Sbmltools: A Sbml Integration Tool for Kbase

Liu, F., Argonne National Laboratory
Faria, J. P., Argonne National Laboratory
Zhang, Q., Argonne National Laboratory
Rocha, M., University of Minho
Rocha, I., ITQB NOVA -Instituto de Tecnologia Química e Biológica António Xavier
Henry, C. S., Argonne National Laboratory
Since the release of the first version of System Biology Markup Language (SMBL) it become the de facto exchange format to store and share Genome Scale Metabolic Models (GSM). However, due to limitations in earlier versions of the SBML users adopted their own strategies to represent important attributes regarding to GSMs: gene-protein-reaction rules (GPR), metabolite/reaction annotation and model constraints. While most of these features were addressed in the latest version of SBML it left a heterogenous community of SBML models.

The SBMLTools provides methods to import and integrate existing SBML models into the Department of Energy Systems Biology Knowledgebase (KBase). The purpose of the SBMLTools is to reshape SBML models to fit the KBase demands: separation of the exchange reactions for the media formulation, integration of the metabolic network with the ModelSEED biochemistry, integration of GPR genes to match with a compatible genome and normalize the compartments with the vocabulary in KBase.

The tool compiles an internal in-house built integrated biochemistry database that compiles existing compound and reaction databases (ModelSEED, KEGG, MetaCyc, BiGG, etc) for annotation purposes. It also takes advantage of the KBase genome catalog that hosts more than 70.000 RefSeq bacterial genomes, indexing several attributes regarding to their genes (e.g., gene aliases).

While the main purpose of the SBMLTools is to improve the compatibility of the existing tools in KBase with external built models, it can also be used by researchers to normalize SBML models regarding to identifiers (compounds and reactions), exchange media, compartments and genes.