FSK-ML Food Safety Knowledge Markup Language

de Alba Aparicio, M.; Correia Carreira, G.; Falenski, A.; Käsbohrer, A.; Filter, M.

SBML is the leading standard for models in Systems Biology. Unlike there, other scientific areas face the challenge that the majority of models have been developed in specific scripting languages like R or Matlab. In order to promote the standardized description and exchange of models in the domain of microbial risk assessment (MRA) we developed the Food Safety Knowledge Markup Language (FSK-ML) by extension and adaption of SBML. FSK-ML now allows to export and exchange executable script-based MRA models with well-structured meta-data. Built on top of the Combine Archive concept, the FSKX archive serves as a container to provide meta-data on MRA models, default values, simulation scenarios, experimental data or data generated by running a model simulation. Models programmed in scripting languages, such as R, Python or Matlab, are stored together with linked resources (e.g. R libraries) allowing to execute the original model scripts in a proper simulation environment. Finally a reference implementation using JSBML has been developed and will be showcased. A number of example applications have been deployed in the open-source data analytics platform Konstanz Information Miner (KNIME) making use of it.

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de Alba Aparicio, M. / Correia Carreira, G. / Falenski, A. / et al: FSK-ML Food Safety Knowledge Markup Language. 2016.

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