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. 2011 Feb;44(1):146-54.
doi: 10.1016/j.jbi.2010.06.007. Epub 2010 Jun 30.

Multiple Ontologies in Action: Composite Annotations for Biosimulation Models

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Free PMC article

Multiple Ontologies in Action: Composite Annotations for Biosimulation Models

John H Gennari et al. J Biomed Inform. .
Free PMC article

Abstract

There now exists a rich set of ontologies that provide detailed semantics for biological entities of interest. However, there is not (nor should there be) a single source ontology that provides all the necessary semantics for describing biological phenomena. In the domain of physiological biosimulation models, researchers use annotations to convey semantics, and many of these annotations require the use of multiple reference ontologies. Therefore, we have developed the idea of composite annotations that access multiple ontologies to capture the physics-based meaning of model variables. These composite annotations provide the semantic expressivity needed to disambiguate the often-complex features of biosimulation models, and can be used to assist with model merging and interoperability. In this paper, we demonstrate the utility of composite annotations for model merging by describing their use within SemGen, our semantics-based model composition software. More broadly, if orthogonal reference ontologies are to meet their full potential, users need tools and methods to connect and link these ontologies. Our composite annotations and the SemGen tool provide one mechanism for leveraging multiple reference ontologies.

Figures

Fig 1
Fig 1
A snippet of SBML code showing three MIRIAM annotations to ChEBI, KEGG & PubChem. The entity (species) is 2-phospho-D-glycerate.
Fig 2
Fig 2
A schema showing the structure of a composite annotation (top), with the example of aortic blood pressure (bottom).
Fig 3
Fig 3
A snippet of the OWL representation for a single composite annotation, Paorta (as in Figure 2). The snippet shows four individuals; the first corresponds to the named variable itself, while the other three correspond to the three reference ontology classes shown on the left. For brevity, we have omitted prefix declarations that provide URIs for ontologies such as OPB, FMA, and RO.
Fig 4
Fig 4
A screen from our SemGen annotation tool, showing the composite annotation for Paorta in the CV model. The composite annotation is independent from the source code (shown in top panel).
Fig 5
Fig 5
A screen showing how users assemble composite annotations. As highlighted on the left, the user has just selected the FMA term “Lumen of aorta” to fill the third spot in the composite annotation for Paorta.
Fig 6
Fig 6
A screen from the SemGen merger tool, showing three suggested matches between variables in the CV model and those in the BARO model.
Fig 7
Fig 7
A trace of the aortic blood pressure under two conditions—with and without a stimulated level of calcium in the smooth muscle of the arterioles.

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