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  • 1.
    Dragisic, Zlatan
    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.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    A System for Debugging Missing Is-a Structure in EL Ontologies2014In: Proceedings of the Third International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM14, 2014, p. 51-58Conference paper (Refereed)
  • 2.
    Dragisic, Zlatan
    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.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Completing the is-a structure of biomedical ontologies2014In: Data Integration in the Life Sciences 10th International Conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014. Proceedings / [ed] Helena Galhardas, Erhard Rahm, Berlin: Springer Science+Business Media B.V., 2014, p. 66-80Conference paper (Refereed)
    Abstract [en]

    Ontologies in the biomedical domain are becoming a key element for data integration and search. The usefulness of the applications which use ontologies is often directly influenced by the quality of ontologies, as incorrect or incomplete ontologies might lead to wrong or incomplete results for the applications. Therefore, there is an increasing need for repairing defects in ontologies. In this paper we focus on completing ontologies. We provide an algorithm for completing the is-a structure in TeX ontologies which covers many biomedical ontologies. Further, we present an implemented system based on the algorithm as well as an evaluation using three biomedical ontologies.

  • 3.
    Freire, Sergio Miranda
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Departamento de Tecnologia da Informação e Educação em Saúde, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
    Teodoro, Douglas
    Departamento de Tecnologia da Informação e Educação em Saúde, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil .
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Sundvall, Erik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Region Östergötland.
    Karlsson, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0150069Article in journal (Refereed)
    Abstract [en]

    This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

  • 4.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. Swedish e-Science Research Centre, Linköping University, Sweden .
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Completing the is-a structure in light-weight ontologies2015In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 6, article id 12Article in journal (Refereed)
    Abstract [en]

     Background: With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologies are a key technology in this effort. However, developing ontologies is not an easy task and often the resulting ontologies are not complete. In addition to being problematic for the correct modelling of a domain, such incomplete ontologies, when used in semantically-enabled applications, can lead to valid conclusions being missed.

    Results: We consider the problem of repairing missing is-a relations in ontologies. We formalize the problem as a generalized TBox abduction problem. Based on this abduction framework, we present complexity results for the existence, relevance and necessity decision problems for the generalized TBox abduction problem with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

    Conclusions: Semantically-enabled applications need high quality ontologies and one key aspect is their completeness. We have introduced a framework and system that provides an environment for supporting domain experts to complete the is-a structure of ontologies. We have shown the usefulness of the approach in different experiments. For the two Anatomy ontologies from the Ontology Alignment Evaluation Initiative, we repaired 94 and 58 initial given missing is-a relations, respectively, and detected and repaired additionally, 47 and 10 missing is-a relations. In an experiment with BioTop without given missing is-a relations, we detected and repaired 40 new missing is-a relations.

  • 5.
    Lambrix, Patrick
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    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.
    Repairing missing is-a structure in ontologies is an abductive reasoning problem2013In: Proceedings of the Second International Workshop on Debugging Ontologies and Ontology Mappings / [ed] Patrick Lambrix; Guilin Qi; Matthew Horridge; Bijan Parsia, Rheinisch-Westfaelische Technische Hochschule Aachen University , 2013, p. 33-44Conference paper (Refereed)
    Abstract [en]

    With the increased use of ontologies in semantically-enabled applications, the issue of debugging defects in ontologies has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Debugging consists of the phases of detection and repairing. In this paper we focus on the repairing phase of a particular kind of defects, i.e., the missing relations in the is-a hierarchy. We show that this can be formalized as an abduction problem. Further, we define properties for the ontology, the set of is-a relations to repair and the domain expert, as well as preference criteria on solutions and discuss the influences of these properties and criteria on the existence of solutions for the abduction problem. We also discuss the consequences of our analyses of the repairing problem for the development and use of debugging systems.

  • 6.
    Meier, Michael
    et al.
    University of Freiburg, Germany.
    Schmidt, Michael
    University of Freiburg, Germany.
    Wei, Fang
    University of Freiburg, Germany.
    Lausen, Georg
    University of Freiburg, Germany.
    Semantic query optimization in the presence of types2013In: Journal of computer and system sciences (Print), ISSN 0022-0000, E-ISSN 1090-2724, Vol. 79, no 6, p. 937-957Article in journal (Refereed)
    Abstract [en]

    Both semantic and type-based query optimization rely on the idea that queries may exhibit non-trivial rewritings if the state space of the database is restricted. While these two problems have always been studied as separate problems in previous work, in this paper we present a unifying, logic-based query optimization framework that builds upon the classical chase algorithm and brings both problems together. As a major challenge, our novel setting requires chasing conjunctive queries with union and negation in the presence of dependencies containing negation and disjunction. Tackling this problem, we study the applicability of the chase in this setting, develop novel conditions that guarantee its termination, identify fragments for which minimal query computation (w.r.t. a generic cost function) is always possible, and investigate the complexity of related decision problems.

  • 7.
    Sundvall, Erik
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Freire, Sergio Miranda
    Universidade do Estado do Rio de Janeiro, Brazil.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, Faculty of Science & Engineering.
    Querying archetype-based Electronic Health Records using Hadoop and Dewey encoding of openEHR models2017In: Informatics for Health: Connected Citizen-Led Wellness and Population Health / [ed] Rebecca Randell; Ronald Cornet; Colin McCowan; Niels Peek; Philip J. Scott, Amsterdam, The Netherlands: IOS Press, 2017, p. 406-410Conference paper (Refereed)
    Abstract [en]

    Archetype-based Electronic Health Record (EHR) systems using generic reference models from e.g. openEHR, ISO 13606 or CIMI should be easy to update and reconfigure with new types (or versions) of data models or entries, ideally with very limited programming or manual database tweaking. Exploratory research (e.g. epidemiology) leading to ad-hoc querying on a population-wide scale can be a challenge in such environments. This publication describes implementation and test of an archetype-aware Dewey encoding optimization that can be used to produce such systems in environments supporting relational operations, e.g. RDBMs and distributed map-reduce frameworks like Hadoop. Initial testing was done using a nine-node 2.2 GHz quad-core Hadoop cluster querying a dataset consisting of targeted extracts from 4+ million real patient EHRs, query results with sub-minute response time were obtained.

  • 8.
    Wei, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    TEDI: Efficient Shortest Path Query Answering on Graphs2012In: Graph Data Management: Techniques and Applications, IGI Global, 2012Chapter in book (Other academic)
  • 9.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Contributions of LiU/ADIT to Steiner Tree Computation over Large Graphs2012In: Advances in secure and networked information systems: the ADIT perspective ; Festschrift in honor of professor Nahid Shahmehri / [ed] Patrick Lambrix, Linköping: Linköping University Electronic Press, 2012, p. 131-138Chapter in book (Other academic)
    Abstract [en]

    This book contains contributions by current and former colleagues and PhD students of professor Nahid Shahmehri in celebration of her 60th birthday. Although it would be difficult to cover the full range of her academic contributions, we have at least been able to hint the importance and the breadth of her work. We have chosen the title ‘Advances in Secure and Networked Information Systems - The ADIT Perspective’ as many of the contributions of Nahid and her group have been in these areas, given a fairly broad interpretation of “networked information systems”. In this collection we have gathered both republications of past work as well as newly written articles.

  • 10.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Finding nearest neighbors in road networks: a tree decomposition method2013In: EDBT '13 Proceedings of the Joint EDBT/ICDT 2013 Workshops, New York: Association for Computing Machinery (ACM), 2013, p. 233-240Conference paper (Refereed)
    Abstract [en]

    Finding k Nearest Neighbors in one category of POIs (point of interests) belongs to the most frequently issued queries in the navigating systems or online maps. This problem can be formulated as given a graph G(V, E), a vertex u and SV, finding k nearest neighbors of u in S. Classic Dijkstra's algorithm offers an optimal solution if S = V holds, but the performance deteriorates as S is of smaller size. Other approaches such as pre-computing and storing all the shortest distances require too much storage, thus suffer from drawbacks of scalability.

    To address these problems, we propose TIkNN (stands for Tree decomposition-based Indexing for kNN), an indexing and query processing scheme for kNN query answering. TIkNN is based on the tree decomposition methodology. The graph is first decomposed into a tree in which each node (a.k.a. bag) contains more than one vertex from graph. The shortest paths are stored in such bags and these local paths together with the tree are the components of the index of the graph. Based on this index, step-wise query processing over the tree can be executed to find the nearest neighbors.

    Our experimental results show that TIkNN offers orders-of-magnitude performance improvement over Dijkstra's algorithm on query answering, while the storage requirement for the index structure is relatively small.

  • 11.
    Wei-Kleiner, Fang
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Tree decomposition-based indexing for efficient shortest path and nearest neighbors query answering on graphs2016In: Journal of computer and system sciences (Print), ISSN 0022-0000, E-ISSN 1090-2724, Vol. 82, no 1, p. 23-44Article in journal (Refereed)
    Abstract [en]

    We propose TEDI, an indexing for solving shortest path, and k Nearest Neighbors (kNN) problems. TEDI is based on the tree decomposition methodology. The graph is first decomposed into a tree in which the node contains vertices. The shortest paths are stored in such nodes. These local shortest paths together with the tree structure constitute the index of the graph. Based on this index, algorithms can be executed to solve the shortest path, as well as the kNN problem more efficiently. Our experimental results show that TEDI offers orders-of-magnitude performance improvement over existing approaches on the index construction time, the index size and the query answering. (C) 2015 Elsevier Inc. All rights reserved.

  • 12.
    Wei-Kleiner, Fang
    et al.
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Dragisic, Zlatan
    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.
    Abduction Framework for Repairing Incomplete EL Ontologies:  Complexity Results and Algorithms2014In: Proceedings of the 28th AAAI Conference on Artificial Intelligence, Palo Alto, CA, USA: AAAI Press, 2014, p. 1120-1127Conference paper (Refereed)
    Abstract [en]

    In this paper we consider the problem of repairing  missing is-a relations in ontologies.We formalize the problem as a generalized TBox abduction problem (GTAP). Based on this abduction framework, we  present complexity results for the existence, relevance and necessity decision problems for the GTAP with and without some specific preference relations for ontologies that can be represented using a member of the EL family of description logics. Further, we present algorithms for finding solutions, a system as well as experiments.

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