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

Database (Oxford). 2015 Mar 8:2015:bau130. doi: 10.1093/database/bau130. Print 2015.


Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models' structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried. Database URL:

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Ontologies*
  • Data Curation / methods*
  • Databases, Factual*
  • Models, Biological*
  • Systems Biology / methods*