A Viewbased Methodology for Collaborative Ontology Engineering VIMeth

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

INTRODUCTION ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü 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 VIMeth. COE 2

NEW DIMENSIONS IN THE DEVELOPMENT ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology 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. ü Knowledge Spaces ü The View Mechanism ü Conclusions VIMeth. COE 3

ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü Conclusions HOW TO ACHIEVE A GOOD BALANCE BETWEEN DIMENSIONS? 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 VIMeth. COE 4

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

LOCAL ADAPTATION ü Introduction ü Methodology Requirements ü Modularization ü Local Adaptation ü Knowledge Abstraction ü Views ü Argumentation and Consensus ü Related Work ü Phases of the Methodology 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. ü Knowledge Spaces ü The View Mechanism ü Conclusions i. e. : Protégé editor VIMeth. COE 6

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

VIEWS (PERSONAL MODULES) ü Introduction ü Methodology Requirements ü Modularization ü Local Adaptation ü Knowledge Abstraction ü Views ü Argumentation and Consensus ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü 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 VIMeth. COE – Reuse of Knowledge 8

ARGUMENTATION AND CONSENSUS ü Introduction ü Methodology Requirements ü Modularization ü Local Adaptation ü Knowledge Abstraction ü Views ü Argumentation and Consensus ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism 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. ü Conclusions VIMeth. COE 9

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

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

COLLABORATIVE APPROACHES ü Introduction ü Methodology Requirements ü Related Work ü Classic Methodologies ü Collaborative Approaches ü Web-based Systems ü Characteristics ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü Conclusions Co 4, DILIGENT, HCOME, Divergence Occurrences Methodology, (KA)2, the Onto. Edit 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). VIMeth. COE 12

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

CHARACTERISTICS OF RELATED WORK ü Introduction MODULARIZATION LOCAL ADAPTATION DILIGENT HCOME ü Collaborative Approaches Div. Occurr. Onto. Edit ü Web-based Systems Ontolingua ü Characteristics Web. Onto Web. ODE ü Methodology Requirements ü Related Work ü Classic Methodologies ü Phases of the Methodology ü Knowledge Spaces CO 4 (KA)2 KNOWLEDGE ABSTRACTION VIEWS ARGUMENT. CONSENSUS Wiki@nt VIMeth. COE ü The View Mechanism ü Conclusions VIMeth. COE 14

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 VIMeth. COE 15

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

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

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

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

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

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

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

KNOWLEDGE SPACES ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü 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. VIMeth. COE 23

KNOWLEDGE SPACES ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü 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. VIMeth. COE 24

THE VIEW MECHANISM ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü 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 VIMeth. COE of the proposed 25

THE VIEW HIERARCHY ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism 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. ü View Hierarchy ü Changes over Views ü Argumentation ü View Language ü Prototype ü Conclusions VIMeth. COE 26

SITUATION IN VIEW HIERARCCHY ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü View Hierarchy ü Changes over Views ü Argumentation ü View Language ü Prototype ü 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 VIMeth. COE inconsistencies conflict view. 27

ARGUMENTATION PROCESS ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü View Hierarchy ü Changes over Views ü Argumentation ü View Language ü Prototype ü 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 VIMeth. COE 28

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

DEFINITION OF VIEWS ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü View Hierarchy Query definitions are paths over the ontology graph with operators over concepts, properties and instances. – “CPT_II Protein”/{component. Of=“Mithocondrial. Me mbrane”} ü Changes over Views ü Argumentation ü View Language ü Prototype ü Conclusions Inference rules may involve the extraction of concepts, properties and instances that are not explicitly indicated in. VIMeth. COE the views: 30

SOME TESTS ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü View Hierarchy ü Changes over Views ü Argumentation ü View Language ü Prototype ü Conclusions Some tests have been realized with a simple prototype. – A plug-in that connects the semistructured database G with the ontology editor Protégé – Views are defined over small ontologies. More Information: http: //www 3. uji. es/~ejimenez/GProtege. Plugin/ VIMeth. COE 31

CONCLUSIONS ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü 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 32 requirements VIMeth. COE

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

FUTURE WORK ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü Conclusions ü Work in Progress 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. ü Future Work ü Some Questions – 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 VIMeth. COE Cuenca Grau. et. al. ) 34

FUTURE WORK ü Introduction ü Methodology Requirements ü Related Work ü Phases of the Methodology ü Knowledge Spaces ü The View Mechanism ü Conclusions ü Work in Progress ü Future Work ü 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: : VIMeth. COE 35

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

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