Master Thesis semanticSBML a Tool for Creating, Checking, Annotating and Merging of SBML Documents

The System Biology Markup Language (SBML) is a common language for expressing biochemical sets of reactions that are accompanied by mathematical statements such as kinetic infomation. The program semanticSBML provides the systems biology community with the ability to integrate (merge) and annotate models with MIRIAM annotations. User interfaces are provided on multiple levels: application programming interface (API), console interface (CI), graphical user interface (GUI). This work aims to enable a full support of SBML level 2 version 3 for the merging of models (including mathematical statements) and the manipulation of MIRIAM annotations (including annotation qualifiers). It is based on the previous work of the Computational Systems Biology Group (Max Planck Institute for Molecular Genetics) SBMLmerge. In its first development phase it extended SBMLmerge with a cross platform GUI and CI for all existing algorithms as well as a simplified API. In its second phase the underlying library (libSBML) was updated. The MIRIAM annotation manipulation as well as the merging algorithm was rewritten. The concept of annotation qualifiers was integrated. For the annotation and merging of models independent abstractions of systems biology models were developed. The merge abstraction is used for a better detection and resolution of conflicts in matching biological objects. Experiments were conducted to show the functional efficiency of the new algorithms as well as to show its possible uses.