Integrating systems biology models and biomedical ontologies

Robert Hoehndorf*, Michel Dumontier, John H. Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


Background: Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology.Results: We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models.Conclusions: We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

Original languageEnglish (US)
Article number124
JournalBMC systems biology
StatePublished - Aug 11 2011

Bibliographical note

Funding Information:
We thank Maxwell Neal for his input and critical discussions, and two anonymous reviewers for valuable comments on our manuscript. Funding for RH, SW, JHG, DLC, BdB was provided by the European Commission’s 7th Framework Programme, RICORDO project, grant number 248502. Funding for MD was provided by a NSERC Discovery Grant. Funding for GVG was provided by BBSRC grant BBG0043581.

ASJC Scopus subject areas

  • Structural Biology
  • Modeling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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