Annotation of SBML models through rule-based semantic integration.

Journal of Biomedical Semantics
Allyson L ListerAnil Wipat

Abstract

The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here we present rule-based mediation, a method of semantic data integration applied to systems biology model annotation. The heterogeneous data sources are first syntactically converted into ontologies, which are then aligned to a small domain ontology by applying a rule base. We demonstrate proof-of-principle of this application of rule-based mediation using off-the-shelf semantic web technology through two use cases for SBML model annotation. Existing tools and technology provide a framework around which the system is built, reducing development time and increasing usability. Integrating resources in this way accommodates multiple formats with different semantics, and provides richly-modelled biological knowledge suitable for annotation of SBML models. This initial work establishes the feasibility of rule-based mediation as part of an autom...Continue Reading

References

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Sep 8, 2009·Bioinformatics·Allyson L ListerAnil Wipat
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Jul 16, 2010·Journal of Biomedical Semantics·Allyson L ListerAnil Wipat
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Citations

Jan 6, 2011·Rejuvenation Research·Georg FuellenAnil Wipat
May 2, 2012·BMC Bioinformatics·Renato UmetonC Forbes Dewey
Mar 8, 2007·BMC Bioinformatics·Nicolas RodriguezNicolas Le Novère
Aug 13, 2011·BMC Systems Biology·Robert HoehndorfGeorgios V Gkoutos
Jul 16, 2010·Journal of Biomedical Semantics·Larisa N SoldatovaNigam H Shah
Jan 19, 2012·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Douglas B Kell
Oct 27, 2011·Molecular Systems Biology·Mélanie CourtotNicolas Le Novère
Jul 16, 2010·Journal of Biomedical Semantics·Allyson L ListerAnil Wipat
Mar 11, 2015·Database : the Journal of Biological Databases and Curation·Ron HenkelDagmar Waltemath

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Software Mentioned

SWRL
UniProtKB
BYU - Local as View ( BGLaV )
MIRIAM
SQWRLQueryTab
XMLMapper
BioPAX
Pathway Commons
XMLTab
Protégé

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