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The Loreley Of Ontology Design Patterns

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March 2009

March 2009

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  • 1. The Loreley of the Ontology Design Patterns Double vocal projection: http://ontologydesignpatterns.org http://www.gong.manchester.ac.uk/odp/html/index.html Dr. Violeta Damjanovic Salzburg Research Forschungsgesellschaft m.b.H. Jakob Haringer Straße 5/3 | 5020 Salzburg, Austria T +43.662.2288-427 | F +43.662.2288-222 violeta.damjanovic@salzburgresearch.at www.salzburgresearch.at
  • 2. Preamble | Ontology Design Pattern -> ODP | ODP: a new testament to known problems in ontology engineering | ODP: a practical solution to semantic interoperability of different knowledge configurations (components and approaches) 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 2
  • 3. Outline | Ontology Engineering | History of Using Patterns in Ontology Engineering | ODP: General Remarks | Bio-Ontology Engineering | Classification of ODP for Bio-Ontologies Adapted SET Triple in Action | | The Advantages of Using ODP in Bio-Ontology Engineering | ODP Initiative: Classification of Ontology Patterns | Content ODP | Description Template of SDP Applied to ODP | Conclusions | Literature 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 3
  • 4. Ontology Engineering | Ontologies are engineering artefacts that can formally represent the concepts and their relationships within a given knowledge domain | Ontologies are implemented in different KR (Knowledge Representation) languages differing in properties that can be described along the following axes: Syntax | Semantics | Expressiveness | Reasoning | | Ontologies provide shared and common understanding of a domain 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 4
  • 5. History of Using Patterns in Ontology Engineering: Selected papers | J.R. Reich, 1999: Ontological Design Patterns for the Integration of Molecular Biological Information. GCB’99, Germany. introduces the notion of ODP for a particular problem domain in Biology | | S. Staab, M. Erdmann, A. Maedche, 2001: Engineering Ontologies Using Semantic Patterns. IJCAI '01, USA. language independent description of a certain concepts, relation or axiom | | V. Devedzic, 2002: Understanding Ontological Engineering. Communications of the ACM, Vol.45, No.4, 2002, pp. 136-144. similarities between traditional SDP and ontologies | | P. Clark, J. Thompson, B. Porter, 2003: Knowledge Patterns. Springer. International Handbooks on Information Systems. conceptual patterns that are “morphed” into a given knowledge base by a | set of mapping axioms | V. Svatek, 2004: Design Patterns for Semantic Web Ontologies: Motivation and Discussion. 7th Conf.on Business Inform.Systems. | A. Gangemi, 2005: Ontology Design Patterns for Semantic Web Content. LNCS 1729 ISWC 2005, 262-276. | … 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 5
  • 6. Ontology Design Patterns in General (1) | ODP: abstract, formalized and documented solutions to the frequent and typical modelling problems | SDP < --- > ODP | The UML notation to OWL axioms mapping proposed in [Brockmans et al., 2004]: 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 6
  • 7. Ontology Design Patterns in General (2) | ODP: “cookbook recipes” [Aranguren et al., 2008] | ODPs are abstract and implementation independent | Applying a particular ODP, e.g.: Competency questions help in choosing an appropriate ODP | Ontology Processing Language (OPL) can be used to create ODP in a | new ontology | OPL plugin: http://www.co-ode.org/downloads/protege-x/opl/ | ODPs can be classified according to their complexity, granularity, usability, popularity, etc. 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 7
  • 8. Bio-Ontology Engineering | GENE (GEne ontology NExt generation) project “ODP for the formalization of biological ontologies”, Thesis by Mikel | Egaña Aranguren. 2005. Available @ http://www.gong.manchester.ac.uk/doc/MPhil_thesis.pdf.gz) | The ODP Catalog can be explored @ http://odps.sourceforge.net/ | ODPs are classified according to the way they are used: Extensional ODPs (Exception ODP, N-ary Relationship ODP) | Good practice ODPs (Normalization ODP, Value Partition ODP, Upper | Level ODP) Domain Modelling ODPs (List ODP, Adapted SEP Triples ODP) | 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 8
  • 9. Classification of ODP for Bio-Ontologies | Extensional ODPs: N-ary Relationships: to model complex phenomena that have | relationships linking more than one element Exception: to model classes that break canonical classifications | | Good practice ODPs: Normalization: to build modular and reusable ontologies | Value Partition: to model attributes of objects that can only have certain | already known values Upper Level Ontology: to create an ontology than can integrate different | ontologies in itself | Domain Modelling ODPs: List: to model ordered groups of elements | Adapted SEP Triples: propagation of properties along the partonomy | relation 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 9
  • 10. Adapted SEP Triple in Action [Seidenberg & Rector, 2006] 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 10
  • 11. The Advantages of Using ODP in Bio-Ontology Engineering | Design Rich and granular modelling | Semantic encapsulation | Robustness and modularity | Reasoning | Alignment | | Implementation Focused development | Rapid prototyping | Reengineering | | Communication Good communication | Documented modelling | Comprehension of advances in KR | 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 11
  • 12. ODP Initiative: Classification of Ontology Design Patterns [Presutti et al., 2008] 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 12
  • 13. Content Ontology Design Pattern [Gangemi, 2005] | Content ODP shows certain characteristics: Computational components | Small, autonomous components | Hierarchical components | Inference-enabling components | Cognitively relevant components | Linguistically relevant components | Best practice components | | Content ODP ways of creation [Presutti & Gangemi, 2008] Reengineering from other data models | Specialization/Composition of other Content ODP | Extraction from reference ontologies | Creation by combining the above techniques | | Set of operation for creation of Content ODP Covering: connects Content ODP and requirements | Clone: copies an ontology element from an existing ontology | Composition: relates two Content ODPs and results into a new ontology | Specialization & Generalization: defines a partial ordering between Content ODPs | Expansion: relation between CODPs and either ontology elements or axioms | 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 13
  • 14. Catalog of Content Ontology Design Pattern [Presutti et al., 2008] | General: types of entities; description; situation; classification; n-ary classification; object role; | Parts and collections: part of; time indexed part of; composition; constituency; collection entity; | Semiotics: intension extension; information realization; | Quantities and dimensions: region; region overlap; parameter; parameter region; | Participation: participation; co-participation; n-ary participation; | Organization, management, and scheduling: precedence (sequence); agent role; task role; time-indexed person role; basic plan description; basic plan execution; basic plan; | Business: price; sales and purchase order contracts; | Time: time interval; | Space: move; | Life science: linnean taxonomy; | Multimedia: multimedia data segment decomposition 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 14
  • 15. Description Template of SDP Applied to ODP [Aranguren et al., 2008] http://martinfowler.com/articles/writingPatterns.html#CommonPatternForms | Name and classification | Intent | Also known as | Motivation | Applicability | Structure | Participants Elements (in ODP) | | Collaboration Relationships (in ODP) | | Consequences | Implementation | Sample code OWL DL ontology with the whole ODP | The important parts of the ODP described using DL notation (or Manchester | abstract OWL syntax) | Known uses | Related patterns | References (possible publications or web pages where can it be founded) 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 15
  • 16. Conclusion | ODP are ready-made solutions for tackling complex modelling issues when creating and maintaining ontologies | ODP improve ontology engineering in different ways [Brockmans et al., 2004] ODPs are abstractions: faster ontology creation; easy way of dealing with | the complexity of e.g. OWL-DL ODPs produce more modular and robust ontologies: the entities and the | structure of ontologies can be explicitly separated ODPs improve communication between ontology developers | | ODP life-cycle: Identifying ODP | Testing ODP | ODP becomes a part of the system (language) | | Protégé plugin for applying ODPs ? http://www.co-ode.org/downloads/protege-x/patterns/ | 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 16
  • 17. Literature | S. Brockmans, R. Volz, A. Eberhart, P. Löffler, 2004: Visual Modelling of OWL DL Ontologies Using UML. Proc. ISWC 2004, 198-213. | M.E. Aranguren, E. Antezana, M. Kuiper, R. Stevens, 2008. Ontology Design Patterns for Bio-Ontologies: A Case Study on the Cell Cycle Ontology. BMC bioinformatics 2008, 9(Suppl 5):S1. [BMC Bioinformatics] | J. Seidenberg, A. Rector, ´2006. Representing Transitive Propagation in OWL, ER2006. | V. Presutti, A. Gangemi, 2008. Content Ontology Design Patterns as Practical Building Blocks for Web Ontologies, In Proceedings of the 27th International Conference on Conceptual Modeling (ER 2008) | V. Presutti, et al., 2008. NeOn D2.5.1: A Library of Ontology Design Patterns: Reusable Solutions for Collaborative Design of Networked Ontologies. | A. Gangemi, 2005. Ontology Design Patterns for Semantic Web Content. LNCS 1729 ISWC 2005, 262-276. 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 17
  • 18. Contribute to the ODP efforts • http://www.ontologydesignpatterns.org • http://www.w3.org/2001/sw/BestPractices/ 01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 18