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Semantically Linking In Silico Cancer Models
Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
2014 (English)In: Libertas, ISSN 1518-9325, E-ISSN 1980-8518, LA Cancer Informatics, Vol. 13, no S1, 133-143 p.Article in journal (Refereed) Published
Abstract [en]

Multiscale models are commonplace in cancer modeling, where individual models acting on different biological scales are combined within a single, cohesive modeling framework. However, model composition gives rise to challenges in understanding interfaces and interactions between them. Based on specific domain expertise, typically these computational models are developed by separate research groups using different methodologies, programming languages, and parameters. This paper introduces a graph-based model for semantically linking computational cancer models via domain graphs that can help us better understand and explore combinations of models spanning multiple biological scales. We take the data model encoded by TumorML, an XML-based markup language for storing cancer models in online repositories, and transpose its model description elements into a graph-based representation. By taking such an approach, we can link domain models, such as controlled vocabularies, taxonomic schemes, and ontologies, with cancer model descriptions to better understand and explore relationships between models. The union of these graphs creates a connected property graph that links cancer models by categorizations, by computational compatibility, and by semantic interoperability, yielding a framework in which opportunities for exploration and discovery of combinations of models become possible.

Place, publisher, year, edition, pages
Libertas Academica Ltd, 2014. Vol. 13, no S1, 133-143 p.
Keyword [en]
Cancer models, interoperability, semantics, online repositories, linking models
National Category
Medical and Health Sciences Cancer and Oncology
Research subject
Computer Science; Biology
Identifiers
URN: urn:nbn:se:uu:diva-238514DOI: 10.4137/CIN.S13895OAI: oai:DiVA.org:uu-238514DiVA: diva2:771355
Available from: 2014-12-12 Created: 2014-12-12 Last updated: 2017-12-05Bibliographically approved

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Publisher's full texthttp://www.la-press.com/article.php?article_id=4552

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McKeever, Steve

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