Connecting ontologies for the representation of biological pathways

Anna Maria Masci, Mikhail Levin, Alan Ruttenberg, Lindsay G. Cowell

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations


Significant effort has been put into the creation of a multitude of large, publicly available pathway databases. Most make their content available in at least one of several standard representation formats, but there are limitations to existing pathway representation formats, including underutilization of a common set of biomedical ontologies. To address this limitation, we developed an approach to representing biological pathways that relies on the use of ontologies from the Open Biomedical Ontologies (OBO) Foundry, including the Relation Ontology (RO), and adheres to the logical principles of ontology development advocated by the Foundry. To demonstrate the utility of this representation approach, we have curated comprehensive pathway representations for the signal transduction pathways initiated by seven of the mouse Toll-like receptors (TLR). Current efforts include the development of approaches for utilizing these representations for pathway analysis.

Original languageEnglish (US)
Title of host publicationCEUR Workshop Proceedings
Number of pages6
StatePublished - 2011
Event2nd International Conference on Biomedical Ontology, ICBO 2011 - Buffalo, NY, United States
Duration: Jul 26 2011Jul 30 2011


Other2nd International Conference on Biomedical Ontology, ICBO 2011
Country/TerritoryUnited States
CityBuffalo, NY


  • OBO foundry
  • Ontology
  • OWL
  • Semantic web
  • Signal transduction pathway

ASJC Scopus subject areas

  • Computer Science(all)


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