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Hall, David
Publications (8 of 8) Show all publications
Strömbäck, L., Ivanova, V. & Hall, D. (2011). Exploring Statistical Information for Applications-Specific Design and Evaluation of Hybrid XML storage. In: Databases, Knowledge, and Data Applications: . Paper presented at The Third International Conference on Advances in Databases, Knowledge, and Data Applications (pp. 108-113).
Open this publication in new window or tab >>Exploring Statistical Information for Applications-Specific Design and Evaluation of Hybrid XML storage
2011 (English)In: Databases, Knowledge, and Data Applications, 2011, p. 108-113Conference paper, Published paper (Refereed)
Abstract [en]

Modern relational database management systems provide hybrid XML storage, combining relational and native technologies. Hybrid storage offers many design alternatives for XML data and in this paper we explore how to aid the user in effective design of hybrid storage. In particular we investigate how the XML schema and statistical information about the data can support the storage design process. We present an extended version of our tool HShreX that uses statistical information about a data to enable fast evaluation of alternative hybrid design solutions. In addition we show the benefit of the approach by a first evaluation where we discuss how the tool aids in the storage design and evaluation process.

Keywords
XML, Hybrid XML management, indexing, storage design
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-74387 (URN)978-1-61208-115-1 (ISBN)
Conference
The Third International Conference on Advances in Databases, Knowledge, and Data Applications
Funder
Swedish Research Council
Available from: 2012-01-25 Created: 2012-01-25 Last updated: 2018-01-12
Strömbäck, L., Ivanova, V. & Hall, D. (2011). Using Statistical Information for Efficient Design and Evaluation of Hybrid XML Storage. International Journal On Advances in Software, 4(3-4), 389-400
Open this publication in new window or tab >>Using Statistical Information for Efficient Design and Evaluation of Hybrid XML Storage
2011 (English)In: International Journal On Advances in Software, ISSN 1942-2628, E-ISSN 1942-2628, Vol. 4, no 3-4, p. 389-400Article in journal (Refereed) Published
Abstract [en]

Modern relational database management systems provide hybrid XML storage, combining relational and native technologies. Hybrid storage offers many design alternatives for XML data. In this paper we explore how to aid the user in effective design of hybrid storage. In particular we investigate how the XML schema and statistical information about the data can support the storage design process. In our previous work, we presented our tool HShreX that uses statistical information about a data set to enable fast evaluation of alternative hybrid design solutions. In this paper, we extend this work by presenting more details about the tool and results of an extended evaluation. In particular, this paper gives a detailed presentation on how the tool aids in the storage design and evaluation process.

Place, publisher, year, edition, pages
IARIA, 2011
Keywords
XML, Hybrid XML management, indexing, storage design
National Category
Computer Systems
Identifiers
urn:nbn:se:liu:diva-102937 (URN)
Funder
Swedish Research Council
Available from: 2014-01-08 Created: 2014-01-08 Last updated: 2017-12-06
Hall, D. & Strömbäck, L. (2010). Generation of Synthetic XML for Evaluation of Hybrid XML Systems. In: Yoshikawa M, Meng X, Yumoto T, Ma Q, Sun L, Watanabe C (Ed.), Database Systems for Advanced Applications: 15th international conference, DASFAA 2010 International workshops: GDM, BenchmarX, MCIS, SNSMW, DIEW, UDM, Revised selected papers (pp. 191-202). Heidelberg: Springer
Open this publication in new window or tab >>Generation of Synthetic XML for Evaluation of Hybrid XML Systems
2010 (English)In: Database Systems for Advanced Applications: 15th international conference, DASFAA 2010 International workshops: GDM, BenchmarX, MCIS, SNSMW, DIEW, UDM, Revised selected papers / [ed] Yoshikawa M, Meng X, Yumoto T, Ma Q, Sun L, Watanabe C, Heidelberg: Springer , 2010, p. 191-202Chapter in book (Other academic)
Abstract [en]

This book constitutes the workshop proceedings of the 14th International Conference on Database Systems for Advanced Applications, DASFAA 2009, held in Brisbane, Australia, in April 2009. The volume contains six workshops, each focusing on specific research issues that contribute to the main themes of the DASFAA conference: The First International Workshop on Benchmarking of XML and Semantic Web Applications (BenchmarkX'09); The Second International Workshop on Managing Data Quality in Collaborative Information Systems (MCIS'09); The 1st International Workshop on Data and Process Provenance (WDPP'09); The First International Workshop on Privacy-Preserving Data Analysis (PPDA'09); The First International Workshop on Mobile Business Collaboration (MBC'09); and the First Ph.D. Workshop.

Place, publisher, year, edition, pages
Heidelberg: Springer, 2010
Series
LiH-RAD-R - Report / Department of Radiology, Linköping University, ISSN 0348-7679
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 6193
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-60206 (URN)10.1007/978-3-642-14589-6_20 (DOI)9783642042041 (ISBN)
Available from: 2010-10-07 Created: 2010-10-07 Last updated: 2013-04-12Bibliographically approved
Strömbäck, L., Hall, D., Åsberg, M. & Schmidt, S. (2009). Efficient XML data management for systems biology: Problems, tools and future vision. International Journal on Advances in Software, 2(2-3), 217-233
Open this publication in new window or tab >>Efficient XML data management for systems biology: Problems, tools and future vision
2009 (English)In: International Journal on Advances in Software, Vol. 2, no 2-3, p. 217-233Article in journal (Refereed) Published
Abstract [en]

Recently, XML has become a very popular representation format for exchange of data within systems biology. This has made large amounts of XML data available on the Internet and there is a need for tools to easily and efficiently manage this data. In this paper we give an overview of existing standards and analyze the situation. We describe two tools that have been developed to provide and experiment with data management for XML standardized data. We evaluate the efficiency for each of the tools, show that they provide more efficient data management and make a proposal for a future combined solution. The paper is an extended version of [1] where we put the work in a larger context of efficient XML data management for systems biology.

 

Place, publisher, year, edition, pages
IARIA, 2009
Keywords
XML; XQuery; hybrid XML management; graph processing; systems biology
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-60203 (URN)
Available from: 2010-10-07 Created: 2010-10-07 Last updated: 2014-06-24
Strömbäck, L., Åsberg, M. & Hall, D. (2009). HShreX - a Tool for Design and Evaluation of Hybrid XML Storage. PROCEEDINGS OF THE 20TH INTERNATIONAL WORKSHOP ON DATABASE AND EXPERT SYSTEMS APPLICATION, 417-421
Open this publication in new window or tab >>HShreX - a Tool for Design and Evaluation of Hybrid XML Storage
2009 (English)In: PROCEEDINGS OF THE 20TH INTERNATIONAL WORKSHOP ON DATABASE AND EXPERT SYSTEMS APPLICATION, p. 417-421Article in journal (Refereed) Published
Abstract [en]

XML is a commonly used data representation format for web applications. One of the reasons for the attractiveness of XML is its flexibility to store unstructured, semi-structured and structured data. However, supporting this flexibility is challenging from a technical perspective and several approaches have been proposed for storage of XML. The focus of this paper is hybrid storage, combining relational and native solutions as it allows many alternatives for designing the data model. The paper presents our tool HShreX that enables quick design and evaluation of alternative choices by annotating the XML schema. The main benefit of the tool is that it is easy to work with and provides quick design of storage model and import of data. The paper describes the main features of the tool and a use case where we discuss how the tool can be used to design, compare and evaluate Storage alternatives.

Place, publisher, year, edition, pages
IEEE COMPUTER SOC, 2009
Keywords
XML, native XML storage, XML shredding, Hybrid XML storage
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-58428 (URN)10.1109/DEXA.2009.33 (DOI)000275655300078 ()
Available from: 2010-08-12 Created: 2010-08-11 Last updated: 2014-06-24
Strömbäck, L., Hall, D. & Lambrix, P. (2007). A review of standards for data exchange within systems biology. Proteomics, 7(6), 857-867
Open this publication in new window or tab >>A review of standards for data exchange within systems biology
2007 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 7, no 6, p. 857-867Article in journal (Refereed) Published
Abstract [en]

The rapid increase in experimental data within systems biology has increased the need for exchange of data to allow analysis and comparison of larger datasets. This has resulted in a need for standardized formats for representation of such results and currently many formats for representation of data have been developed or are under development. In this paper, we give an overview of the current state of available standards and ontologies within systems biology. We focus on XML-based standards for exchange of data and give a thorough description of similarities and differences of currently available formats. For each of these, we discuss how the important concepts such as substances, interactions, and experimental data can be represented. In particular, we note that the purpose of a standard is often visible in the structures it provides for the representation of data. A clear purpose is also crucial for the success of a standard. Moreover, we note that the development of representation formats is parallel to the development of ontologies and the recent trend is that representation formats make more and more use of available ontologies.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2007
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-37738 (URN)10.1002/pmic.200600438 (DOI):000245331000005 ()17370264 (PubMedID)38205 (Local ID)38205 (Archive number)38205 (OAI)
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2018-01-13Bibliographically approved
Strömbäck, L. & Hall, D. (2006). An evaluation of the Use of XML for Representation, Querying, and Analysis of Molecular Interactions.. In: Lena Strömbäck,David Hall (Ed.), Current Trends in Database Technology - EDBT 2006 Workshops.: EDBT 2006 Workshop PhD, DataX, IIDB, IIHA, ICSNW, QLQP, PIM, PaRMa, and Reactivity on the Web, Munich, Germany, March 26-31, 2006, Revised Selected Papers edited by Tor (pp. 220-233). Berlin: Springer Verlag
Open this publication in new window or tab >>An evaluation of the Use of XML for Representation, Querying, and Analysis of Molecular Interactions.
2006 (English)In: Current Trends in Database Technology - EDBT 2006 Workshops.: EDBT 2006 Workshop PhD, DataX, IIDB, IIHA, ICSNW, QLQP, PIM, PaRMa, and Reactivity on the Web, Munich, Germany, March 26-31, 2006, Revised Selected Papers edited by Tor / [ed] Lena Strömbäck,David Hall, Berlin: Springer Verlag , 2006, p. 220-233Chapter in book (Other academic)
Abstract [en]

Currently, biology researchers rapidly generate new information on how genes, proteins and other molecules interact in living organisms. To completely understand the machinery underlying life it is necessary to integrate and analyze these large quantities of data. As one step in this direction, new standards for describing molecular interactions have been defined based on XML. This work evaluates the usage of the XML Query language XQuery for molecular interactions, as it would be of great benefit to the user to work directly on data represented in the new standards. We use and compare a set of available XQuery implementations, eXist, X-Hive, Sedna and QizX/open for querying and analysis on data exported from available databases. Our conclusion is that XQuery can easily be used for the most common queries in this domain but is not feasible for more complex analyses. In particular, for queries containing path analysis the available XQuery implementations have poor performance and an extension of the GTL package clearly outperforms XQuery. The paper ends with a discussion regarding the usability of XQuery in this domain. In particular we point out the need for more efficient graph handling and that XQuery also requires the user to understand the exact XML format of each dataset.

Place, publisher, year, edition, pages
Berlin: Springer Verlag, 2006
Series
Lecture notes in computer science ; 4254
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-35558 (URN)10.1007/11896548_20 (DOI)27566 (Local ID)3-540-46788-2 (ISBN)978-3-540-46790-8 (ISBN)978-3-540-46788-5 (ISBN)27566 (Archive number)27566 (OAI)
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2018-01-13Bibliographically approved
Strömbäck, L. & Hall, D. (2006). An evaluation of the use of XML for representation, querying, and analysis of molecular interactions. In: Torsten Grust, Hagen Höpfner, Arantza Illarramendi, Stefan Jablonski, Marco Mesiti, Sascha Müller, Paula-Lavinia Patranjan, Kai-Uwe Sattler, Myra Spiliopoulou and Jef Wijsen (Ed.), Current Trends in Database Technology – EDBT 2006: EDBT 2006 Workshops PhD, DataX, IIDB, IIHA, ICSNW, QLQP, PIM, PaRMA, and Reactivity on the Web, Munich, Germany, March 26-31, 2006, Revised Selected Papers (pp. 220-233). Springer Berlin/Heidelberg, 4254
Open this publication in new window or tab >>An evaluation of the use of XML for representation, querying, and analysis of molecular interactions
2006 (English)In: Current Trends in Database Technology – EDBT 2006: EDBT 2006 Workshops PhD, DataX, IIDB, IIHA, ICSNW, QLQP, PIM, PaRMA, and Reactivity on the Web, Munich, Germany, March 26-31, 2006, Revised Selected Papers / [ed] Torsten Grust, Hagen Höpfner, Arantza Illarramendi, Stefan Jablonski, Marco Mesiti, Sascha Müller, Paula-Lavinia Patranjan, Kai-Uwe Sattler, Myra Spiliopoulou and Jef Wijsen, Springer Berlin/Heidelberg, 2006, Vol. 4254, p. 220-233Chapter in book (Refereed)
Abstract [en]

Currently, biology researchers rapidly generate new information on how genes, proteins and other molecules interact in living organisms. To completely understand the machinery underlying life it is necessary to integrate and analyze these large quantities of data. As one step in this direction, new standards for describing molecular interactions have been defined based on XML. This work evaluates the usage of the XML Query language XQuery for molecular interactions, as it would be of great benefit to the user to work directly on data represented in the new standards. We use and compare a set of available XQuery implementations, eXist, X-Hive, Sedna and QizX/open for querying and analysis on data exported from available databases. Our conclusion is that XQuery can easily be used for the most common queries in this domain but is not feasible for more complex analyses. In particular, for queries containing path analysis the available XQuery implementations have poor performance and an extension of the GTL package clearly outperforms XQuery. The paper ends with a discussion regarding the usability of XQuery in this domain. In particular we point out the need for more efficient graph handling and that XQuery also requires the user to understand the exact XML format of each dataset.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2006
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 4254
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-48058 (URN)10.1007/11896548_20 (DOI)978-3-540-46788-5 (ISBN)978-3-540-46790-8 (ISBN)3-540-46788-2 (ISBN)
Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2018-02-09Bibliographically approved
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