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WESO SATBI 2011

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  • 1. Application of the Spreading Activation Technique for RecommendingConcepts of well-known Ontologies in Medical Systems José María Álvarez Rodríguez WESO-Universidad de Oviedo http://purl.org/weso/ First International Workshop on Semantic Applied Technologies on Biomedical Informatics (SATBI 2011) In conjunction with ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB) Chicago, IL, U.S.A. August 1-3, 2011
  • 2. IntroductionPsycho linguistics andSemantic priming
  • 3. Retrieve data as brain can do...a connectionist method
  • 4. New information realm...Semantic Technologies Linked Data... Different scopes...E-Health, E-procurement, etc.
  • 5. E-Health Sector Need to automate processes combine and synthesize complex related pieces of informationfacilitate access to clinical informationidentify patterns within the patient data …
  • 6. How to selectrelated concepts (symptoms & diseases)?
  • 7. Tagging of EHR CDSS
  • 8. Graph Exploration Document Retrieval Information Retrieval Annotation & TaggingRecommending enginesSemantic Search Engines
  • 9. Open GALEN“Ontologies” are consideredcategories: 23,141 concepts 950 relations… to facilitate clinical apps & statistics
  • 10. SNOMED CT765,000 active English-language descriptions 830,000 logically-defining relationships… Data retrieve & analysis, tagging…
  • 11. Summary... Concepts RelationsApps to retrieve, analyze, annotate …a huge amount of medical data
  • 12. GRAPHEXPLORATION?
  • 13. Spreading Activation (SA) 3 Stages Activation functionCalculation of activation value Constrained SA Stop condition
  • 14. 3 Stages PreadjustmentInitial nodes, weights of relations, set functions… Execution Spread the activation value, graph exploration… Postadjustment Rank nodes…
  • 15. Variables & Constants/ E E t
  • 16. Activation functionCalculation of activation value
  • 17. Graphically Activation function
  • 18. Constrained SA DistanceNodes far from an activate node should be penalized Path Path of activation built by the algorithm Fan outNodes highly connected should not be representative Activation-thresholdSpread nodes have an activation value = threshold
  • 19. Stop ConditionThere is no node to spread with an activation value Min Activation Value Threshold
  • 20. ONTOSPREAD http://code.google.com/p/ontospread/ API JavaExtensible (intensive use of design patterns)Add new constraints to SA Context, time, output degradation … 3 Tools library, test module graphical debugger
  • 21. New constraints1) Context of activation2) Min activation value*3) Max Min spread concepts4) Time of execution5) Degradation Functions
  • 22. Degradation Functions1) Generic2) Distance-Based3) Beats-based (k number of iterations)
  • 23. Converging Paths Reward
  • 24. Implementation1) Set of activated nodes2) Set of spread nodes 3) Activation value
  • 25. ONTOSPREAD in Action
  • 26. ^ Z
  • 27. Methodology1. Select well-known ontologies2. Define a set of initial concepts3. Specify the weight of relations4. Combine restrictions5. Select degradation function6. Add reward function7. Test repeat!
  • 28. Open GALEN1. Ontology2. #Advanced-BreastCancer NAMEDSymptom3. Default value 1.04. Constrained SA + New restrictions5. H1 H26. No | Yes
  • 29. SNOMED-CT1. Ontology2. #Articular cartilage of lunate #Articular tissue sample3. Default value 1.04. Constrained SA + New restrictions5. H1 H26. No | Yes
  • 30. Use Cases BOPA Project (semantic searh engine of legal documents) http://www.w3.org/2001/sw/sweo/public/UseCases/CTIC/ 10ders Project(recommendation of public procurement notices) http://purl.org/weso/moldeas/
  • 31. Evaluation1. Close to the human brain behaviour2. Configurable extensible framework3. Flexibility scalability ..but...A domain-expert is still needed
  • 32. Further Steps1. Automatic configuration of the algorithm2. Development of Map- Reduce version of SA (to be published)
  • 33. Application of the Spreading Activation Technique for RecommendingConcepts of well-known Ontologies in Medical Systems José María Álvarez Rodríguez WESO-Universidad de Oviedo http://purl.org/weso/ First International Workshop on Semantic Applied Technologies on Biomedical Informatics (SATBI 2011) In conjunction with ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB) Chicago, IL, U.S.A. August 1-3, 2011

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