A View-based Methodology for Collaborative Ontology Engineering (VIMethCOE)

1. A View-based Methodology for Collaborative Ontology Engineering (VIMethCOE) Ernesto Jiménez Ruiz Rafael Berlanga Llavorí Temporal Knowledge Bases Group http://krono.act.uji.es Universidad Jaume I de Castellón (Spain)

2. INTRODUCTION • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • A collaborative methodology for the development of ontologies, based on Views. • Requirements • Related Work • The Methodology • Phases • Knowledge Spaces • The View Mechanism • State of our work, and future tasks VIMethCOE

3. NEW DIMENSIONS IN THE DEVELOPMENT • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • The work “Ontologies: How can They be Built?” (Sofia Pinto, and João Martins) establishes the need for new methodologies that consider new dimensions in the development. VIMethCOE

4. HOW TO ACHIEVE A GOOD BALANCE BETWEEN DIMENSIONS? • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • We want to achieve a highly dynamic, distributed and partially controlled scenario for the development. • Proposed Requirements: • Modularization • Local Adaptation • Knowledge Abstraction • Personal Views • Argumentation and Consensus VIMethCOE

5. MODULARIZATION • Introduction • Methodology Requirements • Modularization • Local Adaptation • Knowledge Abstraction • Views • Argumentation and Consensus • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Ontologies can involve several thousands of concepts, and require several experts involving different domains (molecular, genomics, organs, diseases, etc.). • The definition of modules would facilitate several aspects: • Maintenance and validation of the ontology • Local reasoning • Collaboration • Reuse of knowledge. VIMethCOE

6. LOCAL ADAPTATION • Introduction • Methodology Requirements • Modularization • Local Adaptation • Knowledge Abstraction • Views • Argumentation and Consensus • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Each participant must be able to deal with knowledge in a local and private working space. • Making changes and local copies independent from the community’s knowledge. • i.e.: Protégé editor VIMethCOE

7. KNOWLEDGE ABSTRACTION • Introduction • Methodology Requirements • Modularization • Local Adaptation • Knowledge Abstraction • Views • Argumentation and Consensus • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • The development of ontologies may involve experts from several areas. • These experts may only have a partial knowledge of the domain. • So they will be able to contribute in the development of only a portion of the ontology. VIMethCOE

8. VIEWS (PERSONAL MODULES) • Introduction • Methodology Requirements • Modularization • Local Adaptation • Knowledge Abstraction • Views • Argumentation and Consensus • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Our methodology propose the operation through a view mechanism • User extend views in their local space • Views are defined by the developer. • This mechanism provides… • Knowledge Abstraction • Facilities for Visualization in ontology editors • Reuse of Knowledge VIMethCOE

9. ARGUMENTATION ANDCONSENSUS • Introduction • Methodology Requirements • Modularization • Local Adaptation • Knowledge Abstraction • Views • Argumentation and Consensus • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Developers extend their knowledge in a local space • Changes over the local knowledge may be published • These changes should be evaluated by the community. • Following a Formal or a semi-formal argumentation model like Ibis. VIMethCOE

10. RELATED WORK • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Classic Methodologies • Collaborative Approaches • Web-based approaches • Fulfilment of the Requirements VIMethCOE

11. CLASSIC METHODOLOGIES • Introduction • Methodology Requirements • Related Work • Classic Methodologies • Collaborative Approaches • Web-based Systems • Characteristics • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Cyc, Kactus, Uschold-King’s method, METHONTOLOGY, On-To-Knowledge (OTK), UPON, etc. • They propose a centralized approach to the ontology development. • They neglect collaboration issues. VIMethCOE

12. COLLABORATIVEAPPROACHES • Introduction • Methodology Requirements • Related Work • Classic Methodologies • Collaborative Approaches • Web-based Systems • Characteristics • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Co4, DILIGENT, HCOME, Divergence Occurrences Methodology, (KA)2, the OntoEdit system, etc. • They do not propose a complete methodology with different phases • But solutions to carry out an agreed definition of the knowledge (mainly the argumentation). VIMethCOE

13. WEB-BASED APPLICATIONS • Introduction • Methodology Requirements • Related Work • Classic Methodologies • Collaborative Approaches • Web-based Systems • Characteristics • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Ontolingua Server, WebOnto, WebODE, Wiki@nt, (KA)2, etc. • They rely completely on the WWW. • So they provide good frameworks for collaboration. VIMethCOE

14. CHARACTERISTICS OFRELATED WORK • Introduction • Methodology Requirements • Related Work • Classic Methodologies • Collaborative Approaches • Web-based Systems • Characteristics • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions VIMethCOE

15. BREAK POINT - SUMMARY • I have presented the requirements for collaborative methodologies. • I have reviewed some related work • Next, I’m going to present the characteristics of our methodology VIMethCOE

16. THE VIMethCOE METHODOLOGY • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Complementary to centralized methodologies • We distinguish 5 different phases: • Requirements • Development • Publication and Argumentation • Evaluation and Maintenance • Application Overlapped Phases VIMethCOE

17. REQUIREMENTS PHASE • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Requirements • Development • Publication • Evaluation • Application • Knowledge Spaces • The View Mechanism • Conclusions • Defining an initial knowledge • Definition of a Top-level ontology, or reusing (e.g.: SUMO, DOLCE). • Reusing of Ontologies (NCI, FMA, GO, etc.). • Modularization of this knowledge. • Applying a partitioning algorithm VIMethCOE

18. DEVELOPMENT PHASE • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Requirements • Development • Publication • Evaluation • Application • Knowledge Spaces • The View Mechanism • Conclusions • Knowledge engineers, ontology engineers, domain experts and final users must take part in this phase. • Each participant will define development views in order to extend them. • They will work in a local and private environment VIMethCOE

19. PUBLICATION - ARGUMENTATION • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Requirements • Development • Publication • Evaluation • Application • Knowledge Spaces • The View Mechanism • Conclusions • Local adaptations of the knowledge can be published, by means of views. • This published knowledge must be discussed by others developers. • Whenever a consensus is reached, the global ontology must be updated. VIMethCOE

20. EVALUATION - MAINTENANCE • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Requirements • Development • Publication • Evaluation • Application • Knowledge Spaces • The View Mechanism • Conclusions • Checking for Consistency • General Argumentation • Redefinition of the initial modules if the growth of the ontology requires it. VIMethCOE

21. APPLICATION PHASE • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Requirements • Development • Publication • Evaluation • Application • Knowledge Spaces • The View Mechanism • Conclusions • In this phase we define views with an application purpose. • They will represent a complementary knowledge. • These views may present divergences with other views and with the global knowledge. VIMethCOE

22. KNOWLEDGE SPACES • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • In VIMethCOE we propose the coexistence of several overlapped knowledge spaces: VIMethCOE

23. KNOWLEDGE SPACES • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Private Space • The working space of developers. • The set of views in development and not published • Public Space • Shared knowledge, which can be used by the community. • Agreed Space • Knowledge that is in consensus. • Composed by the ontology modules, and the agreed views over them. VIMethCOE

24. KNOWLEDGE SPACES • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Development Views. • Composed by the set of views that aims of extending the ontology. • Application Views. • Composed by the set of views for a specific application. • Old Versions. • To analyse the evolution of knowledge. VIMethCOE

25. THE VIEW MECHANISM • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Allows a collaborative evolution of the ontology with dynamism and distribution • But also enables control over the global knowledge. • Control in the definition of views  Abstraction • Control in changes over views  Argumentation • Next, I’m going to comment the operation of the proposed mechanism VIMethCOE

26. THE VIEW HIERARCHY • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • View Hierarchy • Changes over Views • Argumentation • View Language • Prototype • Conclusions • Views can be defined over modules or over other views (agreed or not). • Views are grouped inside a hierarchy depending on their definition and the changes made. VIMethCOE

27. SITUATION IN VIEW HIERARCCHY • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • View Hierarchy • Changes over Views • Argumentation • View Language • Prototype • Conclusions • When users publish their extended views, their situations in the view hierarchy are inferred. • If extensions increases the knowledge or causes reversible changes is-a view or derived view. • i.e.: union of two views • If the view extensions causes some kind of loss of information or inconsistencies  conflict view. • i.e.: deleting a property of a class VIMethCOE

28. ARGUMENTATION PROCESS • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • View Hierarchy • Changes over Views • Argumentation • View Language • Prototype • Conclusions • Achieve a consensus is a very important aspect for the Methodology. • If consensus: • Public View  Agreed View • Global Knowledge is updated • No Consensus • Divergent Alternatives (Conflict) • Alternatives may coexist but some control is necessary  the view hierarchy VIMethCOE

29. DEFINITION OF VIEWS • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • View Hierarchy • Changes over Views • Argumentation • View Language • Prototype • Conclusions • One of the main characteristics of VIMethCOE is the ability to operate through views. • We have designed and implemented a traversal-based view definition language. • Views consist of: • the union of a set of queries • and a set of inference rules VIMethCOE

30. DEFINITION OF VIEWS • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • View Hierarchy • Changes over Views • Argumentation • View Language • Prototype • Conclusions • Query definitions are paths over the ontology graph with operators over concepts, properties and instances. • “CPT_II Protein”/{componentOf=“MithocondrialMembrane”} • Inference rules may involve the extraction of concepts, properties and instances that are not explicitly indicated in the views: • Objective: Obtain Closed and Complete views. VIMethCOE

31. SOME TESTS • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • View Hierarchy • Changes over Views • Argumentation • View Language • Prototype • Conclusions • Some tests have been realized with a simple prototype. • A plug-in that connects the semi-structured database G with the ontology editor Protégé • Views are defined over small ontologies. More Information: http://www3.uji.es/~ejimenez/GProtegePlugin/ VIMethCOE

32. CONCLUSIONS • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • We take into account new dimensions (dynamism, distribution and control) in the ontology development and evolution. • We have propose several Requirement in order to achieve a good balance between the dimensions : • Modularization • Local Adaptation • Knowledge Abstraction • Personal Views • Argumentation and Consensus • We have presented a View-based Methodology that aims to realize the above requirements VIMethCOE

33. A GOOD STATE OF THE ART, AND A GOOD PROPOSAL? • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Work in Progress • Future Work • Some Questions • In this work we have carried out a documentation about the state of art in ontology engineering. • And we have proposed a new work for this state of the art. • But, we have only implemented a simple prototype, so we have got more work to do. VIMethCOE

34. FUTURE WORK • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Work in Progress • Future Work • Some Questions • Formal Definition of Views: • The kind of views proposed is mainly oriented to frame-based ontologies. • So it is necessary to refine the definition of views to take advantage of description logic characteristics. • Formal definition of modules or views around a concept or a set of concepts. • i.e.: e-modules (Modularizing OWL ontologies with E-Connections, Bernardo Cuenca Grau. et.al.) VIMethCOE

35. FUTURE WORK • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Work in Progress • Future Work • Some Questions • Application Scenario • The biomedicine domain is an excellent scenario for applying this methodology. • Large Ontologies like NCI, FMA, GO, GALEN, etc. • The development of ontologies may involve experts from several areas • i.e.: Molecular, cellular, tissue, organ, individual and population  Modules • Health-e-Child Project:: http://www.health-e-child.org/ VIMethCOE

36. APPLICATION SCENARIO • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Work in Progress • Future Work • Some Questions VIMethCOE

37. SOME QUESTIONS AND CONTACT • Introduction • Methodology Requirements • Related Work • Phases of the Methodology • Knowledge Spaces • The View Mechanism • Conclusions • Work in Progress • Future Work • Some Questions • Questions?: • Contact: Ernesto Jiménez Ruiz (ejimenez@uji.es) Rafael Berlanga Llavorí (berlanga@uji.es) Temporal Knowledge Bases Group http://krono.act.uji.es Universidad Jaume I de Castellón (Spain) VIMethCOE