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Ontology Alignment and Merging

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Anatomy Ontologies for Bioinformatics

Part of the book series: Computational Biology ((COBO,volume 6))

Summary

In recent years many biomedical ontologies, including anatomy ontologies, have been developed. Many of these ontologies contain overlapping information and often we would want to be able to use multiple ontologies. This requires finding the relationships between terms in the different ontologies, i.e. we need to align them. Sometimes we also want to merge ontologies into a new one.

In this chapter we give an overview of current ontology alignment and merging systems. We focus on systems that compute similarities between terms in the different ontologies. We present a general framework for these kind of systems and discuss the existing strategies. We also present such a system (SAMBO) and discuss its use using anatomy ontologies. Further, we take a first step in dealing with the problem of using the best alignment algorithms for the ontologies we want to align. We present and illustrate the use of a framework and a tool (KitAMO) for comparative evaluation of ontology alignment strategies and their combinations.

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References

  • Ashpole B (2004) Ontology translation protocol (ontrapro). In: Proceedings of the PerformanceMetrics for Intelligent Systems Workshop.

    Google Scholar 

  • Chen B, Tan H, Lambrix P (2006) Structure-based filtering for ontology alignment. In:Proceedings of the IEEE WETICEWorkshop on Semantic Technologies in CollaborativeApplications, pp 364-369.

    Google Scholar 

  • Doan A, Madhavan J, Domingos P, Halevy A (2003) Ontology matching: A machinelearning approach. In: Staab, Studer (eds) Handbook on Ontologies in Information Systems,pp 397-416. Springer.

    Google Scholar 

  • Collins F, Green E, Guttmacher A, Guyer M (2003) A vision for the future of genomicsresearch. Nature 422:835-847.148 Patrick Lambrix and He Tan

    Article  Google Scholar 

  • Ehrig M, Haase P, Stojanovic N, Hefke M (2005) Similarity for Ontologies - A ComprehensiveFramework. In: Proceedings of the 13th European Conference on InformationSystems.

    Google Scholar 

  • Euzenat J (2004) Introduction to the EON ontology alignment context. In: Proceedingsof the 3rd International Workshop on the Evaluation of Ontology-based Tools.

    Google Scholar 

  • Euzenat J (2004) An API for ontology alignment. In: Proceedings of the 3rd InternationalSemantic Web Conference, pp 698-712.

    Google Scholar 

  • Euzenat J, Stuckenschmidt H, Yatskevich M (2005) Introduction to the Ontology AlignmentEvaluation 2005. In: Proceedings of the K-CAP Workshop on Integrating Ontologies.

    Google Scholar 

  • FOAM. http://www.aifb.uni-karlsruhe.de/WBS/meh/foam/

    Google Scholar 

  • Foundational Model of Anatomy. http://sig.biostr.washington.edu/projects/fm/

    Google Scholar 

  • The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology.Nature Genetics 25(1):25-29. http://www.geneontology.org/.

    Google Scholar 

  • Giunchiglia F, Shvaiko P, Yatskevich M (2004) S-Match: an algorithm and an implementationof semantic matching. In: Proceedings of the European SemanticWeb Symposium,LNCS 3053, pp 61-75.

    Google Scholar 

  • Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M (2005) The Adult MouseAnatomical Dictionary: a tool for annotating and integrating data. Genome Biology6(3):R29.

    Article  Google Scholar 

  • I3CON (2004) http://www.atl.lmco.com/projects/ontology/i3con.html

    Google Scholar 

  • Jakoniene V, Lambrix P (2005) Ontology-based Integration for Bioinformatics. In: Proceedingsof the VLDB Workshop on Ontologies-based techniques for DataBases andInformation Systems, pp 55-58.

    Google Scholar 

  • Kalfoglou Y, Schorlemmer M (2003) IF-Map: an ontology mapping method based oninformation flow theory. Journal on Data Semantics 1:98-127.

    Google Scholar 

  • Kotis K, Vouros GA (2004) The HCONE Approach to Ontology Merging. In: Proceedingsof the European Semantic Web Symposium, LNCS 3053, pp 137-151.

    Google Scholar 

  • Lambrix P (2004) Ontologies in Bioinformatics and Systems Biology. In: Dubitzky W,Azuaje F (eds) Artificial Intelligence Methods and Tools for Systems Biology, pp 129-146, chapter 8. Springer.

    Google Scholar 

  • Lambrix P (2005) Towards a Semantic Web for Bioinformatics using Ontology-basedAnnotation. In: Proceedings of the 14th IEEE International Workshops on EnablingTechnologies: Infrastructures for Collaborative Enterprises, pp 3-7. Invited talk.

    Google Scholar 

  • Lambrix P, Edberg A (2003) Evaluation of ontology merging tools in bioinformatics. In:Proceedings of the Pacific Symposium on Biocomputing 8:589-600.

    Google Scholar 

  • Lambrix P, Tan H (2006) SAMBO - A System for Aligning and Merging Biomedical Ontologies.Journal of Web Semantics, Special issue on semantic web for the life sciences,4(3):196-206.

    Google Scholar 

  • Lambrix P, Tan H (2007) A Tool for Evaluating Ontology Alignment Strategies. Journalon Data Semantics, VIII:182-202.

    Google Scholar 

  • Lambrix P, Tan H, Jakonien?e V, Strömbäck L (2007) Biological Ontologies. In: BakerC, Cheung K-H (eds) Semantic Web: Revolutionizing Knowledge Discovery in the LifeSciences, pp 85-99, chapter 4. Springer.

    Google Scholar 

  • Le BT, Dieng-Kuntz R, Gandon F (2004) On ontology matching problem (for buildinga corporate semantic web in a multi-communities organization). In: Proceedings of 6thInternational Conference on Enterprise Information Systems.

    Google Scholar 

  • McGuinness D, Fikes R, Rice J, Wilder S (2000) An Environment for Merging and TestingLarge Ontologies. In: Proceedings of the 7th International Conference on Principlesof Knowledge Representation and Reasoning, pp 483-493.6 Ontology Alignment and Merging 149

    Google Scholar 

  • Medical Subject Headings. http://www.nlm.nih.gov/mesh/

    Google Scholar 

  • Mitra P, Wiederhold G (2002) Resolving terminological heterogeneity in ontologies. In:Proceedings of the ECAI Workshop on Ontologies and Semantic Interoperability.

    Google Scholar 

  • Noy NF, MusenM(2000) PROMPT: Algorithm and Tool for Automated Ontology Mergingand Alignment. In: Proceedings of 17th National Conference on Artificial Intelligence,pp 450-455.

    Google Scholar 

  • Noy NF, Musen M (2001) Anchor-PROMPT: Using Non-Local Context for SemanticMatching. In: Proceedings of the IJCAI Workshop on Ontologies and Information Sharing,pp 63-70.

    Google Scholar 

  • OBO - Open Biomedical Ontologies. http://obo.sourceforge.net/

    Google Scholar 

  • OntoWeb Consortium (2002) Deliverables 1.3 (A survey on ontology tools) and 1.4 (Asurvey on methodologies for developing, maintaining, evaluating and reengineering ontologies).http://www.ontoweb.org

    Google Scholar 

  • OpenGalen. http://www.opengalen.org/

    Google Scholar 

  • Prasad S, Peng Y, Finin T (2002) Using Explicit Information To Map Between TwoOntologies. In: Proceedings of the AAMAS Workshop on Ontologies in Agent Systems.

    Google Scholar 

  • REWERSE. EU Network of Excellence on Reasoning on the Web with Rules and Semantics.Deliverables of the A2 Working Group. http://www.rewerse.net/

    Google Scholar 

  • Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F,Rector A, Rosse C (2005) Relations in biomedical ontologies. Genome Biology 6:R46.

    Google Scholar 

  • SOFG, Standards and Ontologies for Functional Genomics. http://www.sofg.org/

    Google Scholar 

  • Stumme G, Mädche A (2001) FCA-Merge: Bottom-up merging of ontologies. In: Proceedingsof the 17th International Joint Conference on Artificial Intelligence, pp 225-230.

    Google Scholar 

  • Su XM, Hakkarainen S, Brasethvik T (2004) Semantic enrichment for improving systemsinteroperability. In: Proceedings of the ACM Symposium on Applied Computing, pp1634-1641.

    Google Scholar 

  • UMLS. http://www.nlm.nih.gov/research/umls/about umls.html

    Google Scholar 

  • WordNet. http://wordnet.princeton.edu/

    Google Scholar 

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Authors
  1. Patrick Lambrix
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  2. He Tan
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Editor information

Albert Burger BSc, MSc, PhD Duncan Davidson BSc, PhD Richard Baldock BSc, PhD

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© 2008 Albert Burger, Duncan Davidson, Richard Baldock

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Lambrix, P., Tan, H. (2008). Ontology Alignment and Merging. In: Burger, A., Davidson, D., Baldock, R. (eds) Anatomy Ontologies for Bioinformatics. Computational Biology, vol 6. Springer, London. https://doi.org/10.1007/978-1-84628-885-2_6

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  • DOI: https://doi.org/10.1007/978-1-84628-885-2_6

  • Publisher Name: Springer, London

  • Print ISBN: 978-1-84628-884-5

  • Online ISBN: 978-1-84628-885-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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