Integrating systems biology models and biomedical ontologies View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12

AUTHORS

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

ABSTRACT

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. More... »

PAGES

124

References to SciGraph publications

  • 2000-05. Gene Ontology: tool for the unification of biology in NATURE GENETICS
  • 2005-02. An ontology for cell types in GENOME BIOLOGY
  • 2007-11. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration in NATURE BIOTECHNOLOGY
  • 2008-07-01. Ontology (Science) in NATURE PRECEDINGS
  • 2002-11. Computational systems biology in NATURE
  • 2005-05. Relations in biomedical ontologies in GENOME BIOLOGY
  • 2008-10. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology in NATURE BIOTECHNOLOGY
  • 2008. SED-ML – An XML Format for the Implementation of the MIASE Guidelines in COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY
  • 2010-01. Integrating phenotype ontologies across multiple species in GENOME BIOLOGY
  • 2010-12. IntelliGO: a new vector-based semantic similarity measure including annotation origin in BMC BIOINFORMATICS
  • 1917-12. Axiomatisches Denken in MATHEMATISCHE ANNALEN
  • 2009. Towards Enhanced Retrieval of Biological Models through Annotation-Based Ranking in DATA INTEGRATION IN THE LIFE SCIENCES
  • 2007-12. METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks in BMC SYSTEMS BIOLOGY
  • 2010-12. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models in BMC SYSTEMS BIOLOGY
  • 2008-12. Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data in BMC BIOINFORMATICS
  • 2010-12. Applying the functional abnormality ontology pattern to anatomical functions in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2005-12. Minimum information requested in the annotation of biochemical models (MIRIAM) in NATURE BIOTECHNOLOGY
  • 2009-04-22. Beyond Structure: KiSAO and TEDDY—Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology in NATURE PRECEDINGS
  • 2006-10. Model storage, exchange and integration in BMC NEUROSCIENCE
  • 2006. CEL — A Polynomial-Time Reasoner for Life Science Ontologies in AUTOMATED REASONING
  • 2010-06. Annotation of SBML models through rule-based semantic integration in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2007-04. Systems biology standards—the community speaks in NATURE BIOTECHNOLOGY
  • 2010-12. Relations as patterns: bridging the gap between OBO and OWL in BMC BIOINFORMATICS
  • 2010-12. Ranked retrieval of Computational Biology models in BMC BIOINFORMATICS
  • 2010-09. The BioPAX community standard for pathway data sharing in NATURE BIOTECHNOLOGY
  • 2007-12. SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML) in BMC BIOINFORMATICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1752-0509-5-124

    DOI

    http://dx.doi.org/10.1186/1752-0509-5-124

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1003298763

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21835028


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