@incollection{Draeger2020a,
  author    = {Dr\"ager, Andreas and Waltemath, Dagmar},
  title     = {{Overview: Standards for Modeling in Systems Medicine}},
  booktitle = {Systems Medicine},
  editor    = {Wolkenhauer, Olaf},
  publisher = {Academic Press},
  address   = {Oxford},
  pages     = {345--353},
  year      = {2020},
  month     = sep,
  volume    = {3},
  isbn      = {978-0-12-816078-7},
  doi       = {10.1016/B978-0-12-816077-0.00001-7},
  url       = {https://www.sciencedirect.com/science/article/pii/B9780128160770000017},
  keywords  = {CellML, COMBINE, Computational biology, Data formats, MIASE, MIRIAM,
    Reproducibility, SBGN, SBML, SED-ML, Standardization},
  abstract  = {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.},
}