Skip to main content

Systems Biology Pathway Exchange (SBPAX)

  • Reference work entry

Synonyms

SBPAX

Definition

Systems Biology Pathway Exchange (SBPAX) is an ontology and data format designed to store and organize systems biology knowledge data related to biological pathways, quantitative modeling, and the relationships between these two. Originally developed as an extension to BioPAX Level 2, it is now being developed as an extension to BioPAX Level 3 (the current BioPAX version) and proposed as an addition to the upcoming BioPAX Level 4. SBPAX enables broad interoperation between BioPAX and other systems biology modeling formats by creating hierarchies into which data, terms, and data objects from other formats can be inserted. While technically, SBPAX can incorporate any controlled vocabulary, some are better suited for this purpose than others. The preferred choice is the Systems Biology Ontology (SBO). Other suitable sources of terms would be the Systems Biology Markup Language (SBML), the Virtual Cell Markup Language (VCML), CellML, and MathML.

Characteristics

By...

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4419-9863-7_1112
  • Chapter length: 5 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   949.99
Price excludes VAT (USA)
  • ISBN: 978-1-4419-9863-7
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Hardcover Book
USD   999.99
Price excludes VAT (USA)
Systems Biology Pathway Exchange (SBPAX), Fig. 1
Systems Biology Pathway Exchange (SBPAX), Fig. 2
Systems Biology Pathway Exchange (SBPAX), Fig. 3
Systems Biology Pathway Exchange (SBPAX), Fig. 4

References

  • Blinov ML, Ruebenacker O (2009) Integrating BioPAX pathway knowledge with SBML models. IET Syst Biol 3(5):317–328

    PubMed  CrossRef  Google Scholar 

  • Blinov ML, Ruebenacker O, Moraru II (2008) Complexity and modularity of intracellular networks – a systematic approach for modeling and simulation. IET Syst Biol 2(5):363–368

    PubMed  CAS  CrossRef  Google Scholar 

  • Blinov ML, Ruebenacker O, Schaff JC, Moraru II (2010) Modeling without borders: creating and annotating VCell models using the web. Lect Notes Comput Sci, Vol 6053

    Google Scholar 

  • Ruebenacker O, Moraru II, Schaff JC, Blinov ML (2007) Kinetic modeling using BioPAX ontology. Proceedings of the IEEE international conference on bioinformatics and biomedicine, pp 339–348

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Oliver Ruebenacker .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this entry

Cite this entry

Ruebenacker, O. (2013). Systems Biology Pathway Exchange (SBPAX). In: Dubitzky, W., Wolkenhauer, O., Cho, KH., Yokota, H. (eds) Encyclopedia of Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-9863-7_1112

Download citation