Combining computational models, semantic annotations, and associated simulation experiments in a graph database

13 Model repositories such as the BioModels Database or the CellML Model Repository are 14 frequently accessed to retrieve computational models describing biological systems. However, 15 the current designs of these databases limit the types of supported queries, and many data 16 in these repositories cannot easily be accessed. Computational methods for model retrieval 17 cannot be applied. In this paper we present a storage concept that meets this challenge. It 18 grounds on a graph database, re ects the models' structure, incorporates semantic annotations 19 and experiment descriptions, and ultimately connects di erent types of model-related data. 20 The connections between heterogeneous model-related data and bio-ontologies enable e cient 21 search via biological facts and grant access to new model features such as network structure. 22 The introduced concept notably improves the access of computational models and associated 23 simulations in a model repository. This has positive e ects on tasks such as model search, 24 retrieval, ranking, matching, ltering etc. We exemplify how CellMLand SBML-encoded 25 models can be maintained in one database, how these models can be linked via annotations, 26 and queried. 27 2 PeerJ PrePrints | http://dx.doi.org/10.7287/peerj.preprints.376v2 | CC-BY 4.0 Open Access | rec: 6 Oct 2014, publ: 6 Oct 2014 P re P rin ts