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Ontology based semantics and graphical notation as directed graphs


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Ontology based semantics and graphical notation as directed graphs

  1. 1. Ontology based semantics and graphical notation as directed graphs Johann Höchtl, research fellow, Danube University Krems, Austria [email_address]
  2. 2. Overview <ul><li>The Business Problem with Ontology, Semantics and Interoperability
  3. 3. An Information Preparation Methodology
  4. 4. Visualization of Ontologies </li><ul><li>Tool Overview </li></ul><li>Ontology Similarity </li><ul><li>Selected Methodologies and Tools </li></ul></ul>
  5. 5. The Business Problem of (Semantic) Interoperability Application <ul><li>The leaders do not understand what it is all about
  6. 6. Sometimes even not your customers </li><ul><li>Plethora of definitions, common understanding but definition varies from organization to organization
  7. 7. IEEE: “Interoperability is the ability of two or more systems to exchange information and to use the information that has been exchanged”
  8. 8. ISO, ETSI, EICTA, … </li></ul></ul>
  9. 9. The Business Problem of (Semantic) Interoperability Application <ul><li>Quotes from a study </li><ul><li>“Interoperability is not yet a well-defined subject that can easily be applied to project work. It remains an innovative process in which conceptual issues have to be clarified on the job”
  10. 10. “At all phases of the project awareness of the results and benefits to potential users have to be widely publicised to ensure comprehensive marketing to the client base and maximum user take up.”
  11. 11. “differences between stakeholder groups or countries of different sizes or between different levels of government do exist [...] could cause problems of mutual understanding”
  12. 12. Herbert Kubicek, and Ralf Cimander, “Interoperability in eGovernment - A Survey on Information Needs of Different EU Stakeholders.” European Review of Political Technologies 2005 / 3, no. 2005/3 (March 2005): 17. </li></ul></ul>
  13. 13. Get your message through <ul><li>Ever heard of Information Maps?
  14. 14. The method to have your say in a concise manner, even your customer (boss) will understand you </li><ul><li>Obviously you still need the chance to be heard </li></ul><li>research-based approach for creating structured documents and communications that are clear, concise, and user-focused </li><ul><li>200 common “block types”
  15. 15. Information Mapping produces measurable results, changing the way people write and work </li></ul></ul>
  16. 16. Get your message through <ul><li>Key element: Visualization, more precise visual preparation of information
  17. 17. Home of Robert Horn: </li></ul><ul><li>Probably wont get a design price
  18. 18. More examples: </li><ul><li> </li></ul><li>NOT NOW! </li></ul>
  19. 19. Visualization is Key <ul><li>Chris Bennett & Jody Ryall & Leo Spalteholz & Amy Gooch / Aesthetics of Graph Visualization, Computational Aesthetics in Graphics, Visualization, and Imaging (2007), p. 2, D. W. Cunningham, G. Meyer, L. Neumann (Editors) </li></ul>
  20. 20. Visualization is Key <ul><li>Visual representation of information and knowledge is nothing new
  21. 21. Directed graphs are a natural way to represent knowledge
  22. 22. All OWLs/RDFs/... can be transformed to Directed Acyclic Graphs </li><ul><li>Want a formal prove? </li></ul><li>Actually every DAG is_a DG, tautologies do not add information so are omitted -> DAG </li><ul><li>An Ontology is_a Ontology is_a Ontology is_a ... </li></ul></ul>
  23. 23. Ontology Visualization <ul><li>Tools Overview </li><ul><li>Licensed, Closed Source: </li><ul><li>SemanticWorks (Altova)
  24. 24. TopBraid Composer (TopQuadrant)
  25. 25. Integrated Ontology Development Toolkit (IODT) (IBM)
  26. 26. Integrated Ontology Development Environment (IODE) (Ontology Works) </li></ul></ul></ul>
  27. 27. Ontology Visualization <ul><li>Free, Open Source Tools Overview </li><ul><li>IsaViz (W3C)
  28. 28. Protégé (Stanford University) </li><ul><li>Various Plugins for Visualiztion: Jambalaya, OWLViz, TGViz </li></ul></ul><li>IsaViz and various Protégé plugins (but not all!) use Graphviz as the underlying rendering engine
  29. 29. Graphviz (AT&T) </li><ul><li>Based by AT&T research, released under a liberal “Common Public License” with sources
  30. 30. Domain free – no affiliation to semantic knowledge representation
  31. 31. Uses proprietary scripting language – DOT Language – to render directed graphs </li></ul></ul>
  32. 32. Ontology Visualization digraph finite_state_machine { rankdir=LR; size=&quot;8,5&quot; node [shape = doublecircle]; LR_0 LR_3 LR_4 LR_8; node [shape = circle]; LR_0 -> LR_2 [ label = &quot;SS(B)&quot; ]; LR_0 -> LR_1 [ label = &quot;SS(S)&quot; ]; LR_1 -> LR_3 [ label = &quot;S($end)&quot; ]; LR_2 -> LR_6 [ label = &quot;SS(b)&quot; ]; LR_2 -> LR_5 [ label = &quot;SS(a)&quot; ]; LR_2 -> LR_4 [ label = &quot;S(A)&quot; ]; LR_5 -> LR_7 [ label = &quot;S(b)&quot; ]; LR_5 -> LR_5 [ label = &quot;S(a)&quot; ]; LR_6 -> LR_6 [ label = &quot;S(b)&quot; ]; LR_6 -> LR_5 [ label = &quot;S(a)&quot; ]; LR_7 -> LR_8 [ label = &quot;S(b)&quot; ]; LR_7 -> LR_5 [ label = &quot;S(a)&quot; ]; LR_8 -> LR_6 [ label = &quot;S(b)&quot; ]; LR_8 -> LR_5 [ label = &quot;S(a)&quot; ]; } Perfect layout – here: Finite State Machine Input File The DOT processor Magic happens - in various graphics formats
  33. 33. Tool Overview: IsaViz (W3C) <ul><li>Visual representation and modeling of RDFs in N3, N-Triple and RDF-XML Notation
  34. 34. ONLY RDF, no OWL!
  35. 35. Merge and Extend support – a real editor!
  36. 36. Visual component of knowledge representation (DAGs) is a first class citizen through GSS – Graph Style Sheets: IsaViz parses SVG output of GraphViz
  37. 37. Implemented in Java
  38. 38. Uses Xerces (Apache) and Jena
  39. 39. W3C license, GPL compatible </li></ul>
  40. 40. Tool Overview: IsaViz <ul><li>GSS – Combination of Scalable Vector Graphics (SVG) and CSS allows dynamic visualizations and 'views' </li><ul><li>Operates on Node-Edge principle of RDFs </li></ul><li>Fresnel – Successor of GSS, defined in OWL </li><ul><li>Representation independent, no Node-Edge principle
  41. 41. What to display – “Lense”
  42. 42. How to represent
  43. 43. Has it's own selector language opposed to SPARQL </li></ul></ul>
  44. 44. Tool Overview: IsaViz – GSS Transformation <rdf:RDF xmlns:rdf=&quot;; xmlns:foaf=&quot;; xmlns:dc=&quot;;> <rdf:Description rdf:about=&quot;;> <dc:title>Tony Benn</dc:title> <dc:publisher>Wikipedia</dc:publisher> <foaf:primaryTopic> <foaf:Person> <foaf:name>Tony Benn</foaf:name> </foaf:Person> </foaf:primaryTopic> </rdf:Description> </rdf:RDF> Load GSS Stylesheet from file
  45. 45. Tool Overview: IsaViz – Fresnel Transformation Apply Fresnel Lens and style Information
  46. 46. Tool Overview: Protégé (Stanford University / Manchester) <ul><li>An Umbrella Project – Pluggable Architecture like Eclipse Platform
  47. 47. Two distinct modeling methodologies: </li><ul><li>Frames-Editor, rather “object-oriented”, everything is disallowed until specified
  48. 48. OWL-Editor: everything is allowed until restricted (“open world” principle) </li></ul><li>Supports Import of OWL(Lite, DL, Full), RDF, RDFS
  49. 49. Implemented in Java </li><ul><li>Uses familiar Open Sourced libraries like Xerces, Jena, Lucene
  50. 50. Provides the “de-factor standard OWL API” </li></ul><li>Released under Mozilla Public License, MPL
  51. 51. Visualization Tools: OWLViz, Jambalaya, and more! </li></ul>
  52. 52. Tool Overview: Protégé: OWLViz <ul><li>Enables class hierarchies in an OWL Ontology to be viewed and incrementally navigated
  53. 53. uses Graphviz as layout engine
  54. 54. Unlike IsaViz no editor, viewer only
  55. 55. Here: Pizza Example of Protégé </li></ul>
  56. 56. Tool Overview: Protégé:Jambalaya <ul><li>Fundamentally different visualization principle </li><ul><li>domain-independent visualization technique designed to enhance how people browse and explore complex information spaces
  57. 57. uses a nested graph view to present hierarchically structured information.
  58. 58. introduces the concept of nested interchangeable views to allow a user to explore multiple perspectives of information at different levels of abstraction. </li></ul><li>University of Victoria's Department of Computer Science, Canada
  59. 59. A Protégé-Plugin as well a tool on it's own </li></ul>
  60. 60. Tool Overview: Protégé:Jambalaya Nested View Nested Treemap Nested Composite View useful ontology information is ubiquitous
  61. 61. Visualization Technologies <ul><li>Treeviews: </li><ul><li>easy to construct
  62. 62. easy to collapse, “focus” on certain aspects </li></ul><li>Network views </li><ul><li>identify similarity
  63. 63. full potential when employed interactively </li></ul><li>Cluster Maps </li><ul><li>identify similarity
  64. 64. query result visualization
  65. 65. complex ontologies </li></ul></ul>
  66. 66. Ontology Similarity – DAG Similarity <ul><li>As OWLs can be reliably represented as DAGs, comparing DAGs for similarity solves the problem of OWL comparison
  67. 67. Research in graph theory as old as IT research (compiler construction), boost through search engine research </li><ul><li>eg. Map-Reduce algorithm by Google </li></ul><li>However: Not all algorithms applicable to Graphs make sense in Ontology context </li><ul><li>Optimizations (“Graph rewriting”), shortest path (traveling salesman), … </li></ul><li>Brief overview over research projects </li><ul><li>COMA++
  68. 68. BayesOWL
  69. 69. SOQA-SimPack </li></ul></ul>
  70. 70. Notions of Similarity – Structural <ul><li>Tree Edit Distance - Number of Edits to transform one tree into another </li><ul><li>Operations: insert, delete, relabel
  71. 71. purely structural, no notion of synonymy
  72. 72. Here: Add F, relabel A->G, delete C </li></ul><li>Maximum common subgraph/ Minimum common supergraph </li><ul><li>identifying the `smallest’ graph that contains both graphs </li></ul><li>Adjacent Matrix </li><ul><li>Two graphs are similar if the neighborhoods for every Node are similar. </li><ul><li>1st. Graph: Vertice from Node N to M?
  73. 73. Establish a Matrix for all 1 .. N nodes and their interconnection
  74. 74. Do so for second graph
  75. 75. “ Compare” Matrices using mathematics </li></ul></ul></ul>
  76. 76. DAG/OWL Similarity <ul><li>Structural Similarity is not enough
  77. 77. But there clearly is similarity
  78. 78. Measure similarity through combined approaches </li><ul><li>Adjacent Matrices, String matches, full text similarity match (stemming algorithms!), distance of concepts within ontologies, … </li></ul><li>Still not enough </li><ul><li>Abbreviations, AssocWords with delimiters (ArrivalAirportIn), Suffix/Prefix (hasName), misspellings, free invented words </li></ul></ul>vs. vs. no structural similarity! means means
  79. 79. COMA++ <ul><li>Graphical user interface
  80. 80. Map SQL, XSD, XDR and OWL
  81. 81. compose, merge and compare of mappings
  82. 82. Repository to persistently store all match-related data, Model and Mapping Pools to manage schemas, ontologies and mappings in memory, the Match Customizer to configure matchers and match strategies, and the Execution Engine to perform match operations
  83. 83. Models are uniformly represented by directed graphs!
  84. 84. Mapping Pool maintains all generated mappings </li><ul><li>Operations to manipulate them: Diff / Intersect, Merge, MatchCompose -> find common minimum </li></ul><li>Matchers </li><ul><li>Taxonomy Matcher: Intermediary Ontology for similarity lookup. No use of WordNet, “Hand-taylored Matching Ontology”
  85. 85. Experiments with different Lexical Matchers: </li><ul><li>Budanitsky A.: Lexical Semantic Relatedness and Its Application in Natural Language Processing. Tech. Report, Univ. Toronto, 1999
  86. 86. Weeds, J., D. Weir, D. McCarthy: Characterising Measures of Lexical Distributional Similarity. Int. Conf. of Computational Linguistics (COLING) 2004 </li></ul><li>Divide and Conquer-Strategy: Divide large matching problems into smaller schema fragments </li><ul><li>Identify similar fragments
  87. 87. Each identified similar fragment represents a match problem on its own </li></ul><li>Reuse-Oriented Matching: Based on automated learning and component statistics, reuse previous match results </li></ul></ul>
  88. 88. COMA++ <ul><li> </li></ul>
  89. 89. BayesOWL <ul><li>Based on the principle of uncertainty matching
  90. 90. quantify the degree of the overlap or inclusion between two concepts
  91. 91. augment OWLs with uncertainty for reasoning in Baysian Networks (BN)
  92. 92. Convert OWL into DAG and enhance with conditional probability table (CPT) to form a BN
  93. 93. The CPT is constructed entirely on the information of rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith (structural evaluation) and owl:unionOf, owl:intersectionOf, and owl:complementOf (logical relations) </li><ul><li>No evaluation of properties and datatypes </li></ul><li>Structural Nodes are translated 1:1 to BN (DAG) nodes, logical relations are constructed using an algorithmus
  94. 94. The so constructed BN is enhanced with probabilities from the CPT </li><ul><li>Using the iterative proportional fitting procedure IPFP as a basis, the hierarchy nature of ontologies requires conditional fitting procedures CIPF-P described in Bock HH (1989) A Conditional Iterative Proportional Fitting (CIPF) Algorithm with Applications in the Statistical Analysis of Discrete Spatial Data. Bull. ISI, Contributed papers of 47th Session in Paris, 1:141{142 </li></ul><li>The actual mapping of two enriched BN is still an area of research: </li><ul><li>Valtorta M, Kim Y, Vomlel J (2002) Soft Evidential Update for Probabilistic Multiagent Systems. International Journal Approximate Reasoning 29(1): 71-106
  95. 95. Xiang Y (2002) Probabilistic Reasoning in Multiagent Systems: A Graphical Models Approach. Cambridge University Press </li></ul><li>Sources: </li></ul>
  96. 96. SOQA-SimPack Toolkit <ul><li>Operates on Ontologies encoded in OWL, PowerLoom, DAML, WordNet
  97. 97. Supports different concepts of similarity </li><ul><li>Vector Similarity: Mapping of OWL properties of two ontologies, encoding as binary vectors, calculate vector similarity eg. cosine, jaccard or overlap algorithm
  98. 98. String based similarity: Traverses the underlying graph representation of the ontology resources ie. concepts or data values. The string similarity is expressed as the edit distance, calculated by the levenshtein distance
  99. 99. Full text similarity: The whole ontology is expressed in textual representation, normalized using the porter-stemmer and indexed using the Apache Lucene full text indexer
  100. 100. Distance based Similarity: A very intuitive measure as the number of sub- or superconcepts in between two ontonologies. Evectively means finding the shortest path between two concepts and measure the distance.
  101. 101. Supports lexical ontologies like WordNet and ontologies supplied by knowledge bases like CYC </li></ul><li>Architectural overview: </li><ul><li>SOQA:SIRUP Ontology Query API Defines it's own Query Language, similar to SQL
  102. 102. Uses the generic SimPack Java class library </li></ul></ul>
  103. 103. SOQA-SimPack Toolkit
  104. 104. Thank you! Questions & Discussion ?
  105. 105. Links and further reading: Visualization <ul><li>GraphSynth: the first publicly available approach to creating graph grammars
  106. 106. OntoSphere: more than a 3D ontology visualization tool:SWAP 2005:
  107. 107. Ontology-based Information Visualization: Towards Semantic Web Applications:
  108. 108. SIMILE
  109. 109. Cluster Maps: F. van Harmelen, C. Fluit, M. Sabou: Ontology-based Information Visualisation. Visualizing the Semantic Web, Spring Verlag. 2002. </li></ul>
  110. 110. Links and further reading: Graph Similarity <ul><li>
  111. 111.
  112. 112. , </li><ul><li>Overview about mapping tools as well as visualization support, no in-depth analysis though </li></ul><li> </li><ul><li>Good introductory stuff about semantic matching </li></ul><li> </li><ul><li>The Aesthetics of Graph Visualization – Why good visualization matters for the performance of understanding </li></ul><li>Further readings:
  113. 113.
  114. 114.
  115. 115. </li></ul>