A corpus-driven approach for design, evolution and alignment of ontologies
Proceedings of the 38th conference on Winter simulation
A method for comparison of standardized information within systems biology
Proceedings of the 38th conference on Winter simulation
Challenges for modeling and simulation methods in systems biology
Proceedings of the 38th conference on Winter simulation
A database ontology for signal transduction pathways
International Journal of Bioinformatics Research and Applications
Pathway knowledge base: An integrated pathway resource using BioPAX
Applied Ontology - Towards a Metaontology for the Biomedical Domain
Information integration in bioinformatics with ontologies and standards
Semantic techniques for the web
Protein-to-protein interactions: Technologies, databases, and algorithms
ACM Computing Surveys (CSUR)
An efficient storage model for the SBML documents using object databases
VDMB'06 Proceedings of the First international conference on Data Mining and Bioinformatics
An evaluation of the use of XML for representation, querying, and analysis of molecular interactions
EDBT'06 Proceedings of the 2006 international conference on Current Trends in Database Technology
Pathway knowledge base: An integrated pathway resource using BioPAX
Applied Ontology - Towards a Metaontology for the Biomedical Domain
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Motivation: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. Results: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data. Contact: lestr@ida.liu.se