SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format

Abstract

Abstract Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite for model merging, which would be a major step towards the construction of large-scale cell models. The software tool semanticSBML allows users to check and edit MIRIAM annotations and SBO terms, the most common forms of annotation in SBML models. It uses a large collection of biochemical names and database identifiers to support modellers in finding the right annotations. Annotated SBML models can also be built from lists of chemical reactions. In model merging, semanticSBML suggests a preliminary merged model based on MIRIAM annotations in the original models. This model provides a starting point for manually aligning the elements of all input models. To resolve conflicting element properties, conflicts are highlighted and categorised. The user can navigate through the models, change the matching of model elements, check the conflicts between them and decide how they should be resolved. Alternatively, the software can resolve all conflicts automatically, selecting each time the attribute value from the input model with highest priority.URL: "http://www.semanticsbml.org/":http://www.semanticsbml.org/