Publications

  <h3> If you wish to cite cTAKES in a publication, please use: </h3>
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+     <p> Savova, Guergana; Masanz, James; Ogren, Philip; Zheng, Jiaping; Sohn, Sunghwan; Kipper-Schuler, Karin and Chute, Christopher. 2010. Mayo Clinic Clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. JAMIA 2010;17:507-513 doi:10.1136/jamia.2009.001560 </p>
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+  <h3> Other cTAKES publications describing different components and applications: </h3>
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+     <p> Chen Lin, Helena Canhao, Timothy Miller, Dmitriy Dligach, Robert M. Plenge, Elizabeth W. Karlson, Guergana Savova. 2012. Feature Engineering and Selection for Rheumatoid Arthritis Disease Activity Classification Using Electronic Medical Records. International Conference of Machine Learning (ICML) Workshop on Machine Learning for Clinical Data. </p>
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+     <p> Chen Lin, Timothy Miller, Dmitriy Dligach, Robert M. Plenge, Elizabeth W. Karlson, Guergana Savova. 2012. Maximal Information Coefficient for Feature Selection for Clinical Document Classification. International Conference on Machine Learning Workshop on Machine Learning for Clinical Data. </p>
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+     <p> Miller, Timothy; Dligach, Dmitriy; Savova, Guergana. 2012. Active learning for Coreference Resolution in the Biomedical Domain. BioNLP workshop at the Conference of the North American Association of Computational Linguistics (NAACL 2012). </p>
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+     <p> Ashwin N. Ananthakrishnan, Tianxi Cai, Su-Chun Cheng, Pei Jun Chen, Guergana Savova, Raul Guzman Perez, Vivian S. Gainer, Shawn N. Murphy, Peter Szolovits, Katherine Liao, Elizabeth W. Karlson, Susanne Churchill, Isaac Kohane, Robert M. Plenge. 2012. Improving Case Definition of Crohn's Disease and Ulcerative Colitis in Electronic Medical Records using Natural Language Processing - A Novel Informatics Approach. Digestive Disease Week (DDW). </p>
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+     <p> Zheng, Jiaping; Chapman, Wendy; Miller, Timothy; Lin, Chen; Crowley, Rebecca; Savova, Guergana. 2012. A system for coreference resolution for the clinical narrative. Journal of the American Medical Informatics Association. </p>
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+     <p> Savova, Guergana; Olson, Janet; Murphy, Sean; Cafourek, Victoria; Couch, Fergus; Goetz, Matthew; Ingle, James; Suman, Vera; Chute, Christopher and Weinshilboum, Richard. 2011. The electronic medical record and drug response research: automated discovery of drug treatment patterns for endocrine therapy of breast cancer. Journal of American Medical Informatics Association. </p>
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+     <p> Sohn, Sunghwan; Kocher, Jean-Pierre; Chute, Christopher; Savova, Guergana. 2011. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. Journal of American Medical Informatics Association. </p>
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+     <p> Wu, Stephen; Kaggal, Vinod; Savova, Guergana; Liu, Hongfang; Dligach, Dmitriy; Zheng, Jiaping; Chapman, Wendy; Chute, Christopher. 2011. Generality and reuse in a common type system for clinical natural language processing. Managing Interoperability and Complexity in Health Systems (MIXHS 2011), In conjuction with the 20th ACM International conference on information and knowledge management. October 28, 2011. Glasgow, UK. </p>
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+     <p> Chute, Christopher; Pathak, Jyoti; Savova, Guergana; Bailey Kent; Schor Marshall; Hart, Lacey; Beebe, Calvin and Huff, Stan. 2011. The SHARPn project on secondary use of electronic medical record data: progress, plans an possibilities. AMIA ann symp. </p>
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+     <p> Cairns, Brian ; Nielsen, Rodney; Masanz, James; Martin, James; Palmer, Martha; Ward, Wayne; Savova, Guergana. 2011. The MiPACQ Clinical Question Answering System. AMIA Annual Symposium. Washington, DC. </p>
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+     <p> Wilke, Russell; Xu, Hua; Denny, Joshua; Roden, Daniel; Krauss, Ronald M; McCarty, Catherine A; Davis, R; Skaar, Todd; Lamba Jatinder and Savova, Guergana. 2011. The emerging role of electronic medical records in pharamacogenomics. Journal of Clinical Pharmacology and Therapeutics. </p>
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+     <p> Nielsen, Rodney; Masanz, James; Ogren, Philip; Ward, Wayne; Martin, James; Palmer, Martha; Savova, Guergana. 2010. An architecture for complex clinical question answering. 1st Annual ACM International Conference on Health Informatics (IHI 2010). Washington, DC. </p>
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+     <p> Kullo, Iftikar; Fan, Jin; Pathak, Jyotishman; Savova, Guergana; Ali, Zeenat; Chute, Christopher. 2010. Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. JAMIA. DOI:10.1136/jamia.2010.004366. </p>
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+     <p> Sohn, Sunghwan; Murphy, Sean; Masanz, James; Kocher, Jean-Pierre; Savova, Guergana. 2010. Classification of medication status change in clinical narratives. AMIA Fall symposium. </p>
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+     <p> Savova, Guergana; Fan, Jin; Ye, Zi; Murphy, Sean; Zheng, Jiaping; Chute, Christopher and Kullo, Iftikhar. 2010. Discovering peripheral arterial disease cases from radiology notes using natural language processing. AMIA Fall symposium. </p>
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+     <p> Savova, Guergana; Masanz, James; Ogren, Philip; Zheng, Jiaping; Sohn, Sunghwan; Kipper-Schuler, Karin and Chute, Christopher. 2010. Mayo Clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. JAMIA 2010;17:507-513 doi:10.1136/jamia.2009.001560 </p>
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+     <p> Cheng, Lionel; Zheng, Jiaping; Savova, Guergana and Erickson, Bradley. 2010. Discerning tumor status from unstructured MRI reports â completeness of information in existing reports and utility of natural language processing. Journal of Digital Imaging of the Society of Imaging Informatics in Medicine, ISSN: 0897-1889: 23(2), 119-133. PMID: 19484309. (Best paper 2010 award of the Journal of Digital Imaging). http://www.ncbi.nlm.nih.gov/pubmed/19484309 </p>
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+     <p> Sohn, Sunghwan and Savova, Guergana. 2009. Mayo Clinic smoking status classification system. Proc. AMIA, Nov. 2009. </p>
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+     <p> Garla, V. et al. The Yale cTAKES extensions for document classification: architecture and application. Journal of the American Medical Informatics Association (2011). doi:10.1136/amiajnl-2011-000093 </p>
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+     <p> Garla, V and Brandt, C. Ontology-Guided Feature Engineering for Clinical Text Classification (2012) http://dx.doi.org/10.1016/j.jbi.2012.04.010. </p>
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