Forschungsinformationssystem Universität Greifswald

Dräger A, Waltemath D¹

1 - Institut für Community Medicine / Abteilung Medizininformatik

Computational analyses of digital information constitute the foundation for modern scientific research. The analysis of computer models can, for instance, guide experimentalists or predict biological functions such as novel drug targets or recovery from external stress. In many cases, such analyses require several bioinformatics tools to interoperate in complex workflows. To this end, the scientific community has been developing clear standards for automatic interpretation and use of computer models within complex computer analysis pipelines for systems biomedicine. The standard development process follows two fundamental design decisions: (i) to organize the information in a modular fashion and (ii) to strictly separate models from methods for their analysis. Following these principles, a complex ecosystem of modeling guidelines, annotation schemes, and representation formats has evolved, for which enthusiastic community members create and maintain rich documentation and necessary software infrastructure. The resulting standards cover model development, storage, the exchange between different analysis programs, the display, automated validity and plausibility checks, publication and review, and many other aspects of computational modeling and simulation. The umbrella organization COMBINE coordinates the evolution of and communication between new and existing standards. In this chapter, we introduce the reader to commonly used data formats, guidelines, and ontologies for the storage and exchange of computational models in systems medicine. We focus on models of biological systems, including their structures, annotation, visualization, and interpretation. Additional chapters in this book offer more detailed information on selected data formats. For the construction of models or the integration of data, further literature needs to be consulted.