Dr. Lucas Zamboulis Postdoctoral Researcher Tel:   +44 - (0)20 - 7763 2102 Fax:   +44 - (0)20 - 7242 2754 E-mail:   LKL (main) address: (map)   London Knowledge Lab 23-29 Emerald Street WC1N 3QS London       Birkbeck address: (map)   Department of Computer Science & Information Systems Birkbeck College Malet Street WC1E 7HX London

Short Bio

After finishing my B.Sc. in Informatics (A.U.Th. 2002), I did a Ph.D. in XML data transformation and integration at the Department of Computer Science and Information Systems at Birkbeck. I am a researcher in the Pervasive Navigation project and a member of the AutoMed project. I have supervised the Advances in Data Management course labs (Oracle Database Programming and Heterogeneous Data Integration), and have also supervise a number of MSc projects related to the AutoMed project. My research interests are in the area of data management, including XML and heterogeneous data transformation and integration, distributed query processing and optimisation and query language translation.

Ph.D. Research

My Ph.D. research involves the development of an XML schema and data transformation and integration approach. The approach uses the Both-As-View (BAV) data integration approach and is being developed within the AutoMed heterogeneous data integration system (see below).

The approach is able to use domain expert input for the automatic transformation and integration of XML data, supplied e.g. from schema matching tools or from correspondences to ontologies. The approach is able to utilise any subtyping information this input may contain. The approach is also able to avoid loss of data that may be caused by structural incompatibilities of the data sources.

The approach is currently being evaluated against a number of different settings: for the virtual integration of relational and XML bioinformatics data sources within the BioMap project, for the transformation and materialisation of crime data and for bioinformatics service reconciliation in the ISPIDER project.

Research Projects

• Pervasive Navigation (April 2009 - December 2009)

• ASSIST - Asssociation Studies assisted by Inference and Semantic Technologies (March 2008 - January 2009)

Project contributions:
• Integrate three medical relational databases into the ASSIST OWL-DL domain ontology using AutoMed
• Develop a SeRQL-to-IQL query language translator for AutoMed
• Provide efficient query processing for SeRQL queries submitted to the domain ontology, expanded using domain knowledge

• ISPIDER - In Silico Proteome Integrated Data Environment Resource (October 2004 - March 2008)

Project contributions:
• Developed wrappers allowing the interoperation of AutoMed with OGSA-DAI and OGSA-DQP
• Query processing and query optimisation in Automed, related to the ISPIDER integration setting
• Service deployment over the AutoMed query processor through ISPIDER Central
• Working on bioinformatics service reconciliation and the interoperation of AutoMed and Taverna

• AutoMed - Automatic Generation of Mediator Tools for Heterogeneous Database Integration (mailing list) (April 2003 - December 2009)
  

Project contributions:
• Query processing (reformulation, optimisation, planning, parallelisation, query language translation, query language semantics)
• XMLDSS schema type (supports DTD and XML Schema), XML wrappers (DOM, SAX, XQuery for eXist NXD)
• XML schema and data transformation and integration

Collaborations

• MyPlan - Personal Planning for Learning throughout Life
  
  Collaborated with members of the MyPlan project to evaluate my ontology-assisted service reconciliation approach against an e-Learning data transformation setting. In particular, my approach was evaluated in the exchange of data between e-learning systems that expose their repositories using services that conform to different ontologies.


BioMap - BioMap Data Warehouse: Functional and Structural Resources for BioInformatics

Collaborated with members of the BioMap project to evaluate my XML data transformation and integration approach against real-world biological data sources. In particular, a number of relational data sources were semi-automatically integrated under an XMLDSS global schema, given input from a BioMap domain expert.


Crime Informatics

Collaborated with Prof. Peter King to evaluate my XML data transformation and integration approach against real-world crime data. In particular, the XML output of a relational data source was first transformed to a target XML format, and was then materialised.

     Ph.D. Thesis

1. L. Zamboulis
   XML data transformation and integration - A schema transformation approach (pdf)
   Birkbeck College, University of London, 2009

     Peer-Reviewed Journals

1. L. Zamboulis, N. Martin and A. Poulovassilis
   Query Performance Evaluation of an Architecture for Fine-Grained Integration of Heterogeneous Grid Data Sources (pdf preprint,DOI)
   Future Generation Computer Systems 26(8), pp 1073-1091, 2010
2. J.A. Siepen, K. Belhajjame, J.N. Selley, S. Embury, N.W. Paton, C. Goble, S.G. Oliver, R. Stevens, L. Zamboulis,
   N. Martin, A. Poulovassillis, P. Jones, R. Cote, H. Hermjakob, M. Pentony, D.T. Jones, C. Orengo and S.J. Hubbard
   ISPIDER Central: an integrated database web-server for proteomics (pdf, BibTeX)
   Nucleic Acids Research 36(2), pp 485-490, 2008

     Peer-Reviewed Conferences/Workshops

1. L. Zamboulis, A. Poulovassilis, J. Wang
   Ontology-Assisted Data Transformation and Integration (pdf, ps, pps, BibTeX)
   Proc. ODBIS Workshop at VLDB'08, pp 29-36, August 2008
2. L. Zamboulis, A. Poulovassilis, G. Roussos
   Flexible Data Integration and Ontology-Based Data Access to Medical Records (pdf, ps, BibTeX)
   Proc. IEEE Int. Conference on Bioinformatics and BioEngineering (BIBE'08), pp 1-6, October 2008
3. L. Zamboulis, N. Martin, A. Poulovassilis
   A Uniform Approach to Workflow and Data Integration (paper pdf, poster)
   Proc. U.K. e-Science All Hands Conference 2007, pp 656-663, September 2007
4. L. Zamboulis, N. Martin, A. Poulovassilis
   Bioinformatics Service Reconciliation By Heterogeneous Schema Transformation (pdf, ps, pps, BibTeX)
   Proc. Data Integration in the Life Sciences 2007. LNCS/LNBI 4544, pp 89-104, June 2007
5. L. Zamboulis, H. Fan, K. Belhajjame, J. Siepen, A. Jones, N. Martin, A. Poulovassilis, S. Hubbard, S. M. Embury, N. W. Paton
   Data Access and Integration in the ISPIDER Proteomics Grid (pdf, ps, BibTeX)
   Proc. Data Integration in the Life Sciences 2006. LNCS/LNBI 4075, pp 3-18, July 2006
6. L. Zamboulis, A. Poulovassilis
   Information Sharing for the Semantic Web - a Schema Transformation Approach (pdf, ps, BibTeX)
   Proc. DISWeb Workshop, CAiSE'06 Workshop Proceedings , pp 275-289, June 2006
7. K. Belhajjame, S.M. Embury, H. Fan, C. Goble, H. Hermjakob, S.J. Hubbard, D. Jones, P. Jones, N. Martin, S. Oliver, C. Orengo, N.W. Paton, A. Poulovassilis, J. Siepen, R.D. Stevens, C. Taylor, N. Vinod, L. Zamboulis, W. Zhu
   Proteome Data Integration: Characteristics and Challenges (pdf)
   Proc. U.K. e-Science All Hands Conference 2005, pp 418-425, September 2005
8. M. Maibaum, L. Zamboulis, G. Rimon, N. Martin, A. Poulovassilis
   Cluster based Integration of Heterogeneous Biological Databases using the AutoMed toolkit (pdf, ps, BibTeX)
   Proc. Data Integration in the Life Sciences 2005. LNCS/LNBI 3615, pp 191-207, July 2005
9. L. Zamboulis, A. Poulovassilis
   Using AutoMed for XML Data Transformation and Integration (pdf, ps, BibTeX)
   Proc. DIWeb Workshop, at CAiSE'04. LNCS 3084, pp 58-69, June 2004
10. L. Zamboulis
    XML Data Integration By Graph Restructuring (pdf, ps, BibTeX)
    Proc. BNCOD21, LNCS 3112, pp 57-71, July 2004

     Technical Reports

1. L. Zamboulis, S. Mittal, E. Jasper, H. Fan, A. Poulovassilis
   Processing IQL Queries in the AutoMed toolkit v1.2 (pdf, ps)
   AutoMed Technical Report 35, July 2008
2. A. Poulovassilis, L. Zamboulis
   A Tutorial on the IQL Query Language v1.2 (pdf, ps)
   AutoMed Technical Report 28, July 2008
3. E. Jasper, A. Poulovassilis, L. Zamboulis, H. Fan, S. Mittal
   Processing IQL Queries and Migrating Data in the AutoMed toolkit v1.1 (pdf, ps)
   AutoMed Technical Report 20, October 2006
4. E. Jasper, A. Poulovassilis, L. Zamboulis
   Processing IQL Queries and Migrating Data in the AutoMed toolkit v1.0 (pdf, ps)
   AutoMed Technical Report 20, July 2003

     Technical Reports (long versions of published papers)

1. L. Zamboulis, A. Poulovassilis, J. Wang
   Ontology-Assisted Data Transformation and Integration (pdf, ps)
   Birkbeck Technical Report BBKCS-08-05, July 2008
2. L. Zamboulis, N. Martin, A. Poulovassilis
   Query Processing and Optimisation in Integrated Heterogeneous Grid Resources (pdf, ps)
   Birkbeck Technical Report BBKCS-08-04, July 2008
3. L. Zamboulis, N. Martin, A. Poulovassilis
   Bioinformatics Service Reconciliation By Heterogeneous Schema Transformation (pdf,ps)
   Birkbeck Technical Report BBKCS-07-03, March 2007
4. L. Zamboulis, A. Poulovassilis
   Information Sharing for the Semantic Web - A Schema Transformation Approach (pdf,ps)
   AutoMed Technical Report 31, February 2006
5. M. Maibaum, L. Zamboulis, G. Rimon, C. Orengo, N. Martin, A. Poulovassilis
   Cluster based integration of Heterogeneous Biological Databases using the AutoMed toolkit (pdf)
   Birkbeck Technical Report BBKCS-04-07, October 2004
6. L. Zamboulis, A. Poulovassilis
   XML Data Integration By Graph Restructuring (pdf, ps)
   AutoMed Technical Report 27, February 2004

     Ph.D. Progress Reports

1. XML Data Transformation & Integration for the Semantic Web. Viva Report, Birkbeck College, July 2005.
2. XML Data Transformation & Integration For The Semantic Web. Viva Report, Birkbeck College, July 2004.
3. XML Schema Matching & XML Data Migration & Integration: A Step Towards The Semantic Web Vision. Viva Report, Birkbeck College, October 2003.

     Reviewing

• UK e-Science All Hands Meeting 2009
• E-Infrastructures and Technologies for Lifelong Learning
• Pervasive and Mobile Computing Journal (PMC) 2009
• International Conference on Conceptual Modelling (ER) 2008 (external)
• International Workshop on Integrative Bioinformatics 2007 (external)
• Transactions on Knowledge and Data Engineering (TKDE) 2006 (external)

     Invited Talks

1. Data Transformation & Integration (pdf,pps)
   Vienna University of Economics & Business Administration, Vienna, 14th April 2005
2. Using AutoMed for XML Data Transformation & Integration (pdf, pps)
   University of Glasgow, 13th December 2004

     Posters

1. A Uniform Approach to Bioinformatics Workflow and Data Integration (poster)
   ISMB retreat, Cambridge, 19-20 June 2007
2. Integration and Analysis of Biological Data Sources (pdf)
   ISMB retreat, Cambridge, 28 June 2005

     Presentations - other

1. A Uniform Approach to Data and Workflow Integration for the Life Sciences (abstract,presentation)
   Hellenic Bioinformatics & Medical Informatics Meeting, 4-5 October 2007
2. XML Data Transformation and Integration - A Schema Transformation Approach
   London Knowledge Lab Ph.D. Networking Session, London, 17th May 2007
3. Data Access and Integration in the ISPIDER Proteomics Grid (pdf,pps)
   Bioinformatics Retreat, Sussex, 6th June 2006
4. ISPIDER: Grid-based Integration of Biological Data (pdf,pps)
   Dept. of Informatics, Aristotle University of Thessaloniki, 14th April 2006
5. Data Access and Integration in the ISPIDER Proteomics Grid (pdf,pps)
   2nd DIALOGUE Workshop, e-Science Institute, Edinburgh, 8-9 February 2006
6. ISPIDER: Grid-Based Integration of Biological Data Using AutoMed (pdf, pps)
   Bioinformatics and the DAIT (BioDA) Project Workshop, CCLRC Daresbury Laboratory, Warrington, Cheshire, 26th September 2005
7. The BioMap Data Warehouse: Integration of Relational & XML Data Using AutoMed (pdf,pps)
   Birkbeck School of Comp. Science & I.S., Research Day, 11th July 2005
8. ISPIDER: Grid-Based Integration of Biological Data Using AutoMed (pdf,pps)
   ISMB retreat, Cambridge, 28th June 2005

     Presentations - publications

1. Ontology-Assisted Data Transformation and Integration
   ODBIS Workshop, at VLDB'08, 23rd August 2008, Auckland, New Zealand
2. A Uniform Approach to Bioinformatics Workflow and Data Integration
   U.K. e-Science All Hands Conference 2007, Nottingham, September 2007
3. Bioinformatics Service Reconciliation By Heterogeneous Schema Transformation
   Data Integration in the Life Sciences 2007, Philadelphia, June 2007
4. Data Access and Integration in the ISPIDER Proteomics Grid
   Data Integration in the Life Sciences 2006, EBI, Hinxton, July 2006
5. Information Sharing for the Semantic Web - a Schema Transformation Approach
   DISWeb Workshop, at CAiSE'06, Luxembourg, June 2006
6. Using AutoMed for XML Data Transformation and Integration
   DIWeb Workshop, at CAiSE'04, Riga, June, 2004
7. XML Data Integration By Graph Restructuring
   BNCOD21, Edinburgh, July 2004

     Presentations - project meetings

1. Project update (pdf,pps)
   ISPIDER project meeting, Manchester, 30th April 2007
2. Bionformatics Service Alignment By Schema Transformation (pdf,pps)
   AutoMed project meeting, Imperial College, London, 2nd February 2007
3. Query Processing in AutoMed (pdf,pps)
   AutoMed project meeting, Imperial College, London, 2nd February 2007
4. Integration, Optimisation and Evolution in the ISPIDER Proteomics Grid (pdf,pps)
   ISPIDER project meeting, EBI, Cambridge, 17th November 2006
5. Data Access & Integration in the ISPIDER Proteomics Grid (pdf,pps)
   ISPIDER project meeting, UCL, London, 15th May 2006
6. Data Integration Using Automed, OGSA-DAI & DQP (pdf,pps)
   ISPIDER project meeting, Wellcome Trust Centre, Hinxton, Cambridge, 14th July 2005
7. The AutoMed Query Processor (pdf, pps)
   AutoMed project meeting, Imperial College, London, 16th February 2005
8. XML Data Transformation & Integration (pdf, pps)
   AutoMed project meeting, Birkbeck College, London, 15th December 2004

     Conference/Workshop Attendances

• Ontologies-based Techniques for DataBases in Inf. Systems and Knowledge Systems (ODBIS), at VLDB'08, 23rd August 2008, Auckland, New Zealand
• All Hands Conference 2007, 10-13 September 2007, Nottingham
• Data Integration in the Life Sciences 2007, 27-29 June 2007, Univ. of Pennsylvania, Philadelphia
• ISMB Retreat, 19-20 June 2007, EBI, Hinxton, Cambridge
• Data Integration in the Life Sciences 2006, 20-22 July 2006, EBI, Hinxton
• DISWeb Workshop, at CAiSE'06, 5 June 2006 Luxembourg
• 2nd DIALOGUE Workshop, 8-9 February 2006, e-Science Institute, Edinburgh
• ISMB Retreat, 27-28 June 2005, EBI, Hinxton
• 2nd IST Workshop on Metadata Management in Grid and P2P systems (MMGPS'04), 17th December 2004, London
• BioInformatics Workshop at INA, CERTH, 30th September- 1st October 2004, Thessaloniki, Greece
• British National Conference On Databases (BNCOD'04), 7-9 July 2004, Edinburgh
• International Conference on Advanced Information Systems Engineering (CAiSE'04), 7-11 June 2004, Riga, Latvia
• Data Integration over the Web Workshop (DIWeb), at CAiSE'04, 8th June 2004, Riga, Latvia

     MSc Project Supervision (with Prof. Alexandra Poulovassilis)

1. Lambert Dean (2007)
   Implementation of Schema and Data Evolution in the AutoMed Heterogeneous Data Integration Toolkit
2. Dimitris Fourkiotis (2007)
   Implementation of Parallel and Distributed Query Processing in the AutoMed Heterogeneous Data Integration Toolkit (pdf)
3. Jamie Walters (2007)
   Implementation of an SQL to IQL Query Translation Component for the AutoMed Toolkit (pdf)
4. Dheeraj Mudgil (2006)
   Implementation of Schema Evolution in the AutoMed Heterogeneous Data Integration Toolkit

     Lecturing

• XML Databases (Advances in Data Management course, 2007, 2008)

     Lab Supervision

• Oracle Database Programming (Advances in Data Management course, 2007, 2008)
  1. Oracle PL/SQL and Database Programming
  2. Triggers and Java in Oracle
  3. Oracle XML DB - XML in Oracle 10g
• Heterogeneous Data Integration Lab (Advances in Data Management course, 2004-2008)
  1. Example Integration
  2. Exercise Integration

Links

• Research, tech and other links