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Open biomedical pluralism: formalising knowledge about breast cancer phenotypes
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 o...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448532/ https://www.ncbi.nlm.nih.gov/pubmed/23046572 http://dx.doi.org/10.1186/2041-1480-3-S2-S3 |
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author | Sojic, Aleksandra Kutz, Oliver |
author_facet | Sojic, Aleksandra Kutz, Oliver |
author_sort | Sojic, Aleksandra |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3448532 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34485322012-09-24 Open biomedical pluralism: formalising knowledge about breast cancer phenotypes Sojic, Aleksandra Kutz, Oliver J Biomed Semantics Proceedings 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. BioMed Central 2012-09-21 /pmc/articles/PMC3448532/ /pubmed/23046572 http://dx.doi.org/10.1186/2041-1480-3-S2-S3 Text en Copyright ©2012 Sojic and Kutz; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Proceedings Sojic, Aleksandra Kutz, Oliver Open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
title | Open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
title_full | Open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
title_fullStr | Open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
title_full_unstemmed | Open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
title_short | Open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
title_sort | open biomedical pluralism: formalising knowledge about breast cancer phenotypes |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448532/ https://www.ncbi.nlm.nih.gov/pubmed/23046572 http://dx.doi.org/10.1186/2041-1480-3-S2-S3 |
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