Publications

• Ontologies in the Life Sciences
• SAMBO
• KitAMO
• Recommendation of alignment strategies
• Related

• Ontologies in the Life Sciences
  • RECOMMENDED 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, pp 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. and Azuaje, F. (eds.) Artificial Intelligence Methods and Tools for Systems Biology, pp 129-146, Springer, 2004. ISBN 1-4020-2859-8 (hard cover) / 1-4020-2959-4 (soft cover). publisher's book page.
    
    
  • Lambrix P, Edberg A, `Evaluation of ontology merging tools in bioinformatics', Proceedings of the Pacific Symposium on Biocomputing - PSB03, pp 589-600, Kauai, Hawaii, USA, 2003.
    
    
  • Lambrix P, Habbouche M, Perez M, `Evaluation of ontology development tools for bioinformatics', Bioinformatics, 19(12):1564-1571, 2003. (Also best paper selection for and re-publication in the 2005 edition of the IMIA Yearbook, pp 547-554.)
    
    
• SAMBO
  • RECOMMENDED Lambrix P, Liu Q, Using partial reference alignments to align ontologies, Proceedings of the 6th European Semantic Web Conference, LNCS 5554, 188-202, Heraklion, Greece, 2009.
    
    
  • RECOMMENDED Lambrix P, Tan H, `Ontology alignment and merging', chapter 6 in Burger, Davidson, Baldock, (eds), Anatomy Ontologies for Bioinformatics: Principles and Practice, pp 133-150, Springer, 2008. publisher's book page.
    
    
  • Lambrix P, Liu Q, Tan H, Aligning Anatomy Ontologies in the Ontology Alignment Evaluation Initiative, 25th Workshop of the Swedish Artificial Intelligence Society, Linköping, Sweden, 2009.
    
    
  • Lambrix P, Tan H, Liu Q, 'SAMBO and SAMBOdtf results for the Ontology Alignment Evaluation Initiative 2008', Proceedings of the Third International Workshop on Ontology Matching, 190-198, Karlsruhe, Germany, 2008.
    
    
  • Lambrix P, Tan H, Xu W, 'Literature-based alignment of ontologies'. Proceedings of the Third International Workshop on Ontology Matching, 219-223, Karlsruhe, Germany, 2008. extended version.
    
    
  • Tan H, Lambrix P, 'SAMBO results for the Ontology Alignment Evaluation Initiative 2007', Proceedings of the Second International Workshop on Ontology Matching, pp 236-243, Busan, Korea, 2007.
    
    
  • Chen B, Tan H, Lambrix P, `Structure-based filtering for ontology alignment', Proceedings of the IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications, pp 364-369, 2006. errata figure 4.
    
    
  • RECOMMENDED Lambrix P, Tan H, `SAMBO - A System for Aligning and Merging Biomedical Ontologies', Journal of Web Semantics, Special issue on Semantic Web for the Life Sciences, 4(3):196-206, 2006. pre-print, journal page
    
    
  • Tan H, Jakoniene V, Lambrix P, Aberg J, Shahmehri N, `Alignment of Biomedical Ontologies using Life Science Literature', Proceedings of the International Workshop on Knowledge Discovery in Life Science Literature, LNBI 3886, pp 1-17, Singapore, 2006.
    
    
  • Lambrix P, Tan H, `Merging DAML+OIL Ontologies', in Barzdins, J. and Caplinskas, A. (eds.) Databases and Information Systems (Selected Papers from the Sixth International Baltic Conference DB&IS'2004), pp 249-258, IOS Press, 2005. ISBN: 1 58603 485 5.
    
    
  • Lambrix P, Tan H, `A Framework for Aligning Ontologies', Proceedings of the Third Workshop on Principles and Practice of Semantic Web Reasoning, LNCS 3703, pp 17-31, Dagstuhl, Germany, 2005.
    
    
  • Lambrix P, Edberg A, Manis C, Tan H, `Merging DAML+OIL bio-ontologies', Proceedings of the International Workshop on Description Logics, Rome, Italy, 2003.
    
    
• KitAMO
  • RECOMMENDED Lambrix P, Tan H, `A Tool for Evaluating Ontology Alignment Strategies', Journal on Data Semantics, LNCS 4380, VIII:182-202, 2007. pre-print, journal page.
    
    
• Recommendation of alignment strategies
  • RECOMMENDED Tan H, Lambrix P, `A method for recommending ontology alignment strategies', Proceedings of the 6th International Semantic Web Conference, LNCS 4825, pp 494-507, Busan, Korea, 2007.
    
    
• Related
  • 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, Springer, 2009. In press.
    
    
  • Strömbäck L, Hall D, Lambrix P, `A review of standards for data exchange within systems biology', Proteomics, 7(6):857-867, 2007. Invited contribution.
    
    
  • Doms A, Jakoniene V, Lambrix P, Schroeder M, Wächter T, `Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences', Reasoning Web, Second International Summer School, LNCS 4126, pp 164-183, 2006.
    
    
  • Strömbäck L, Jakoniene V, Tan H, Lambrix P, `Representing, storing and accessing molecular interaction data: a review of models and tools', Briefings in Bioinformatics, 7(4):331-338, 2006. Invited contribution.
    
    
  • Wächter T, Tan H, Wobst A, Lambrix P, Schroeder M, `A Corpus-driven Approach for Design, Evolution and Alignment of Ontologies', Proceedings of the Winter Simulation Conference, pp 1595-1602, 2006. Invited contribution.
    
    
  • Jakoniene V, Lambrix P, `Ontology-based Integration for Bioinformatics', Proceedings of the VLDB Workshop on Ontologies-based techniques for DataBases and Information Systems - ODBIS 2005, pp 55-58, Trondheim, Norway, 2005.
    
    
  • Lambrix P, `Towards a Semantic Web for Bioinformatics using Ontology-based Annotation', Proceedings of the 14th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises, pp 3-7, Linköping, Sweden, 2005. Invited talk.
    
    
  • Strömbäck L, Lambrix P, `Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX', Bioinformatics, 21(24):4401-4407, 2005.