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 (4):

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 (6):

  • Semantic Web, Databases and Ontologies for the Life Sciences
    • 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):

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 (74):

  • Semantic Web, Databases and Ontologies (for the Life Sciences)
  • Semantic Web and Workflows
  • Knowledge-Based Information Retrieval
    • Lambrix P, Shahmehri N, Querying Document Bases using Content, Structure and Properties, Ontologies and Search - Proceedings of the 2nd OntoQuery Workshop, 15-21, Copenhagen, Denmark, 2001. Invited contribution.
    • Lambrix P, Shahmehri N, Jacobsen S, Querying Document Bases by Content, Structure and Properties, Proceedings of the Eleventh International Symposium on Methodologies for Intelligent Systems - ISMIS99, LNAI 1609, 123-132, Warsaw, Poland, 1999. © Springer-Verlag.
    • Lambrix P, Shahmehri N, TRIFU: The Right Information For yoU, Proceedings of the 31st Hawaii International Conference on System Sciences, Volume IV - Internet and the Digital Economy Track, 505-512, Hawaii, 1998.
    • Lambrix P, Padgham L, A Description Logic Model for Querying Knowledge Bases for Structured Documents, Proceedings of the Tenth International Symposium on Methodologies for Intelligent Systems - ISMIS97, LNAI 1325, 72-83, Charlotte, North Carolina, USA, 1997.
    • Lambrix P, Shahmehri N, Wahllöf N, Dwebic: An Intelligent Search Engine based on Default Description Logics, Proceedings of the International Workshop on Description Logics, 119-121, Gif sur Yvette, France, 1997.
    • Lambrix P, Shahmehri N, Wahllöf N, A Default Extension to Description Logics for Use in an Intelligent Search Engine, Proceedings of the 31st Hawaii International Conference on System Sciences, Volume V - Modeling Technologies and Intelligent Systems Track, 28-35, Hawaii, 1998. Extended Abstract in Proceedings of the Tenth International Symposium on Methodologies for Intelligent Systems - Poster Session - ISMIS 97, 97-104, Charlotte, North Carolina, USA, 1997.
    • Lambrix P, Shahmehri N, Åberg J, Towards Creating a Knowledge Base for World-Wide Web Documents, Proceedings of the IASTED International Conference on Intelligent Information Systems, 507-511, Freeport, Bahamas, 1997.
    • Lambrix P, Padgham L, A Knowledge Base for Structured Documents, Proceedings of the First Australian Document Computing Symposium, Melbourne, Australia, 1996.
  • Knowledge Representation
    • Lambrix P, Introduction to Description Logics, Ontologies and Search - Proceedings of the 2nd OntoQuery Workshop, 53-56, Copenhagen, Denmark, 2001. Invited tutorial.
    • Lambrix P, Larocchia P, Learning Composite Concepts, Proceedings of the International Workshop on Description Logics, 147-152, Trento, Italy, 1998.
    • Lambrix P, Padgham L, Using Knowledge Representation for Agent World Model, Proceedings of the International Conference on Multi Agent Systems - ICMAS 98, 443-444, Paris, France, 1998.
    • Lambrix P, Some Notes on Parts, Wholes and Time, Proceedings of the Tenth International Symposium on Methodologies for Intelligent Systems - Poster Session - ISMIS97, 85-96, Charlotte, North Carolina, USA, 1997.
    • Lambrix P, Maleki J, Learning Composite Concepts in Description Logics: A First Step, Proceedings of the 9th International Symposium on Methodologies for Intelligent Systems - ISMIS96, LNAI 1079, 68-77, Zakopane, Poland, 1996. © Springer-Verlag.
    • Lambrix P, Padgham L, A Description Logic for Composite Objects for Domain Modeling in an Agent-Oriented Application, Proceedings of the International Workshop on Description Logics, 146-149, Boston, MA, USA, 1996.
    • Lambrix P, Padgham L, Analysis of Part-of Reasoning in Description Logics for Use in a Document Management Application, Proceedings of the Eighth International Symposium on Artificial Intelligence, 102-110, Monterrey, Mexico, 1995.
    • Lambrix P, Padgham L, Part-of Reasoning in Description Logics: A Document Management Application, Proceedings of the International Workshop on Description Logics, 106-108, Roma, Italy, 1995.
    • Padgham L, Lambrix P, Kalmelid S, Integrating a Description Logic System and an Object-Centered Database System, Proceedings of the International KRUSE Symposium - Knowledge Retrieval, Use and Storage for Efficiency, 40-48, Santa Cruz, California, USA, 1995.
    • Lambrix P, Extending Standard Description Logics, Proceedings of the International Workshop on Description Logics, 42-44, Bonn, Germany, 1994.
    • Padgham L, Lambrix P, A Framework for Part-of Hierarchies in Terminological Logics, Principles of Knowledge Representation and Reasoning - Proceedings of the Fourth International Conference - KR 94, 485-496, Bonn, Germany, 1994.
    • Lambrix P, Rönnquist R, Terminological Logic Involving Time and Evolution: A Preliminary Report, Proceedings of the Seventh International Symposium on Methodologies for Intelligent Systems - ISMIS93, LNAI 689, 162-171, Trondheim, Norway, 1993. © Springer-Verlag.
  • Agent Theory
  • Education
    • Lambrix P, Strömbäck L, Teaching databases to hundreds of engineering students, Proceedings of the 2nd Workshop on Computer Science Education, Linköping, Sweden, 2007.
    • Hoffmann Y, Lambrix P, Takkinen, J., Kamkar, M., Muddy Cards en praktisk användning, 5:e universitetspedagogiska konferensen vid Linköpings universitet, 146-150, Linköping, Sweden, 2001.
    • Shahmehri N, Åberg J, Lambrix P, Projects as a means for subject learning and personal development under student responsibility, Proceedings of Second International Conference on Problem-based Learning in Higher Education, 66, Linköping, Sweden, 2000.
    • Lambrix P, Ouchterlony U, Samarbete Teknik - Psykologi - Ekonomi, 3:e universitetspedagogiska konferensen vid Linköpings universitet, 7-9, Linköping, Sweden, 1999.
    • Lambrix P, Kamkar M, Computer Science as an Integrated Part of Engineering Education, Proceedings of the Third ACM SIGCSE/SIGCUE Conference on Integrating Technology into Computer Science Education, 153-156, Dublin, Ireland, 1998.
    • Lambrix P, Göthe Lundgren M, Kamkar M, Integrated Engineering Education, Verklighet och Vision - 1:a universitetspedagogiska konferensen vid Linköpings universitet, Linköping, Sweden, 1997.
      An abstract of this paper appeared under the title Computer Science as an Integrated Part of Engineering Education Proceedings of the ACM SIGCSE/SIGCUE Conference on Integrating Technology into Computer Science Education - Poster Session, Uppsala, Sweden, 1997.
  • Security and Safety
    • Chisalita I, Shahmehri N, Lambrix P., Traffic Accidents Modeling and Analysis using Temporal Reasoning, IEEE Conference on Intelligent Transportation Systems, 378-383, Washington, D.C., USA, 2004.
    • Duma, C, Shahmehri N, Lambrix P, Efficient Storage for Category-Based Group Key Management, Fifth Ph.D. Student Conference on Computer Science and Systems Engineering, 139-146, Norrköping, Sweden, 2004.
    • Duma C, Shahmehri N, Lambrix P, A Flexible Category-Based Collusion-Resistant Key Management Scheme for Multicast, Proceedings of the 18th IFIP International Information Security Conference, 133-144, Athens, Greece, 2003.
    • Duma C, Shahmehri N, Lambrix P, A Hybrid Key Tree Scheme for Multicast to Balance Security and Efficiency Requirements, Proceedings of the IEEE WETICE Workshop on Enterprise Security, 208-213, Linz, Austria, 2003.
  • Debugging of Real-Time Systems
    • Timmerman M, Gielen F, Lambrix P, High Level Tools for the Debugging of Real-Time Multiprocessor Systems, Proceedings of the Fifth IEEE Euromicro Workshop on Real-Time Systems, 140-146, Oulu, Finland, 1993, and Proceedings of the Third ACM/ONR Workshop on Parallel and Distributed Debugging, SIGPLAN Notices, 28(12):151-157, San Diego, CA, USA, 1993.
    • Timmerman M, Gielen F, Lambrix P, A Knowledge-Based Approach for the Debugging of Real-Time Multiprocessor Systems, Proceedings of the First IEEE Workshop on Real-Time Applications, Manhattan, New York, USA, 1993.
  • Version Management in Object-Oriented Databases
    • Lambrix P, Temporal Aspects of Composite Objects, Proceedings of the Second Golden West Conference on Intelligent Systems, 97-103, Reno, Nevada, USA, 1992. LiTH-IDA-R-91-14.
    • Lambrix P, Versioning of Strongly Connected Composite Objects, Proceedings of the Second Golden West Conference on Intelligent Systems, 116-125, Reno, Nevada, USA, 1992.
    • Lambrix P, Versioning Aspects of Strongly Connected Composite Objects, Proceedings of the Third Information Systems Developers Workbench, Gdansk, Poland, 1992.

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, Linköpings universitet, 2007.
    • Jakoniene V, Integration of Biological Data, Ph.D. Thesis 1035, Department of Computer and Information Science, Linköpings universitet, 2006.
  • Lic. theses (supervisor)
    • Liu Q, Dealing with Missing Mappings and Structure in a Network of Ontologies, Lic. Thesis 1468, Department of Computer and Information Science, Linköpings universitet, 2011.
    • Tan H, Aligning and Merging Biomedical Ontologies, Lic. Thesis 1225, Department of Computer and Information Science, Linköpings universitet, 2006.
    • Jakoniene V, A Study in Integrating Multiple Biological Data Sources, Lic. Thesis 1149, Department of Computer and Information Science, Linköpings universitet, 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, Linköpings universitet, 2011.
    • Åberg C, An Evaluation Platform for Semantic Web Technology, Ph.D. Thesis 1061, Department of Computer and Information Science, Linköpings universitet, 2007.
    • Takkinen J, From Information Management to Task Management in Electronic Mail, Ph.D. Thesis 732, Department of Computer and Information Science, Linköpings universitet, 2002.
    • Andre-Jönsson H, Indexing strategies for time series data, Ph.D. Thesis 757, Department of Computer and Information Science, Linköpings universitet, 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, Linköpings universitet, 2005.
    • Takkinen J, CAFE: Towards a Conceptual Model for Information Management in Electronic Mail, Lic. thesis 640, Department of Computer Science and Information Science, Linköpings universitet, 1997.
    • Wahllöf N, A Default Extension to Description Logics and its Applications, Lic. thesis 591, Department of Computer Science and Information Science, Linköpings universitet, 1996.
  • M.Sc. theses
    • Rundqvist D, Grouping biological data, Undergraduate thesis, Department of Computer and Information Science, Linköpings universitet, 2006. LITH-IDA-EX--06/029--SE. Best Undergraduate Thesis Award 2006 at the Department of Computer and Information Science, Linköpings universitet.
    • Edberg A, Förening av ontologier inom bioinformatik. Undergraduate thesis, Department of Computer and Information Science, Linköpings universitet, 2002. LiTH-IDA-Ex-02/62. Best Undergraduate Thesis Award 2002 at the Department of Computer and Information Science, Linköpings universitet.
    • Jacobsen S, A Hybrid System for Knowledge-Based Information Retrieval, Undergraduate thesis, Department of Computer and Information Science, Linköpings universitet, 1997. LiTH-IDA-Ex-97/59. Best Undergraduate Thesis Award 1997 at the Department of Computer and Information Science, Linköpings universitet.

Other Presentations and Panels:

(Most presentations are in connection to conference papers. They are not listed here.)
  • 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

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