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Publications (since 2003)

Proceedings:

Journal Publications:

Video Journal Publications:

Book Chapters:

  • 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.
  • Pena J, Sonntag D, Contributions of LiU/ADIT to Chain Graphs, in Lambrix, (ed), Advances in Secure and Networked Information Systems - The ADIT Perspective, 121-130, LiU Tryck / LiU Electronic Press, 2012. publisher's book page.
  • Wei-Kleiner F, Contributions of LiU/ADIT to Steiner Tree Computation over Large Graphs, in Lambrix, (ed), Advances in Secure and Networked Information Systems - The ADIT Perspective, 131-138, 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, pp 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, 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, Azuaje F, (eds), Artificial Intelligence Methods and Tools for Systems Biology, pp 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:

  • 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), pp 249-258, IOS Press, 2005. ISBN: 1 58603 485 5.

Magazine Publications:

  • Lambrix P, Strömbäck L, 'Where is my protein? - Issues in Information Integration', BIOforum Europe, 7-8/07:24-26, 2007. Invited contribution. Also republished in the 2007 Highlights Issue, 12(1-2):24-25, 2008.

Conference Publications:

  • Marcus Bendtsen and Jose M. Pena Learning Gated Bayesian Networks for Algorithmic Trading In Proceedings of the seventh European Workshop on Probabilistic Graphical Models - PGM 2014, 17-19 September 2014, Utrecht, The Netherlands.
  • Dragisic Z, Lambrix P, Wei-Kleiner F, Completing the is-a structure of biomedical ontologies, Proceedings of the 10th International Conference on Data Integration in the Life Sciences, LNBI 8574, 66-80, Lisbon, Portugal, 2014.
  • Dragisic Z, Lambrix P, Wei-Kleiner F, A System for Debugging Missing Is-a Structure in EL Ontologies, Proceedings of the 3rd International Workshop on Debugging Ontologies and Ontology Mappings, CEUR Workshop Proceedings Volume 1162, 51-58, Anissaras/Hersonissou, Greece, 2014. [Demonstration paper.]
  • Ivanova V, Lambrix P, User involvement for large-scale ontology alignment, International Workshop on Visualizations and User Interfaces for Knowledge Engineering and Linked Data Analytics, CEUR Workshop Proceedings Volume 1299, 34-47, Linköping, Sweden, 2014.
  • Wei-Kleiner F, Dragisic Z, Lambrix P, Abduction Framework for Repairing Incomplete EL Ontologies: Complexity Results and Algorithms, Proceedings of the 28th AAAI Conference on Artificial Intelligence, 1120-1127, Quebec, Canada, 2014. extended version.
  • Bendtsen, M. and Pena, J. M. (2013). Gated Bayesian Networks. In Proceedings of the 12th Scandinavian Conference on Artificial Intelligence (SCAI 2013), 35-44.
  • Cuenca Grau B, Dragisic Z, Eckert K, Euzenat J, Ferrara A, Granada R, Ivanova V, Jimenez-Ruiz E, Kempf A, Lambrix P, Nikolov A, Paulheim H, Ritze D, Scharffe F, Shvaiko P, Trojahn C, Zamazal O, Results of the Ontology Alignment Evaluation Initiative 2013, International Workshop on Ontology Matching - OM 2013,CEUR Workshop Proceedings Volume 1111, 61- 100, Sydney, Australia, 2013.
  • Ivanova V, Lambrix P, A unified approach for aligning taxonomies and debugging taxonomies and their alignments, Tenth Extended Semantic Web Conference - ESWC 2013, LNCS 7882, 1-15, Montpellier, France, 2013. slides, video.
  • Ivanova V, Lambrix P, A system for aligning taxonomies and debugging taxonomies and their alignments, Tenth Extended Semantic Web Conference - ESWC 2013 Satellite Events, LNCS 7955, 152-156, Montpellier, France, 2013. [Demonstration paper.] © Springer-Verlag.
  • Lambrix P, Kaliyaperumal R, A Session-based Approach for Aligning Large Ontologies, Tenth Extended Semantic Web Conference - ESWC 2013, LNCS 7882, 46-60, Montpellier, France, 2013. slides, video.
  • Lambrix P, Wei-Kleiner F, Dragisic Z, Ivanova V, Repairing missing is-a structure in ontologies is an abductive reasoning problem. Second International Workshop on Debugging Ontologies and Ontology Mappings, CEUR Workshop Proceedings Volume 999, 33-44, Montpellier, France, 2013.
  • Pena, J. M. (2013). Approximate Counting of Graphical Models Via MCMC Revisited. In Proceedings of the 15th Conference of the Spanish Association for Artificial Intelligence (CAEPIA 2013) - Lecture Notes in Artificial Intelligence 8109, 383-392. Best paper award. Software.
  • Sonntag, D. and Pena, J. M. (2013). Chain Graph Interpretations and their Relations. In Proceedings of the 12th European Conference on Symbolic and Quantitative Approaches to Reasoning under Uncertainty (ECSQARU 2013) ÔÇô Lecture Notes in Artificial Intelligence 7958, 510-521. Best student paper award (ex-aequo). Extended version.
  • Freire S, Sundvall E, Karlsson D, Lambrix P, Performance of XML Databases for Epidemiological Queries in Archetype-Based EHRs, Scandinavian Conference on Health Informatics, 51-57, Linköping, Sweden, 2012.
  • Ivanova V, Lambrix P, A System for Debugging Taxonomies and their Alignments, First International Workshop on Debugging Ontologies and Ontology Mappings, 37-42, Galway, Ireland, 2012. Demonstration.
  • Ivanova V, Laurila Bergman J, Hammerling U, Lambrix P, Debugging Taxonomies and their Alignments: the ToxOntology - MeSH Use Case, First International Workshop on Debugging Ontologies and Ontology Mappings, 25-36, Galway, Ireland, 2012.
  • Lambrix P, Dragisic Z, Ivanova V, Get my pizza right: Repairing missing is-a relations in ALC ontologies, Second Joint International Semantic Technology Conference, LNCS 7774, 17-32, Nara, Japan, 2012. extended version, slides.
  • Tan H, Kaliyaperumal R, Benis N, 'Ontology-driven Construction of Corpus with Frame Semantics Annotations'. A. Gelbukh (Ed.): CICLing 2012, Part I, LNCS 7181, pp. 54--65. Springer, Heidelberg (2012)
  • Ivanova V, Strömbäck L, Creating infrastructure for tool-independent querying and exploitation of scientific workflows, 7th IEEE International Conference on e-Science, Stockholm, Sweden, 2011.
  • Lambrix P, A framework for session-based ontology alignment, Sixth International Workshop on Ontology Matching - OM 2011 , Bonn, Germany, 2011.
  • Lambrix P, Liu Q, Debugging is-a structure in networked taxonomies, Proceedings of the Fourth International Workshop on Semantic Web Applications and Tools for Life Sciences - SWAT4LS11, 58-65, London, UK, 2011.
  • Lambrix P, Liu Q, RepOSE: A System for Debugging is-a Structure in Networked Taxonomies, Demo at the 10th International Semantic Web Conference - ISWC 2011, Bonn, Germany, 2011.
  • Pe├▒a, J. M. (2011). Faithfulness in Chain Graphs: The Gaussian Case. In Proceedings of the 14th International Conference on Artificial Intelligence and Statistics (AISTATS 2011), 588-599.
  • Strömbäck L, Ivanova V, Hall D (2011) 'Exploring Statistical Information for Applications-Specific Design and Evaluation of Hybrid XML storage'. Databases, Knowledge, and Data Applications DBKDA 2011, published by IEEE, January 2011, St Maarten, The Netherlands.
  • He Tan, Rajaram Kaliyaperumal, Nirupama Benis, Building frame-based corpus on the basis of ontological domain knowledge, Proceedings of the Workshop on BioNLP, 74-82, Portland, Oregon, USA, 2011.
  • Tan H, Kaliyaperumal R, Benis N, 'Ontology-driven Construction of Corpus with Frame Semantics Annotations'. poster at The Fourth International Symposium on Languages in Biology and Medicine (LBM 2011). Singapore, 2011.
  • Freire J, Provenance management for data exploration, Proceedings of the Seventh International Conference on Data Integration in the Life Sciences - DILS 2010, LNBI 6254, 1-2 Gothenburg, Sweden, 2010. Invited talk.
  • David Hall, Lena Strömbäck: Generation of Synthetic XML for Evaluation of Hybrid XML Systems. DASFAA Workshops 2010: 191-202
  • Liu Q, Lambrix P, A system for debugging missing is-a structure in networked ontologies, Proceedings of the Seventh International Conference on Data Integration in the Life Sciences - DILS 2010, LNBI 6254, 50-57, Gothenburg, Sweden, 2010. © Springer-Verlag.
  • Liu Q, Lambrix P, Debugging the missing is-a structure of networked ontologies, Proceedings of the 7th Extended Semantic Web Conference - ESWC10, Part II, LNCS 6089, 478-482, Heraklion, Greece, 2010.
  • Pe├▒a, J. M. (2010). Reading Dependencies from Polytree-Like Bayesian Networks Revisited. In Proceedings of the 5th European Workshop on Probabilistic Graphical Models (PGM 2010), 225-232.
  • Tan H, A study on the relation between linguistics-oriented and domain-specific semantics, Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10, 2010.
  • Mikael ├ůsberg, Lena Strömbäck: Interoperable and Easy-to-Use Web Services for the Bioinformatics Community - A Case Study. DBKDA 2010: 16-21
  • Baker C, Lambrix P, Laurila Bergman J, Kanagasabai R, Ang WT, Slicing through the scientific literature, Proceedings of the 6th International Workshop on Data Integration in the Life Sciences - DILS09, LNBI 5647, 127-140, Manchester, UK, 2009. slides.
  • Ellkvist, T, Koop, D, Freire, J, Silva, C T, and Strömbäck, L (2009) Using Mediation to Achieve Provenance Interoperability, In IEEE International Workshop on Scientific Workflows, 2009.
  • Ellkvist, T, Lena Strömbäck, L, Didier Lins, L, and Freire J (2009) A First Study on Strategies for Generating Workflow Snippets. The first International Workshop on Keyword Search on structured data KEYS 2009, Collocated with ACM SIGMOD/PODS, June 28th, 2009, Providence, Rhode Island, USA
  • Lambrix P, Liu Q, Using partial reference alignments to align ontologies, Proceedings of the 6th European Semantic Web Conference - ESWC09, LNCS 5554, 188-202, Heraklion, Greece, 2009. slides, video.
  • Lambrix P, Liu Q, Tan H, Repairing the missing is-a structure of ontologies, Proceedings of the 4th Asian Semantic Web Conference - ASWC09, LNCS 5926, 76-90, Shanghai, China, 2009.
  • Lambrix P, Liu Q, Tan H, RepOSE: an environment for repairing missing ontological structure, Proceedings of the 4th Asian Semantic Web Conference - ASWC09, LNCS 5926, 365-366, Shanghai, China, 2009.
  • Lambrix P, Liu Q, Tan H, A system for repairing missing is-a structure in ontologies, Semantic Web Applications and Tools for Life Sciences - SWAT4LS09, Amsterdam, Netherlands, 2009.
  • Lambrix P, Liu Q, Tan H, Aligning Anatomy Ontologies in the Ontology Alignment Evaluation Initiative, 25th Workshop of the Swedish Artificial Intelligence Society, 13-20, Linköping, Sweden, 2009.
  • Strömbäck, L, Schmidt S (2009) An Extension of XQuery for Graph Analysis of Biological, Proc. The First International Conference on Advances in Databases, Knowledge, and Data Applications, DBKDA 2009, March 1-6, 2009, Cancun, Mexico Best paper award
  • Strömbäck, L, ├ůsberg, M, Hall, D (2009) HShreX: a Tool for Design and Evaluation of Hybrid XML Storage, FLexDBIST 2009, Linz Austria.
  • Tan H, Lambrix P, Selecting an Ontology for Biomedical Text Mining, Proceedings of the Workshop on BioNLP, 55-62, Boulder, Colorado, USA, 2009.
  • Ellqvist T, Freire J, Koop D, Silva C, Strömbäck L (2008) Using Mediation to Achieve Provenance Interoperability Proc. 4th IEEE International Conference on e-Science

  • Tommy Ellkvist, David Koop, Erik W. Anderson, Juliana Freire, and Claudio Silva, Using Provenance to Support Real-Time Collaborative Design of Workflow, Proceedings of the International Provenance and Annotation Workshop (IPAW), June 17-18, 2008, Salt Lake City.
  • Köhn D, Strömbäck L (2008) 'A method for Semi-automatic Standard Integration in Systems Biology', Proc. 19th Intern. Conf. on Database and Expert Systems Applications, pp 745 - 752, Turin, Italy, paper, DOI 10.1007/978-3-540-85654-2_66
  • 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.
  • Pe├▒a, J. M. (2008). Learning Gaussian Graphical Models of Gene Networks with False Discovery Rate Control. Proceedings of the 6th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2008), LNCS 4973, 165-176.
  • Strömbäck, L Eifr├ęm E, Faraglia P (2008) 'Custmizable XML Management on a Navigational Database Framework', Proc. 19th International Workshop on Database and Expert Systems Applications, Turin, Italy pp 261 - 265, paper, DOI 10.1109/DEXA.2008.48

  • Tan H, 'Knowledge-based Gene Symbol Disambiguation'. Second International Workshop on Data and Text Mining in Bioinformatics, 73-76, Napa Valley, California, USA, 2008.
  • 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.
  • 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.
  • Sauro H M, Uhrmacher A M, Harel D, Hucka M, Kwiatkowska M, Mendes P, Shaffer C A, Strömbäck L, Tyson J J. (2006) Challenges for Modeling and Simulation Methods in Systems Biology. In: Track on Modeling and Simulation in Computational Biology at the Winter Simulation Conference 2006 , paper, DOI 10.1109/WSC.2006.322948
  • Strömbäck, L. (2006) A classification for comparing standardized XML data. Proc. 17th International Workshop on Database and Expert Systems Applications (DEXA'06), pp 517-521, Krakow, Poland, September 2006, paper, DOI 10.1109/DEXA.2006.5
  • Strömbäck, L. (2006) A method for alignment of standardised XML information within systems biology. Winter Simulation 2006 In: Track on Modeling and Simulation in Computational Biology at the Winter Simulation Conference 2006 , paper, DOI 10.1109/WSC.2006.322933
  • Strömbäck, L, Hall, D. (2006) An evaluation of the Use of XML for Representation, Querying, and Analysis of Molecular Interactions. In T. Grust et. al. (Editors) Current Trends in Database Technology - EDBT 2006 Workshops. LNSC 4254, Springer verlag, paper, DOI 10.1007/11896548_20
  • Aberg C, Aberg J, Lambrix P, Shahmehri N, `A Platform to Evaluate the Technology for Service Discovery in the Semantic Web', Proceedings of the Twenty-First National Conference on Artificial Intelligence - AAAI-2006, pp 1253-1258, Boston, MA, USA, 2006. © AAAI.
  • 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.
  • 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. © Springer-Verlag.
  • Jakoniene V, Rundqvist D, Lambrix P, `A method for similarity-based grouping of biological data', Proceedings of the 3rd International Workshop on Data Integration in the Life Sciences - DILS06, LNBI 4075, pp 136-151, Hinxton, UK, 2006. © Springer-Verlag.
  • 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. © Springer-Verlag.
  • 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.
  • Aberg, C., Lambrix, P., Shahmehri, N., `An Agent-based Framework for Integrating Workflows and Web Services', Proceedings of the IEEE WETICE Workshop on Agent-based Computing for Enterprise Collaboration, pp 27-32, Linköping, Sweden, 2005. Best paper award.
  • Aberg, C., Lambrix, P., Takkinen, J., Shahmehri, N., `sButler: A Mediator between Organizations' Workflows and the Semantic Web', Proceedings of the WWW 2005 Workshop on Web Service Semantics: Towards Dynamic Business Integration, Chiba, Japan, 2005.
  • 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.
  • 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. © Springer-Verlag.
  • Strömbäck, L. (2005) Possibilities and Challenges Using XML Technology for Storage and Integration of Molecular Interactions16th International Workshop on Database and Expert Systems Applications (DEXA'05), pp 575-579, Copenhagen, Denmark, August 2005.
  • Strömbäck L, Lambrix P, `Modeling for simulation and data storage of cellular pathways: Similarities and differences', Proceedings of the Fourth Modeling and Simulation in Biology, Medicine and Biomedical Engineering Conference - BioMedSim, pp 65-72, Linköping, Sweden, 2005.
  • Lambrix P, Tan H, `Merging DAML+OIL Ontologies', Proceedings of the Sixth International Baltic Conference on Databases and Information Systems, pp 425-435, Riga, Latvia, 2004. (same as book chapter)
  • Strömbäck, L. (2004) XML representations of pathway data: a comparison. In Proceedings of the ACM SIGIR'04 Workshop on Search and Discovery in Bioinformatics . Sheffield, UK.
  • Lambrix P, Edberg A, `Evaluation of ontology merging tools in bioinformatics', Pacific Symposium on Biocomputing - PSB03, 8:589-600, Kauai, Hawaii, USA, 2003.
  • Lambrix P, Edberg A, Manis C, Tan H, `Merging DAML+OIL bio-ontologies', Proceedings of the International Workshop on Description Logics, Rome, Italy, 2003.
  • Lambrix P, Jakoniene V, `Towards transparent access to multiple biological databanks', Proceedings of the First Asia-Pacific Bioinformatics Conference, pp 53-60, Adelaide, Australia, 2003.

PhD Theses:

  • Tan H, Aligning Biomedical Ontologies, PhD thesis No. 1110, Department of Computer and Information Science, Linköpings universitet, Sweden, 2007.
  • Åberg C, An Evaluation Platform for Semantic Web Technology, PhD thesis No. 1061, Department of Computer and Information Science, Linköpings universitet, Sweden, 2007.
  • Jakoniene V, Integration of Biological Data, Ph.D. Thesis 1035, Department of Computer and Information Science, Linköpings universitet, Sweden, 2006.

Page responsible: Patrick Lambrix
Last updated: 2014-11-24