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Free keywords:
model combination; SBML; MIRIAM; metabolic model
Abstract:
The Systems Biology Markup Language (SBML) is an XML-based format for representing
mathematical models of biochemical reaction networks, and it is likely to become a main standard
in the systems biology community. As published mathematical models in cell biology are growing
in number and size, modular modelling approaches will gain additional importance. The main issue
to be addressed in computer-assisted model combination is the specification and handling of model
semantics.
The software SBMLmerge assists the user in combining models of biological subsystems to
larger biochemical networks. First, the program helps the user in annotating all model elements
with unique identifiers pointing to databases such as KEGG or Gene Ontology. Second, during
merging, SBMLmerge detects and resolves various syntactic and semantic problems. Typical problems
are conflicting variable names, elements which appear in more than one input model, and
mathematical problems arising from the combination of equations. If the input models make contradicting
statements about a biochemical quantity, the user is asked to choose between them. In
the end the merging process results in a new, valid SBML model.
