Creating PROV-DM Graphs from Model Databases.

Documenting the provenance of the main products of a simulation study plays a crucial role in improving the understanding of mechanistic, biological models as well as their reproducibility and credibility. With model databases already an ample collection of simulation models, including metainformation and source files, exists. In this paper, we bridge the gap between the information contained in model databases and the PROV-DM provenance standard, which allows making the diverse products and their relationships formally explicit. We present a procedure for creating PROV-DM graphs from model database entries, and illustrate the approach based on ten different models from the BioModels database. These case studies demonstrate the advantages of having a standardized provenance view in addition to the regular database entries, i.e., enhanced means for visualizing the structure of the simulation study and the curation process.