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Ontology alignment

Ontology alignment. Patrick Lambrix Linköpings universitet. GO: Complement Activation. SigO: complement signaling synonym complement activation. Alignment Strategies. Strategies based on linguistic matching Structure-based strategies Constraint-based approaches

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Ontology alignment

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  1. Ontology alignment Patrick Lambrix Linköpings universitet

  2. GO:Complement Activation SigO: complement signaling synonymcomplement activation Alignment Strategies • Strategies based on linguistic matching • Structure-based strategies • Constraint-based approaches • Instance-based strategies • Use of auxiliary information • Combining different approaches • Strategies based on linguistic matching

  3. Alignment Strategies • Strategies based on linguistic matching • Structure-based strategies • Constraint-based approaches • Instance-based strategies • Use of auxiliary information • Combining different approaches

  4. O2 O1 Person Human Animal Animal Alignment Strategies • Strategies based on linguistic matching • Structure-based strategies • Constraint-based approaches • Instance-based strategies • Use of auxiliary information • Combining different approaches

  5. Alignment Strategies • Strategies based on linguistic matching • Structure-based strategies • Constraint-based approaches • Instance-based strategies • Use of auxiliary information • Combining different approaches instance corpus Ontology

  6. dictionary thesauri intermediate ontology alignment strategies Alignment Strategies • Strategies based linguistic matching • Structure-based strategies • Constraint-based approaches • Instance-based strategies • Use of auxiliary information • Combining different approaches

  7. Alignment Strategies • Strategies based on linguistic matching • Structure-based strategies • Constraint-based approaches • Instance-based strategies • Use of auxiliary information • Combining different approaches

  8. Ontology Alignment and Mergning Systems

  9. An Alignment Framework

  10. GO: 70 terms SigO: 15 terms GO-immune defense SigO-immune defense MA: 77 terms GO: 60 terms MA: 112terms MA: 15 terms MeSH: 18 terms MeSH: 45 terms SigO: 10 terms MeSH: 39 terms SigO-behavior MeSH-nose MeSH-ear MeSH-eye Evaluation - cases • GO vs. SigO • MA vs. MeSH GO-behavior MA-nose MA-ear MA-eye

  11. Evaluation • Matchers Term, TermWN, Dom, Learn (Learn+structure), Struc • Parameters Quality of suggestions: precision/recall Threshold filtering : 0.4, 0.5, 0.6, 0.7, 0.8 Weights for combination: 1.0/1.2 KitAMO (http://www.ida.liu.se/labs/iislab/projects/KitAMO)

  12. Evaluation • Terminological matchers

  13. Evaluation • Basic learning matcher

  14. Evaluation • Domain matcher

  15. Evaluation • Comparison of the matchers CS_TermWNCS_Dom CS_Learn • Combinations of the different matchers • combinations give often better results • no significant difference on the quality of suggestions for different weight assignments in the combinations • Structural matcher did not find (many) new correct alignments (but: good results for systems biology schemas SBML – PSI MI)

  16. Evaluation • Matchers TermWN • Parameters Quality of suggestions: precision/recall Double threshold filtering using structure: Upper threshold: 0.8 Lower threshold: 0.4, 0.5, 0.6, 0.7, 0.8 Chen, Tan, Lambrix, Structure-based filtering for ontology alignment, IEEE WETICE workshop on semantic technologies in collaborative applications, pp 364-369, 2006.

  17. Evaluation • The precision is increased after filtering. - a linguistic alignment algorithm using WordNet - the upper threshold is 0.8

  18. Evaluation • The recall is constant in most cases after filtering - a linguistic alignment algorithm using WordNet - the upper threshold is 0.8

  19. Issues • Evaluation methodology: Golden standards e.g. OAEI: Anatomy (FMA – GALEN) • Systems available, but not always the alignment algorithms. • Connections types of algorithms – types of ontologies • Recommending ’best’ alignment strategies

  20. Further reading • http://www.ontologymatching.org • Ontology alignment evaluation initiative: http://oaei.ontologymatching.org • Lambrix, Tan, SAMBO – a system for aligning and merging biomedical ontologies, Journal of Web Semantics, 4(3):196-206, 2006. • Lambrix, Tan, A tool for evaluating ontology alignment strategies, Journal on Data Semantics, VIII:182-202, 2007.

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