Role-based representation and inference of biochemical processes

Talk at the 3rd International Conference of Biomedical Ontology (ICBO) 2012, July 21-25, Graz, Austria

Computational approaches to study biochemistry require machine accessible representations of biochemical knowledge. Based on the requirements for assembling, managing and analysing genome-scale constraint-based models of liver metabolism we developed a semantic data model for representation of liver biochemical knowledge. Adopting a consistent perspective on biochemical processes as molecular events our OWL2-based representation is capable of representing biochemical processes of various complexity in terms of their parts and participants and the various roles they play. We further outline an information model that employs sidecar evidence ontologies to represent the evidence for the asserted properties of and among biochemical entities with great detail and conforming to OWL semantics. Our approach overcomes previous limitations in the modeling of pathways and evidence. We discuss how these elements can be incorporated in resources for representation and analysis of liver biochemistry.

Filename: ICBO_2012-07-24.pdf

Format: PDF document

Size: 407 KB

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[Christian Bölling] [Michael Weidlich] [Hermann-Georg Holzhütter]

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Michel Dumontier

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Views: 1682    Downloads: 0
  • Created: 14th Aug 2012 at 14:34
  • Last updated: 14th Aug 2012 at 14:35
  • Last used: 23rd Aug 2019 at 05:05

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