how DOL supports representations of parthood on various levels of logical expressivity, mapping of terms, merging of ontologies, as well as non-monotonic extensions based on circumscription allowing a transparent formal modelling of the normal/abnormal distinction in phenotypes.