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Semantic Software Lab
Concordia University
Montréal, Canada

Publications from the Semantic Software Lab

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Xylanase
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., and R. Witte, "Mutation mining–A prospector's tale", Information Systems Frontiers (ISF), vol. 8, no. 1, pp. 47–57, February, 2006. Abstract
text mining
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)
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)
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
Semantic Web
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)
querying OWL-DL ontologies
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)
Protein Structure Annotation
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., and R. Witte, "Mutation mining–A prospector's tale", Information Systems Frontiers (ISF), vol. 8, no. 1, pp. 47–57, February, 2006. Abstract
protein mutations
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)
Protein mutation
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
Protein Function
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)
ProSAT
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)
ontology population
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)
Ontology Design
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)
ontological NLP
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 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)
NLP
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)
mutation extraction systems; mutation evaluation tasks; mutation evaluation metrics
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)
Haloalkane dehalogenase
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
description logics
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)
Data mining
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
CSWS2013
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)
Biphenyl dioxygenase
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
automated reasoning in bioinformatics
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)