He Tan's publications

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Thesis

• Tan H, 'Aligning Biomedical Ontologies', Doctoral Thesis 1110, Department of Computer and Information Science, Linköpings universitet, Linköping, 2007.

• Tan H, 'Aligning and Merging Biomedical Ontologies', Licentiate Thesis 1225, Department of Computer and Information Science, Linköpings universitet, Linköping, 2006.

Book Chapters

• 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.
• 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 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.

Journal Papers

• 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].

• Lambrix P, Tan H, 'A Tool for Evaluating Ontology Alignment Strategies', Journal on Data Semantics, LNCS 4380, VIII:182-202, 2007. © Springer-Verlag. [pre-print], [journal page].

• 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. [journal page].

Conference Papers

• Tan H, Kaliyaperumal R, Benis N, 'Ontology-driven Construction of Corpus with Frame Semantics Annotations'. accepted to 13th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2012).
• Tan H, Kaliyaperumal R, Benis N, Building frame-based corpus on the basis of ontological domain knowledge, Proceedings of the 2011 Workshop on Biomedical Natural Language Processing (ACL-HLT 2011) , 74-82, Portland, Oregon, USA.
• 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.
• Tan H, Lambrix P, Selecting an Ontology for Biomedical Text Mining, Proceedings of the Workshop on BioNLP, 55-62, Boulder, Colorado, USA, 2009.
• Lambrix P, Liu Q, Tan H, Repairing the missing is-a structure of ontologies, Proceedings of the 4th Asian Semantic Web Conference, 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, Linköping, Sweden, 2009.
• Tan H, 'Knowledge-based Gene Symbol Disambiguation'. CIKM: Proceedings of the 2nd international workshop on Data and text mining in bioinformatics , pp 73-76, Napa Valley, California, USA, 2008.
• 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 , Karlsruhe, Germany, 2008.
• Lambrix P, Tan H, Xu W, 'Literature-based alignment of ontologies'. Proceedings of the Third International Workshop on Ontology Matching, Karlsruhe, Germany, 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, pp236-243, Busan, Korea, 2007.
• 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.
• 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.
• 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.
• 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.
• 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.
• Lambrix P, Edberg A, Manis C, Tan H, `Merging DAML+OIL bio-ontologies', Proceedings of the International Workshop on Description Logics, Rome, Italy, 2003.

Abstracts

• 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.
• 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.
• Tan H, Lambrix P, `Aligning and merging biomedical ontologies', Seventh Swedish Bioinformatics Workshop for PhD students and PostDocs, pp 18, Stockholm, Sweden, 2006.
• 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, pp 18-19, Linköping, Sweden, 2003.

Project Deliverables

• 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.
• 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.