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Semantic Software Lab
Concordia University
Montréal, Canada

Publications from the Semantic Software Lab

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Book Chapter
Baker, C. J. O., and K. - H. Cheung (Eds.), Witte, R., T. Kappler, and C. J. O. Baker, "Ontology Design for Biomedical Text Mining", Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, New York, NY, USA : Springer Science+Business Media, pp. 281–313, 2007. Abstract  Download: ontology_design_preprint.pdf (811.59 KB)
Conference Paper
Rebholz-Schuhmann, D., A. Jimeno-Yepes, C. Li, S. Kafkas, I. Lewin, N. Kang, P. Corbett, D. Milward, E. Buyko, E. Beisswanger, et al., "Assessment of NER solutions against the first and second CALBC silver standard corpus", Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, vol. 714, Cambridge, United Kingdom, 10/2010.  Download: Paper08_RebholzSchuhmann.pdf (162.5 KB)
Witte, R., and C. J. O. Baker, "Combining Biological Databases and Text Mining to support New Bioinformatics Applications", Natural Language Processing and Information Systems: 10th International Conference on Applications of Natural Language to Information Systems (NLDB 2005), vol. 3513, Alicante, Spain : Springer-Verlag, pp. 310–321, June 15–17, 2005. Abstract  Download: witte_baker_nldb05.pdf (360.06 KB)
Baker, C. J. O., A. Shaban-Nejad, R. Witte, V. Haarslev, and G. Butler, "Empowering the Enzyme Biotechnologist with Ontologies", 10th International Congress on Biotechnology in the Pulp and Paper Industry (ICBPPI 2007), Monona Terrace, Madison, Wisconsin, USA, June 10–14, 2007. Abstract  Download: ICBPPI2007-poster.png (570.97 KB)
Baker, C. J. O., and R. Witte, "Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature", The 3rd Canadian Working Conference on Computational Biology (CCCB'04), Markham, Ontario, Canada, October 4, 2004. Abstract  Download: baker_witte_cccb04.pdf (272.1 KB)
Baker, C. J. O., R. Witte, A. Shaban-Nejad, G. Butler, and V. Haarslev, "The FungalWeb Ontology: Application Scenarios", Eighth Annual Bio-Ontologies Meeting, Detroit, Michigan, USA, pp. 1–2, June 24, 2005. Abstract  Download: Baker-etal-8th-Bio-Ontologies-Abstract.pdf (30.2 KB)
Kouznetsov, A., B. Shoebottom, R. Witte, and C. J. O. Baker, "Leverage of OWL-DL axioms in a Contact Centre for Technical Product Support", OWL: Experiences and Directions (OWLED 2010), San Francisco, California, USA, June 21–22, 2010. Abstract  Download: owled2010_submission_11.pdf (333.95 KB)
Baker, C. J. O., and R. Witte, "Mutation Miner", 13th Annual International conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, Michigan, USA, June 25–29, 2005. Abstract  Download: ISMB2005-poster.png (411.18 KB)
Baker, C. J. O., R. Witte, A. B. Gurpur, and V. Ryzhikov, "Mutation Miner", 5th International Conference of the Canadian Proteomics Initiative (CPI 2005), Toronto, Ontario, Canada, May 13–14, 2005. Abstract  Download: CPI2005-poster.png (397.65 KB)
Baker, C. J. O., and R. Witte, "Mutation Miner – Textual Annotation of Protein Structures", 5th CERMM Annual Symposium, Concordia University, Montréal, Québec, Canada : Centre for Research in Molecular Modeling, pp. 29, February 11–13, 2005. Abstract  Download: cermm-abstracts-2005.pdf (564.91 KB)
Conference Proceedings
Witte, R., C. J. O. Baker, G. Butler, and M. Dumontier (Eds.), "Proceedings of the 4th Canadian Semantic Web Symposium (CSWS 2013)", 4th Canadian Semantic Web Symposium (CSWS 2013), vol. 1054, Montréal, QC, Canada : CEUR-WS.org, 06/2011, 2013.  Download: CSWS2013-complete.pdf (7.49 MB)
Baker, C. J. O., R. Witte, and D. Rebholz-Schuhmann (Eds.), "Proceedings of the European Conference on Computational Biology (ECCB) 2010 Workshop: Annotation, interpretation and management of mutations (AIMM)", ECCB 2010 Workshop: Annotation interpretation and management of mutations (AIMM), BMC Bioinformatics, vol. 12 Suppl 4, 2011.
Journal Article
Witte, R., T. Kappler, and C. J. O. Baker, "Enhanced semantic access to the protein engineering literature using ontologies populated by text mining", Int.\ J.\ Bioinformatics Research and Applications (IJBRA), vol. 3, no. 3, pp. 389–413, 2007. Abstract  Download: witte_etal_ijbra2007.pdf (376.3 KB)
Baker, C. J. O., and R. Witte, "Mutation mining–A prospector's tale", Information Systems Frontiers (ISF), vol. 8, no. 1, pp. 47–57, February, 2006. Abstract
Witte, R., and C. J. O. Baker, "Towards A Systematic Evaluation of Protein Mutation Extraction Systems", Journal of Bioinformatics and Computational Biology (JBCB), vol. 5, no. 6, pp. 1339–1359, December, 2007. Abstract  Download: witte_baker_jbcb2007.pdf (248.69 KB)