Linköpings universitet > Department of Computer and Information Science > Division for Database and Information Techniques > Patrick Lambrix
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Annotated bibliography

Book - monograph (1):

Book - edited (1):

Proceedings (6):

PhD thesis:

    • Lambrix P, Part-Whole Reasoning in Description Logics, Ph.D. Thesis 448, Department of Computer and Information Science, Linköpings universitet, 1996.

Book Chapters (7):

  • Semantic Web, Databases and Ontologies for the Life Sciences
    • Lambrix P, Semantic Web, Ontologies and Linked Data, chapter 6.05 in Brahme (ed in chief), Persson, (ed), Comprehensive Biomedical Physics, Volume 6: Bioinformatics, 67-76, Elsevier, 2014. ISBN: 978-0-444-53633-4. publisher's book page.
    • Lambrix P, Ivanova V, Dragisic Z, Contributions of LiU/ADIT to Debugging Ontologies and Ontology Mappings, in Lambrix, (ed), Advances in Secure and Networked Information Systems - The ADIT Perspective, 109-120, LiU Tryck / LiU Electronic Press, 2012. publisher's book page.
    • Lambrix P, Kaliyaperumal R, Contributions of LiU/ADIT to Ontology Alignment, in Lambrix, (ed), Advances in Secure and Networked Information Systems - The ADIT Perspective, 97-108, LiU Tryck / LiU Electronic Press, 2012. publisher's book page.
    • Lambrix P, Strömbäck L, Tan H, Information integration in bioinformatics with ontologies and standards, chapter 8 in Bry, Maluszynski, (eds), Semantic Techniques for the Web: The REWERSE perspective, LNCS 5500, 343-376, Springer, 2009. ISBN: 978-3-642-04580-6. publisher's book page.
    • Lambrix P, Tan H, Ontology alignment and merging, chapter 6 in Burger, Davidson, Baldock, (eds), Anatomy Ontologies for Bioinformatics: Principles and Practice, 133-150, Springer, 2008. ISBN: 978-1-84628-884-5. publisher's book page.
    • Lambrix P, Tan H, Jakoniene V, Strömbäck L, Biological Ontologies, chapter 4 in Baker, Cheung, (eds), Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, 85-99, Springer, 2007. ISBN-10: 0-387-48436-1, ISBN-13: 978-0-387-48436-5. publisher's book page.
    • Lambrix P, Ontologies in Bioinformatics and Systems Biology, chapter 8 in Dubitzky W, Azuaje F, (eds), Artificial Intelligence Methods and Tools for Systems Biology, 129-146, Springer, 2004. ISBN-10: 1-4020-2859-8, ISBN-13: 978-1-4020-2859-5 (hard cover) / 1-4020-2959-4 (soft cover). publisher's book page.

Book Chapters based on conference articles (1):

  • Semantic Web, Databases and Ontologies for the Life Sciences
    • Lambrix P, Tan H, Merging DAML+OIL Ontologies, in Barzdins J, Caplinskas A, (eds), Databases and Information Systems (Selected Papers from the Sixth International Baltic Conference DB&IS'2004), 249-258, IOS Press, 2005. ISBN: 1 58603 485 5.

Journal Publications (14):

Video Journal Publications (1):

Magazine Publications (1):

  • Semantic Web, Databases and Ontologies for the Life Sciences
    • Lambrix P, Strömbäck L, Where is my protein? - Issues in Information Integration, BIOforum Europe,11(7-8):24-26, 2007. Invited contribution. Also republished in the 2007 Highlights Issue, 12(1-2):24-25, 2008.

Conference and Workshop Publications (80):

Abstracts:

  • Semantic Web, Databases and Ontologies for the Life Sciences
    • Lambrix P, Valentina I, Debugging is-a structure in and mappings between taxonomies, Poster at Scandinavian Conference on Health Informatics, 67, Linköping, Sweden, 2012.
    • Lambrix P, Kaliyaperumal R, Session-based Ontology Alignment, Poster at Scandinavian Conference on Health Informatics, 65, Linköping, Sweden, 2012.
    • Tan H, Lambrix P, Selecting an ontology for biomedical text mining, Poster at the 17th Conference on Intelligent Systems for Molecular Biology, ISMB-2009, Stockholm, Sweden, 2009.
    • Lambrix P, Tan H, Aligning biomedical ontologies, Poster at the 4th Integrative Bioinformatics Workshop, Gent, Belgium, 2007.
    • Jakoniene V, Lambrix P, A tool for evaluating strategies for grouping of biological data, Seventh Swedish Bioinformatics Workshop for PhD students and PostDocs, 23-24, Stockholm, Sweden, 2006.
    • Tan H, Lambrix P, Aligning and merging biomedical ontologies, Seventh Swedish Bioinformatics Workshop for PhD students and PostDocs, 18, Stockholm, Sweden, 2006.
    • Backofen R, Badea M, Barahona P, Badea L, Bry F, Dawelbait G, Doms A, Fages F, Goble C, Henschel A, Hotaran A, Huang B, Krippahl L, Lambrix P, Nutt W, Schroeder M, Soliman S, Will S, Towards a Semantic Web for Bioinformatics, Poster at Bioinformatics 2004, p 26, Linköping, Sweden, 2004.
    • Jakoniene V, Lambrix P, Implementation of a System for Integrated Access to Biological Data Sources, Poster at Bioinformatics 2004, p 44, Linköping, Sweden, 2004.
    • Lambrix P, Tan H, A Semi-Automatic Tool for Merging Bio-Ontologies, Poster at Bioinformatics 2004, p 55, Linköping, Sweden, 2004.
    • Lambrix P, Tan H, A semi-automatic tool for merging bio-ontologies, Fourth Swedish Bioinformatics Workshop for PhD students and PostDocs, 18-19, Linköping, Sweden, 2003.
    • Jakoniene V, Lambrix P, Monitoring performance and access to biological databases, Third Swedish Annual Workshop in Bioinformatics for PhD students and PostDocs, p 17, Stockholm, Sweden, 2002.
    • Lambrix P, Jakoniene V, A databank knowledge base for the integration of biological databanks, Bioinformatics 2002, p 62, Bergen, Norway, 2002.
    • Lambrix P, Querying Multiple Biological Databanks, poster at the 9th International Conference on Intelligent Systems for Molecular Biology - ISMB01, p 64, Copenhagen, Denmark, 2001.
    • Lambrix P, A Query Language and Architecture for Querying Multiple Biological Databanks, Proceedings of Bioinformatics 2001, p 24, Skövde, Sweden, 2001.
    • Lambrix P, Jakoniene V, Lessons learned from the analysis of characteristics of biological databanks, Second Annual National Workshop for PhD students and PostDocs in Bioinformatics in Sweden, p 9, Göteborg, Sweden, 2001.

Project Deliverables:

  • REWERSE
    • Backofen R, Burger A, Busch A, Dawelbait G, Fages F, Jakoniene V, Lambrix P, McLeod K, Soliman S, Tan H, Will S, Implementation of prototypes, REWERSE Deliverable A2-D6, 2007.
    • Dawelbait G, Doms A, Lambrix P, Royer L, Schroeder M, Bioinformatics Demonstrators, REWERSE Deliverable A2-D4, 2006.
    • Backofen R, Badea M, Barahona P, Berndtsson M, Burger A, Dawelbait G, Doms A, Fages F, Hotaran A, Jakoniene V, Krippahl L, Lambrix P, McLeod K, Nutt W, Olsson B, Schroeder M, Schroiff A, Soliman S, Tan H, Tilivea D, Will S, Requirements and specification of use cases, REWERSE Deliverable A2-D3, 2005.
    • Backofen R, Badea M, Barahona P, Burger A, Dawelbait G, Doms A, Fages F, Hotaran A, Jakoniene V, Krippahl L, Lambrix P, McLeod K, Möller S, Nutt W, Olsson B, Schroeder M, Soliman S, Tan H, Tilivea D, Will S, Usage of bioinformatics tools and identification of information sources, REWERSE Deliverable A2-D2, 2005.
    • Backofen R, Badea M, Burger A, Fages F, Lambrix P, Nutt W, Schroeder M, Soliman S, Will S, State-of-the-art in Bioinformatics, REWERSE Deliverable A2-D1, 2004.

Selected Student Publications:

  • Ph.D. theses (supervisor)
    • Tan H, Aligning Biomedical Ontologies, Ph.D. Thesis 1110, Department of Computer and Information Science, Linköping University, 2007.
    • Jakoniene V, Integration of Biological Data, Ph.D. Thesis 1035, Department of Computer and Information Science, Linköping University, 2006.
  • Lic. theses (supervisor)
    • Dragisic Z, Completing the Is-a Structure in Description Logics Ontologies, Lic. Thesis 1683, Department of Computer and Information Science, Linköping University, 2014.
    • Ivanova V, Integration of Ontology Alignment and Ontology Debugging for Taxonomy Networks, Lic. Thesis 1644, Department of Computer and Information Science, Linköping University, 2014.
    • Liu Q, Dealing with Missing Mappings and Structure in a Network of Ontologies, Lic. Thesis 1468, Department of Computer and Information Science, Linköping University, 2011.
    • Tan H, Aligning and Merging Biomedical Ontologies, Lic. Thesis 1225, Department of Computer and Information Science, Linköping University, 2006.
    • Jakoniene V, A Study in Integrating Multiple Biological Data Sources, Lic. Thesis 1149, Department of Computer and Information Science, Linköping University, 2005.
  • Ph.D. theses (co-supervisor)
    • Leifler O, Affordances and constraints of intelligent decision support for military command and control - three case studies of support systems Department of Computer and Information Science, Linköping University, 2011.
    • Åberg C, An Evaluation Platform for Semantic Web Technology, Ph.D. Thesis 1061, Department of Computer and Information Science, Linköping University, 2007.
    • Takkinen J, From Information Management to Task Management in Electronic Mail, Ph.D. Thesis 732, Department of Computer and Information Science, Linköping University, 2002.
    • Andre-Jönsson H, Indexing strategies for time series data, Ph.D. Thesis 757, Department of Computer and Information Science, Linköping University, 2002.
  • Lic. theses (co-supervisor)
    • Åberg C, Integration of Organizational Workflows and the Semantic Web. Lic. thesis 1168, Department of Computer Science and Information Science, Linköping University, 2005.
    • Takkinen J, CAFE: Towards a Conceptual Model for Information Management in Electronic Mail, Lic. thesis 640, Department of Computer Science and Information Science, Linköping University, 1997.
    • Wahllöf N, A Default Extension to Description Logics and its Applications, Lic. thesis 591, Department of Computer Science and Information Science, Linköping University, 1996.
  • M.Sc. theses
    • Rundqvist D, Grouping biological data, Undergraduate thesis, Department of Computer and Information Science, Linköping University, 2006. LITH-IDA-EX--06/029--SE. Best Undergraduate Thesis Award 2006 at the Department of Computer and Information Science, Linköping University.
    • Edberg A, Förening av ontologier inom bioinformatik. Undergraduate thesis, Department of Computer and Information Science, Linköping University, 2002. LiTH-IDA-Ex-02/62. Best Undergraduate Thesis Award 2002 at the Department of Computer and Information Science, Linköping University.
    • Jacobsen S, A Hybrid System for Knowledge-Based Information Retrieval, Undergraduate thesis, Department of Computer and Information Science, Linköping University, 1997. LiTH-IDA-Ex-97/59. Best Undergraduate Thesis Award 1997 at the Department of Computer and Information Science, Linköping University.

Other Presentations and Panels:

(Most presentations are in connection to conference papers. They are not listed here.)
  • Invited talk: Ontologies in the age of linked data, 2nd Linked Data in Sweden event, Linköping, Sweden, 2013. video
  • Debugging is-a structure in ontologies, Ontology Summit 2013.
  • Invited talk: Debugging the structure of ontologies, Laboratory Protocol Standards Workshop, Uppsala, Sweden, 2011.
  • Tutorial: Debugging ontologies and mappings in ontology networks, by Patrick Lambrix, Guilin Qi and Christian Meilicke, at the 10th International Semantic Web Conference - ISWC 2011, Bonn, Germany, 2011.
  • Ontology alignment - state of the art and an application in literature search, GlaxoSmithKline, via Web to US, UK, 2010.
  • Ontology Alignment, Ontology Workshop, Linköping, Sweden, 2010.
  • Invited talk: Ontology alignment - state of the art and an application in literature search, Meeting on Modeling biological systems: Bio-model similarities and differences based on semantic information, Rostock, Germany, 2010.
  • State of the Art in Ontology Alignment, TU Dresden, Germany, 2009.
  • State of the Art in Ontology Alignment, AstraZeneca, via Web to Sweden, UK, US, 2009.
  • State of the Art in Ontology Alignment, Norges Teknisk-Naturvitenskapelige Universitet, Trondheim, Norway, 2008.
  • Ontologies for bioinformatics, BioMedley - Nätverket för LifeScience-teknologi och biomedicin i Östergötland, Linköping, Sweden, 2008.
  • Invited talk: Aligning ontologies, Annual Workshop of the National Graduate School in Computer Science (CUGS), Linköping, Sweden, 2008.
  • Aligning biomedical ontologies, Singapore Agency for Science, Technology and Research (A*STAR), Singapore, 2007.
  • Keynote talk: Aligning biomedical ontologies, Second International Symposium on Language in Biology and Medicine, Singapore, 2007.
  • Panel: `Biomedical Language and Biomedical Knowledge: Emerging Synergies', Second International Symposium on Language in Biology and Medicine, Singapore, 2007.
  • REWERSE A2 Linköping contribution: ontology alignment (SAMBO, KitAMO) and grouping of biological data (KitEGA), Final REWERSE Annual Meeting, Abbey Frauenwörth, Lake Chiemsee, Germany, 2007.
  • Ontology Alignment, Dagstuhl Seminar 07132, Towards Interoperability of Biomedical Ontologies, Dagstuhl, Germany, 2007.
  • SAMBO - System for Aligning and Merging Biomedical Ontologies, REWERSE A2 meeting, Edinburgh, UK, 2005.
  • Invited talk: Towards a Semantic Web for Bioinformatics using Ontology-based Annotation, 14th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprise (WET-ICE 2005). Linköping, Sweden, 2005.
  • Towards a Semantic Web for Bioinformatics, AstraZeneca, Lund, Sweden, 2004.
  • Databases and ontologies in bioinformatics, REWERSE meeting, Munich, Germany, 2004.
  • Invited talk: Document management using part-of reasoning in description logics, OntoQuery Workshop, Copenhagen, Denmark, 2001.
  • Invited tutorial: Introduction to description logics, OntoQuery Workshop, Copenhagen, Denmark, 2001.
  • Integration av psykologi, ekonomi och informationsteknologi, Högskolekonferensen, Linköping, Sweden, 1998.
  • TRIFU: A system for knowledge-based information retrieval, International Workshop on Description Logics, Trento, Italy, 1998.
  • Panel: Description Logics and the World Wide Web, International Workshop on Description Logics, Trento, Italy, 1998.
  • Panel: The Part-Whole Relationship and Composite Objects in Description Logics, International Workshop on Description Logics, Boston, MA, USA, 1996.
  • Panel: Extensions of Description Logics, International Workshop on Description Logics, Bonn, Germany, 1994.

Homepages of my co-authors

Scholar google citations

Scholar google - author (finds most papers)

Microsoft Academic search (finds most papers, but few citations)

DBLP entry (finds more than half of the papers)

Citeseer citations (finds some papers)

Scopus entry (finds some papers)

ISI (finds some papers)

PubMed entry (finds few papers)

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