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  • 1.
    Ellkvist, Tommy
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Koop, David
    University of Utah.
    Freire, Juliana
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. University of Utah.
    Silvia, Claudiu
    University of Utah.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Using Mediation to Achieve Provenance Interoperability2009In: 2009 Congress on Services - I, IEEE Press, 2009, p. 291-298Conference paper (Refereed)
    Abstract [en]

    Provenance is essential in scientific experiments. It contains information that is key to preserving the data, to determining their quality and authorship, and to reproduce as well as validate the results. In complex experiments and analyses, where multiple tools are used to derive data products, provenance captured by these tools must be combined in order to determine the complete lineage of the derived products. In this paper we describe a mediator-based architecture for integrating provenance information from multiple sources. This architecture contains two key components: a global mediated schema that is general and capable of representing provenance information represented in different model; and describe a new system-independent query API that is general and able to express complex queries over provenance information from different sources. We also present a case study where we show how this model was applied to integrate provenance from three provenance-enabled systems and discuss the issues involved in this integration process.

  • 2.
    Ellkvist, Tommy
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Didier Linz, Lauro
    University of Utah.
    Freire, Juliana
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. University of Utah.
    A First Study on Strategies for Generating Workflow Snippets2009In: The first International Workshop on Keyword Search ob structured data KEYS 2009, Collocated with ACM SIGMOD/PODS, Association for Computing Machinery (ACM), 2009, p. 15-20Conference paper (Refereed)
    Abstract [en]

    Workflows are increasingly being used to specify computational tasks, from simulations and data analysis to the creation of Web mashups. Recently, a number of public workflow repositories have become available, for example, myExperiment for scientific workflows, and Yahoo! Pipes. Workflow collections are also commonplace in many scientific projects. Having such collections opens up new opportunities for knowledge sharing and re-use. But for this to become a reality, mechanisms are needed that help users explore these collections and locate useful workflows. Although there has been work on querying workflows, not much attention has been given to presenting query results. In this paper, we take a first look at the requirements for workflow snippets and study alternative techniques for deriving concise, yet informative snippets.

  • 3.
    Ellqvist, Tommy
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Koop, David
    University of Utah, USA.
    Freire, Juliana
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. University of Utah.
    Silva, Claudio
    University of Utah, USA.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Using Mediation to Achieve Provenance Interoperability2008In: 2009 World Conference on Services - I, IEEE , 2008, p. 398-399Conference paper (Refereed)
    Abstract [en]

    Provenance is essential in scientific experiments. It contains information that is key to preserving the data and to determine its quality and uthorship. In complex experiments and analyses, where multiple tools are used to derive data products, provenance captured by these tools must be combined in order to determine the complete lineage of the derived products. We propose a mediator-based architecture to integrate provenance information from multiple sources, which contains two key components: a global mediated schema that is general and capable of representing provenance information represented in different models; and an expressive query interface that supports complex queries over provenance information spread over multiple different sources. We also present a case study where we show how this model was applied to integrate provenance from three provenance-enabled systems.

  • 4.
    Hall, David
    et al.
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Generation of Synthetic XML for Evaluation of Hybrid XML Systems2010In: 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.

  • 5.
    Ivanova, Valentina
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Creating Infrastructure for Tool-Independent Querying and Exploration of Scientific Workflows2011In: 7th IEEE International Conference on e-Science, IEEE , 2011, p. 287-294Conference paper (Refereed)
    Abstract [en]

    Many scientific experiments produce an enormous amount of data that needs to be explored. Scientific workflows and tools for managing workflows have been designed to streamline the computational processes that manipulate this data, from acquisition to analysis. However, the fact that each system has its own workflow format has greatly hampered efficient sharing and re-use. To address this problem, we propose a general model for workflows, based on OPM, which combines features from popular scientific workflow systems. We use this model to build infrastructure that supports system-agnostic workflow repositories. We describe the implementation of the infrastructure and present an experimental evaluation of its performance. We show that the proposed model and its implementation provide efficient support for queries over large repositories.

  • 6.
    Jönsson, Arne
    et al.
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Robust Interaction through Partial Interpretation and Dialogue Management,1998In: Proceedings of Coling-ACL'98, Montrèal, Canada, 1998Conference paper (Refereed)
  • 7.
    Köhn, Dagmar
    et al.
    Institute for Computer Science Universität Rostock.
    Strömbäck, Lena
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    A method for Semi-automatic Standard Integration in Systems Biology2008In: Database and Expert Systems Applications,2008 / [ed] Bhowmick, Sourav S., Küng, Josef, Wagner, Roland, Heidelberg, Germany: Springer , 2008, p. 745-752Conference paper (Refereed)
    Abstract [en]

    The development of standards for biological pathways has led to a huge amount of model data stored in a variety of different formats represented in XML (e. g. SBML) or OWL (e. g. BioPAX). As a result, there is an urgent need for the conversion of data between different formats, especially between XML and OWL data. The fact that that transformation is hard to realize hampers the integration of data in the area. Addressing this problem, the following article proposes a general, semi-automatic solution by suggesting the transformation of XML Schema based data into an OWL format. The general solution presented here will support biologists by offering them a way to query data of any format and as well compare different data files or schemas to each other using OWL as a common format for matching and providing a backwards transformation to XML Schema. The paper presents a first architectural approach and its prototype implementation. The evaluation showed that the approach is promising.

  • 8.
    Köhn, Dagmar
    et al.
    Rostock Universität.
    Strömbäck, Lena
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    A schema matching architecture for the bioinformatics domain2006In: Winter Simulation Conference,2006, New York: ACM , 2006Conference paper (Refereed)
  • 9.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Teaching databases to hundreds of engineering students2007In: Workshop on Computer Science Education,2007, 2007Conference paper (Refereed)
    Abstract [en]

    Yearly, we teach basic database courses to about two to four hundred engineering students with different backgrounds and different requirements. We also have a limited amount of teacher resources. To deal with this situation we have organized our course topics in the form of modules. A database course is then defined by a number of modules together with a mini-project. We discuss this organization and give an evaluation.

  • 10.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Where is my protein? - Issues in Information Integration2008In: BIOFORUM Europe, ISSN 1611-597X, Vol. 12, no 1-2, p. 24-25Article in journal (Other (popular science, discussion, etc.))
  • 11.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Where is my protein? - Issues in Information Integration2007In: BIOFORUM Europe, ISSN 1611-597X, Vol. 11, no 7-8, p. 24-26Article in journal (Other (popular science, discussion, etc.))
  • 12.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Information integration in bioinformatics with ontologies and standards2009In: Semantic Techniques for the Web: The REWERSE perspective, Springer Berlin/Heidelberg, 2009, 1, p. 343-376Chapter in book (Refereed)
    Abstract [en]

    New experimental methods allow researchers within molecular and systems biology to rapidly generate larger and larger amounts of data. This data is often made publicly available on the Internet and although this data is extremely useful, we are not using its full capacity. One important reason is that we still lack good ways to connect or integrate information from different resources. One kind of resource is the over 1000 data sources freely available on the Web. As most data sources are developed and maintained independently, they are highly heterogeneous. Information is also updated frequently. Other kinds of resources that are not so well-known or commonly used yet are the ontologies and the standards. Ontologies aim to define a common terminology for a domain of interest. Standards provide a way to exchange data between data sources and tools, even if the internal representations of the data in the resources and tools are different. In this chapter we argue that ontological knowledge and standards should be used for integration of data. We describe properties of the different types of data sources, ontological knowledge and standards that are available on the Web and discuss how this knowledge can be used to support integrated access to multiple biological data sources. Further, we present an integration approach that combines the identified ontological knowledge and standards with traditional information integration techniques. Current integration approaches only cover parts of the suggested approach. We also discuss the components in the model on which much recent work has been done in more detail: ontology-based data source integration, ontology alignment and integration using standards. Although many of our discussions in this chapter are general we exemplify mainly using work done within the REWERSE working group on Adding Semantics to the Bioinformatics Web.

  • 13.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Jakoniené, Vaida
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Biological Ontologies2007In: Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences / [ed] Christopher J.O. Baker and Kei-Hoi Cheung, Springer , 2007, p. 85-99Chapter in book (Refereed)
    Abstract [en]

    Biological ontologies define the basic terms and relations in biological domains and are being used among others, as community reference, as the basis for interoperability between systems, and for search, integration, and exchange of biological data. In this chapter we present examples of biological ontologies and ontology-based knowledge, show how biological ontologies are used and discuss some important issues in ontology engineering.

  • 14. Laux, Fritz
    et al.
    Strömbäck, LenaLinköping University.
    The Second International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 20102010Conference proceedings (editor) (Other academic)
  • 15. Laux, Fritz
    et al.
    Strömbäck, LenaLinköping University.
    The Second International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 20102010Conference proceedings (editor) (Other academic)
  • 16. Sauro, H M
    et al.
    Uhrmacher, A
    Harel, D
    Hucka, M
    Kwiatkowska, M
    Mendes, P
    Strömbäck, Lena
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Tyson, J J
    Challenges for Modeling and Simulation Methods in Systems Biology.2006In: Winter Simulation Conference,2006, New York: ACM , 2006, p. 1720-Conference paper (Refereed)
  • 17.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    A classification for comparing standardized XML data2006In: Database and Expert Systems Applications, 2006. DEXA '06, Los Alamitos, CA, USA: IEEE Computer Society, 2006, p. 517-524Conference paper (Refereed)
    Abstract [en]

    The increasing amount of XML data provided via the Web imposes a large need for efficient data exchange and import. This has led to an increasing interest in XML standards within a large number of areas. However, in most application domains there are several competing standards capturing the same kind of information. This work presents a method for classification and comparison of standards within an area. The method can be applied to XML-standards in any domain. We report on the situation for two different areas, molecular interactions and digital television and use our method to compare the standards within the two domains. The classification gives information on how similar the standards are, in terms of information content and structure. This information is useful for deciding which kind of methods are interesting for providing automatic matching and efficient development of tools for import of standardised data

  • 18.
    Strömbäck, Lena
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    A method for comparison of standardized information within systems biology2006In: WSC '06 Proceedings of the 38th conference on Winter simulation, New York: ACM , 2006, p. 1603-1610Conference paper (Refereed)
  • 19.
    Strömbäck, Lena
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    Possibilities and Challenges Using XML Technology for Storage and Integration of Molecular Interactions2005In: International Workshop on Database and Expert Systems Applications DEXA05,2005, Los Alamitos, CA, USA: IEEE Computer Society , 2005, p. 575-Conference paper (Refereed)
    Abstract [en]

    The amount of data emerging from experiments on molecular and protein interactions is rapidly growing. It is of high importance to understand these datasets, putting them together to meaningful pathways describing some aspects of the cell physiology. Currently, there is a big interest in XML representations of protein interaction and molecular pathways. New standards, SBML, PSI MI and BioPAX are under development and it is of high importance to build tools for easy integration and analysis of data represented in these standards. There are currently two main approaches for storage of data represented within XML, one is to base the tools directly on XML while the other is to translate the information into a relational database. In this paper we report on experiments with these approaches for storage and analysis of molecular interaction data represented in the standards. The results give important pointers to the possibility of building easy to use tools.

  • 20.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Så tycker kvinnor och män om våra utbildningar2004Report (Other academic)
    Abstract [sv]

    Idag finns ett antal utbildningar inom data på Linköpings universitet med olika inriktning och olika andel kvinnor och män. Under 1998 gjordes en undersökning om hur kvinnor och män trivs på dessa utbildningar. Rapporten sammanfattar denna undersökning och reflekterar över vilka av resultaten som kan påverkas av att man tilhör en minoritetsgrupp på utbildningen.

  • 21.
    Strömbäck, Lena
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems.
    XML representations of pathway data: a comparison2004In: The ACM SIGIR04 Workshop on Search and Discovery in Bioinformatics,2004, 2004Conference paper (Refereed)
    Abstract [en]

    Standardisation and integration of pathway data is currently an interesting topic within bioinformatics with several consortia,e.g.SBML, PSI MI and BioPAX.These groups use or consider XML for representation of their standards. Furthermore, XML is used by many of the existing databases containing pathway information for export and exchange of data. In this paper we compare some of the XML representations used by the standardisation committees and existing databases. The contribution of the paper is the comparison and evaluation of the representations together with a discussion on implications for information discovery and integration.

  • 22.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Eifrém, Emil
    Neo AB, Sweden.
    Faraglia, Piergiorglio
    Universita di Roma, Italy.
    Customizable XML Management on a Navigational Database Framework2008In: Database and Expert Systems Application, 2008. DEXA '08, IEEE Computer Society, 2008, p. 261-265Conference paper (Refereed)
    Abstract [en]

    XML is a commonly used and popular representation format and there is an increasing need for efficient storage and retrieval of XML. Available technology for storage and management of XML includes native XML storage and shredding of XML into relational databases. Evaluations show that there is no easy answer on which solution that is most efficient and that the storage needs to be customized depending on the application. In this paper we investigate a third option, storing XML in a navigational database. With this solution the user can customize the underlying representation for the XML document. We show the feasibility of the approach by giving an overview of our first experimental evaluation with the tool. Our impression of the solution is that it offers an efficient and easy to use storage model for XML.

  • 23.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Freire, Juliana
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. University of Utah.
    XML Management for Bioinformatics Applications2011In: Computing in science & engineering (Print), ISSN 1521-9615, E-ISSN 1558-366X, Vol. 13, no 5, p. 12-22Article in journal (Refereed)
    Abstract [en]

    Scientific exploration has become a data-intensive process, and increasing amounts of data need to be stored, analyzed, and shared. XML can help address these needs. As concrete examples from systems biology show, native XML storage can be combined with traditional relational databases to offer an effective, usable solution for storing scientific data.

  • 24.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Hall, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    An evaluation of the Use of XML for Representation, Querying, and Analysis of Molecular Interactions.2006In: 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.

  • 25.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Hall, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    An evaluation of the use of XML for representation, querying, and analysis of molecular interactions2006In: 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.

  • 26.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Hall, David
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A review of standards for data exchange within systems biology2007In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 7, no 6, p. 857-867Article in journal (Refereed)
    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.

  • 27.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Hall, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Åsberg, Mikael
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Schmidt, Stefan
    Rostock University.
    Efficient XML data management for systems biology: Problems, tools and future vision2009In: International Journal on Advances in Software, Vol. 2, no 2-3, p. 217-233Article in journal (Refereed)
    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.

     

  • 28.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Hall, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Exploring Statistical Information for Applications-Specific Design and Evaluation of Hybrid XML storage2011In: Databases, Knowledge, and Data Applications, 2011, p. 108-113Conference 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.

  • 29.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Ivanova, Valentina
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Hall, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Using Statistical Information for Efficient Design and Evaluation of Hybrid XML Storage2011In: International Journal On Advances in Software, ISSN 1942-2628, E-ISSN 1942-2628, Vol. 4, no 3-4, p. 389-400Article in journal (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. 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.

  • 30.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Jakoniené, Vaida
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tan, He
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Representing, storing and accessing molecular interaction data: a review of models and tools2006In: Briefings in Bioinformatics, ISSN 1467-5463, E-ISSN 1477-4054, Vol. 7, no 4, p. 331-338Article in journal (Refereed)
    Abstract [en]

    One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

  • 31.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Jönsson, Arne
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    Robust Interpretation for Spoken Dialogue Systems1998In: Proceedings of ICSLP'98, Sydney, Australia,, 1998Conference paper (Refereed)
  • 32.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Modeling for simulation and data storage of cellular pathways: Similarities and differences2005In: Proceedings of the Fourth Modeling and Simulation in Biology, Medicine and Biomedical Engineering Conference - BioMedSim,2005, 2005, p. 65-Conference paper (Refereed)
    Abstract [en]

    The amount of information about molecular interactions and cellular pathways is rapidly increasing as experiments in the area are generating new information. To use this large amount of data in an optimal way there is a need for providing standardized descriptions of data. In the future it would also be of high importance to use standardized data descriptions capable of representing results originating from experiments as well as data used for advanced analyses and simulations, to allow for an optimal comparison and reuse of information in various situations. In this paper we compare three XML-based standards provided for exchange of molecular interaction and pathway data with the information provided in BioChem a library for simulation.

  • 33.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX2005In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 24, p. 4401-4407Article in journal (Refereed)
    Abstract [en]

    Motivation: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. Results: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.

  • 34.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Schmidt, Stefan
    Rostock University.
    An Extension of XQuery for Graph Analysis of Biological Pathways2009In: Proc. The First International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 2009,, 2009, p. 22-27Conference paper (Refereed)
    Abstract [en]

     The vast quantity of scientific data produced in life sciences demands the use of sophisticated storage and analysis techniques. In particular, for biological pathways graph analysis plays an important role and data is commonly available in XML-based formats. Thus, there is a growing need to make analysis capabilities available through query languages for XML. This paper presents an approach to extend XQuery for graph analysis with focus on data for biological pathways. A graph model is introduced within the XQuery environment. New built-in functions define the available operations on the graph model. XQuery expressions can be utilized to populate graphs with data and execute graph algorithms. Graph data and results of algorithms can be accessed in an XML representation for further processing. In addition, a reference mechanism can be used to preserve associations from graph data to the original XML data. The approach has been implemented as an extension to exist. First evaluations of the implementation show that the introduced approach is practical and efficient for reaction networks with several thousand vertices and edges.

  • 35.
    Strömbäck, Lena
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Åsberg, Mikael
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Hall, David
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    HShreX - a Tool for Design and Evaluation of Hybrid XML Storage2009In: PROCEEDINGS OF THE 20TH INTERNATIONAL WORKSHOP ON DATABASE AND EXPERT SYSTEMS APPLICATION, p. 417-421Article in journal (Refereed)
    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.

  • 36.
    Turcan, Eduard
    et al.
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Morris, John
    Philips Research Laboratories, Redhill, England.
    Share it! by bringing P2P into the TV-domain2003In: Proceedings of the Third IEEE International Conference on Peer-to-Peer computing, 2003Conference paper (Refereed)
    Abstract [en]

    Share it! is a European project with a focus on developing concepts and solutions for interconnecting digital TV set-top boxes that enable users to share TV-programmes. One important goal of the project is to set future standards, e.g. in content management and rights management, for broadband connected digital television.This paper introduces the project objectives and the consortium, and then focuses on how P2P technology and JXTA platform are used in solving various important issues that help to achieve the project goals.

  • 37.
    Åsberg, Mikael
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Bioinformatics: From Disparate Web Services to Semantics and Interoperability2010In: International Journal of Advances in Software, ISSN 1942-2628, Vol. 3, no 3-4, p. 396-406Article in journal (Refereed)
    Abstract [en]

    In the field of bioinformatics, there exists a large number of web service providers and many competing standards regarding how data should be represented and interfaced. However, these web services are often hard to use for a non-programmer and it can be especially hard to understand how different services can be used together to create scientific workflows. In this paper we have performed a literature study to identify problems involved in developing interoperable webservices for the bioinformatics community and steps taken by other projects to address them. We have also conducted a case study by developing our own bioinformatic web service to further investigate these problems. Based on our case study we have identified a number of design issues important to consider when designing web services. The paper is concluded by discussing current approaches aimed at making web services easier to use and by presenting our own proposal of an easy-to-use solution for integrating information from web services.

  • 38.
    Åsberg, Mikael
    et al.
    Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    Strömbäck, Lena
    Linköping University, Department of Computer and Information Science, IISLAB - Laboratory for Intelligent Information Systems. Linköping University, The Institute of Technology.
    Interoperable and Easy-to-Use Web Services for the Bioinformatics Community - A Case Study2010In: The Second International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 2010, 2010, p. 16-21Conference paper (Refereed)
    Abstract [en]

    In the field of bioinformatics, there exists a large number of web service providers and many competing standards regarding how data should be represented and interfaced. However, these web services are often hard to use for a non-expert programmer and it can be especially hard to see how different services can be used together to create scientific workflows. In this paper we have performed a literature study to identify problems involved in developing interoperable web services for the bioinformatics community and steps taken by other projects to, at least in part, address them. We have also conducted a case study by developing our own bioinformatic web service to further investigate these problems.

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