title: Retrieval, alignment, and clustering of computational models based on semantic annotations.
abstract: 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.
authors.affiliation: Institut für Biologie, Theoretische Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin, Germany.
authors.forename: Marvin
authors.initials: M
authors.lastname: Schulz
authors.forename: Falko
authors.initials: F
authors.lastname: Krause
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
authors.forename: Edda
authors.initials: E
authors.lastname: Klipp
authors.forename: Wolfram
authors.initials: W
authors.lastname: Liebermeister
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D012660:Semantics; D016415:Sequence Alignment / Q000379:methods*; D049490:Systems Biology / Q000379:methods*