Semantically Linking In Silico Cancer Models
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Author(s)
Type
Journal Article
Abstract
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.
Date Issued
2014-12-08
Citation
Cancer Informatics, 2014, Suppl. 1, pp.133-143
ISSN
1176-9351
Publisher
Libertas Academica
Start Page
133
End Page
143
Journal / Book Title
Cancer Informatics
Volume
Suppl. 1
Copyright Statement
© 2014 the authors, publisher and licensee Libertas academica Limited. this is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License
License URL
Description
25.02.15 KB. Ok to add published version to spiral, OA paper
Notes
To appear
Publication Status
Published