A View-based Methodology for Collaborative Ontology Engineering (VIMethCOE) Ernesto Jiménez Ruiz Rafael Berlanga Llavorí Temporal Knowledge Bases Group Universidad Jaume I de Castellón (Spain)

VIMethCOE2 INTRODUCTION 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 Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE3 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.

VIMethCOE4 HOW TO ACHIEVE A GOOD BALANCE BETWEEN DIMENSIONS? We want to achieve a highly dynamic, distributed and partially controlled scenario for the development. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions Proposed Requirements: –Modularization –Local Adaptation –Knowledge Abstraction –Personal Views –Argumentation and Consensus

VIMethCOE5 MODULARIZATION 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. Introduction Methodology Requirements Modularization Local Adaptation Knowledge Abstraction Views Argumentation and Consensus Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE6 LOCAL ADAPTATION 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 Introduction Methodology Requirements Modularization Local Adaptation Knowledge Abstraction Views Argumentation and Consensus Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE7 KNOWLEDGE ABSTRACTION 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. Introduction Methodology Requirements Modularization Local Adaptation Knowledge Abstraction Views Argumentation and Consensus Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE8 VIEWS (PERSONAL MODULES) 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 Introduction Methodology Requirements Modularization Local Adaptation Knowledge Abstraction Views Argumentation and Consensus Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE9 ARGUMENTATION AND CONSENSUS 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. Introduction Methodology Requirements Modularization Local Adaptation Knowledge Abstraction Views Argumentation and Consensus Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE10 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

VIMethCOE11 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.

VIMethCOE12 COLLABORATIVE APPROACHES 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). Introduction Methodology Requirements Related Work Classic Methodologies Collaborative Approaches Web-based Systems Characteristics Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE13 WEB-BASED APPLICATIONS Ontolingua Server, WebOnto, WebODE, (KA)2, etc. They rely completely on the WWW. So they provide good frameworks for collaboration. Introduction Methodology Requirements Related Work Classic Methodologies Collaborative Approaches Web-based Systems Characteristics Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE14 CHARACTERISTICS OF RELATED WORK MODULARIZATION LOCAL ADAPTATION KNOWLEDGE ABSTRACTION VIEWS ARGUMENT. CONSENSUS CO 4  DILIGENT  HCOME  Div. Occurr.  OntoEdit  Ontolingua  (KA) 2  WebOnto  WebODE   VIMethCOE  Introduction Methodology Requirements Related Work Classic Methodologies Collaborative Approaches Web-based Systems Characteristics Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE15 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

VIMethCOE16 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

VIMethCOE17 REQUIREMENTS PHASE 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 Introduction Methodology Requirements Related Work Phases of the Methodology Requirements Development Publication Evaluation Application Knowledge Spaces The View Mechanism Conclusions

VIMethCOE18 DEVELOPMENT PHASE 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 Introduction Methodology Requirements Related Work Phases of the Methodology Requirements Development Publication Evaluation Application Knowledge Spaces The View Mechanism Conclusions

VIMethCOE19 PUBLICATION - ARGUMENTATION 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. Introduction Methodology Requirements Related Work Phases of the Methodology Requirements Development Publication Evaluation Application Knowledge Spaces The View Mechanism Conclusions

VIMethCOE20 EVALUATION - MAINTENANCE Checking for Consistency General Argumentation Redefinition of the initial modules if the growth of the ontology requires it. Introduction Methodology Requirements Related Work Phases of the Methodology Requirements Development Publication Evaluation Application Knowledge Spaces The View Mechanism Conclusions

VIMethCOE21 APPLICATION PHASE 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. Introduction Methodology Requirements Related Work Phases of the Methodology Requirements Development Publication Evaluation Application Knowledge Spaces The View Mechanism Conclusions

VIMethCOE22 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:

VIMethCOE23 KNOWLEDGE SPACES 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. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE24 KNOWLEDGE SPACES 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. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE25 THE VIEW MECHANISM 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 Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE26 THE VIEW HIERARCHY 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. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism View Hierarchy Changes over Views Argumentation View Language Prototype Conclusions

VIMethCOE27 SITUATION IN VIEW HIERARCCHY 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 Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism View Hierarchy Changes over Views Argumentation View Language Prototype Conclusions

VIMethCOE28 ARGUMENTATION PROCESS 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 Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism View Hierarchy Changes over Views Argumentation View Language Prototype Conclusions

VIMethCOE29 DEFINITION OF VIEWS 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 Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism View Hierarchy Changes over Views Argumentation View Language Prototype Conclusions

VIMethCOE30 DEFINITION OF VIEWS 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. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism View Hierarchy Changes over Views Argumentation View Language Prototype Conclusions

VIMethCOE31 SOME TESTS 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. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism View Hierarchy Changes over Views Argumentation View Language Prototype Conclusions More Information:

VIMethCOE32 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 Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions

VIMethCOE33 A GOOD STATE OF THE ART, AND A GOOD PROPOSAL? 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. Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions Work in Progress Future Work Some Questions

VIMethCOE34 FUTURE WORK 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.) Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions Work in Progress Future Work Some Questions

VIMethCOE35 FUTURE WORK 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:: Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions Work in Progress Future Work Some Questions

VIMethCOE36 APPLICATION SCENARIO Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions Work in Progress Future Work Some Questions

VIMethCOE37 SOME QUESTIONS AND CONTACT Questions?: Contact: Ernesto Jiménez Ruiz Rafael Berlanga Llavorí Temporal Knowledge Bases Group Universidad Jaume I de Castellón (Spain) Introduction Methodology Requirements Related Work Phases of the Methodology Knowledge Spaces The View Mechanism Conclusions Work in Progress Future Work Some Questions