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Semantic Software Lab
Concordia University
Montréal, Canada
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Open Mutation Miner

Our Open Mutation Miner (OMM) system for text mining protein mutation related information from the bibliome.

Ontology Design for Biomedical Text Mining

Submitted by witte on Fri, 2010-12-31 08:53
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.
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Mutation mining–A prospector's tale

Submitted by witte on Wed, 2010-12-29 12:22
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.
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Towards A Systematic Evaluation of Protein Mutation Extraction Systems

Submitted by witte on Wed, 2010-12-29 11:59
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.
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Enhanced semantic access to the protein engineering literature using ontologies populated by text mining

Submitted by witte on Wed, 2010-12-29 11:33
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.
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Algorithms and semantic infrastructure for mutation impact extraction and grounding

Submitted by rene on Mon, 2010-12-27 09:57
Laurila, J., N. Naderi, R. Witte, A. Riazanov, A. Kouznetsov, and C. Baker, "Algorithms and semantic infrastructure for mutation impact extraction and grounding", BMC Genomics, vol. 11, no. Suppl 4, pp. S24, 12/2010.
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Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature

Submitted by rene on Tue, 2010-08-24 09:48
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.
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Mutation Miner – Textual Annotation of Protein Structures

Submitted by rene on Mon, 2010-08-23 07:43
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.
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Combining Biological Databases and Text Mining to support New Bioinformatics Applications

Submitted by rene on Sun, 2010-08-22 08:06
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.
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The FungalWeb Ontology: Application Scenarios

Submitted by rene on Sat, 2010-08-21 07:31
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.
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Ontology-Based Extraction and Summarization of Protein Mutation Impact Information

Submitted by rene on Fri, 2010-07-23 09:03
Naderi, N., and R. Witte, "Ontology-Based Extraction and Summarization of Protein Mutation Impact Information", Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP 2010), Uppsala, Sweden : Association for Computational Linguistics (ACL), pp. 128--129, July 15, 2010.
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