Extending SD-Core for Ontology-based Data Integration

This paper describes the main elements of a functional platform for building Semantic Web Applications, the Semantic Directory (additional information can be found at http://khaos.uma.es/SD-Core). A Semantic Directory provides a resource directory, in which web resources are registered and their semantics published. Using the Semantic Directories we provide a solution for publishing the semantics of resources, and interoperating them with some other applications in the same or different domains. The main idea behind this proposal is to help developers build Semantic Web applications by providing them with functional components for this task. This paper also describes some applications that have been developed using an SD-Core extension: SD-Data. Then, we describe the instantiation of the Khaos Ontology-based Mediation Framework (KOMF) in the Systems Biology domain. This framework provides an architecture that enables the research on the development of ontology-based mediators. Thus, an ontology-based mediator has been produced that has demonstrated its utility in two applications developed in the Amine System Project using the SD-Data for registering semantics: AMMO-Prot and SBMM Assistant. The use of ontologies is limited in the current version of the mediator, but its development as a framework enables the implementation of improvements based on the use of reasoning.

[1]  Kai-Uwe Sattler,et al.  Concept-based querying in mediator systems , 2005, The VLDB Journal.

[2]  Christof Bornhövd,et al.  A Prototype for Metadata-Based Integration of Internet Sources , 1999, CAiSE.

[3]  Tomasz Ksiezyk,et al.  InfoSleuth: agent-based system for data integration and analysis , 2001, 25th Annual International Computer Software and Applications Conference. COMPSAC 2001.

[4]  David Maier,et al.  Magic sets and other strange ways to implement logic programs (extended abstract) , 1985, PODS '86.

[5]  Peter Haase,et al.  OMV – Ontology Metadata Vocabulary , 2005 .

[6]  Yun Peng,et al.  Finding and Ranking Knowledge on the Semantic Web , 2005, SEMWEB.

[7]  Tore Risch,et al.  Distributed data integration by object‐oriented mediator servers , 2001, Concurr. Comput. Pract. Exp..

[8]  Jennifer Widom,et al.  The TSIMMIS Approach to Mediation: Data Models and Languages , 1997, Journal of Intelligent Information Systems.

[9]  M. del Roldan-Garcia,et al.  DBOWL: Towards a Scalable and Persistent OWL Reasoner , 2008, 2008 Third International Conference on Internet and Web Applications and Services.

[10]  Alon Y. Halevy,et al.  Answering queries using views: A survey , 2001, The VLDB Journal.

[11]  José Francisco Aldana Montes,et al.  AMMO-Prot: amine system project 3D-model finder , 2008, BMC Bioinformatics.

[12]  Didier Rognan,et al.  sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank , 2006, J. Chem. Inf. Model..

[13]  J. Meigs,et al.  WHO Technical Report , 1954, The Yale Journal of Biology and Medicine.

[14]  Wolfram Wöß,et al.  A Semantic Web middleware for Virtual Data Integration on the Web , 2008, ESWC.

[15]  H. Kitano.  Systems Biology: A Brief Overview , 2002, Science.

[16]  York Sure-Vetter,et al.  Ontology Mapping - An Integrated Approach , 2004, ESWS.

[17]  R. Ramakrishnan,et al.  An Optimizer for Heterogeneous Systems with NonStandard Data and Search Capabilities , 1996 .

[18]  Silvana Castano,et al.  Information Integration: The MOMIS Project Demonstration , 2000, VLDB.

[19]  José Francisco Aldana Montes,et al.  SD-Core: Generic Semantic Middleware Components for the Semantic Web , 2008, KES.

[20]  Asunción Gómez-Pérez,et al.  Oyster: sharing and re-using ontologies in a peer-to-peer community , 2006, WWW '06.

[21]  José Francisco Aldana Montes,et al.  SD-Core: A Semantic Middleware Applied to Molecular Biology , 2008, OTM Workshops.

[22]  Diego Calvanese,et al.  The Description Logic Handbook: Theory, Implementation, and Applications , 2003, Description Logic Handbook.

[23]  Philippe Bonnet,et al.  The distributed information search component (Disco) and the World Wide Web , 1997, SIGMOD '97.

[24]  Vipul Kashyap,et al.  OBSERVER: An Approach for Query Processing in Global Information Systems Based on Interoperation Across Pre-Existing Ontologies , 2000, Distributed and Parallel Databases.