Harmonizing SNOMED CT with BioTopLite: An Exercise in Principled Ontology Alignment

The integration of heterogeneous ontologies is often hampered by different upper level categories and relations. We report on an on-going effort to align clinical terminology/ontology SNOMED CT with the formal upper-level ontology BioTopLite. This alignment introduces several constraints at the OWL-DL level. The mapping was done manually by analysing formal and textual definitions. Descriptive logic classifiers interactively checked mapping steps, using small modules for increasing performance. We present an effective workflow, using modules of several scales. However, only part of the classes and relations could easily be mapped. The implications for future evolution of SNOMED CT are discussed. It seems generally feasible to use a highly constrained upper-level ontology as an upper level for the benefit of future SNOMED CT versions that are more interoperable with other biomedical ontologies.

[1]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[2]  Stefan Schulz,et al.  Medical knowledge reengineering - converting major portions of the UMLS into a terminological knowledge base , 2001, Int. J. Medical Informatics.

[3]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[4]  Catalina Martínez-Costa,et al.  Ontology-based reinterpretation of the SNOMED CT context model , 2013, ICBO.

[5]  Barry Smith,et al.  SNAP and SPAN: Towards Dynamic Spatial Ontology , 2004, Spatial Cogn. Comput..

[6]  Giancarlo Guizzardi,et al.  On the Representation of Temporally Changing Information in OWL , 2010, 2010 14th IEEE International Enterprise Distributed Object Computing Conference Workshops.

[7]  Mathias Brochhausen,et al.  An Ontological Analysis of Reference in Health Record Statements , 2014, FOIS.

[8]  Alan L. Rector,et al.  Web ontology segmentation: analysis, classification and use , 2006, WWW '06.

[9]  Ian Horrocks,et al.  FaCT++ Description Logic Reasoner: System Description , 2006, IJCAR.

[10]  Stefano Borgo,et al.  Ontological Foundations of dolce , 2010 .

[11]  Kent A. Spackman,et al.  Consolidating SNOMED CT's ontological commitment , 2011, Appl. Ontology.

[12]  Bijan Parsia,et al.  Laconic and Precise Justifications in OWL , 2008, SEMWEB.

[13]  Martin Boeker,et al.  Scalable representations of diseases in biomedical ontologies , 2011, J. Biomed. Semant..

[14]  Olivier Bodenreider,et al.  Alignment of the UMLS semantic network with BioTop: methodology and assessment , 2009, Bioinform..

[15]  Kent A. Spackman,et al.  Role grouping as an extension to the description logic of Ontylog, motivated by concept modeling in SNOMED , 2002, AMIA.