Retrieval, alignment, and clustering of computational models based on semantic annotations.

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TitleRetrieval, alignment, and clustering of computational models based on semantic annotations.
Publication TypeJournal Article
Year of Publication2011
AuthorsSchulz, M, Krause, F, Le Novère, N, Klipp, E, Liebermeister, W
JournalMol Syst Biol
Volume7
Pagination512
Date Published2011
ISSN1744-4292
KeywordsAlgorithms, Cluster Analysis, Computer Simulation, Database Management Systems, Databases, Factual, Information Storage and Retrieval, Models, Biological, Natural Language Processing, Semantics, Sequence Alignment, Systems Biology
Abstract

<p>The exploding number of computational models produced by Systems Biologists over the last years is an invitation to structure and exploit this new wealth of information. Researchers would like to trace models relevant to specific scientific questions, to explore their biological content, to align and combine them, and to match them with experimental data. To automate these processes, it is essential to consider semantic annotations, which describe their biological meaning. As a prerequisite for a wide range of computational methods, we propose general and flexible similarity measures for Systems Biology models computed from semantic annotations. By using these measures and a large extensible ontology, we implement a platform that can retrieve, cluster, and align Systems Biology models and experimental data sets. At present, its major application is the search for relevant models in the BioModels Database, starting from initial models, data sets, or lists of biological concepts. Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data.</p>

DOI10.1038/msb.2011.41
Alternate JournalMol. Syst. Biol.
PubMed ID21772260
PubMed Central IDPMC3159965
Grant ListBB/E006248/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom