Title: Apache cTAKES - History Notice: Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. #Related Resources ##Intro This page is a place to put links to info about talks (past and upcoming), tutorials, articles, publications, slides, PDFs, discussions, etc. about cTAKES and related technologies. No endorsements are implied or given. #Useful Links 1. [Apache UIMA][1]: cTAKES is built on top of the UIMA framework. 2. [Apache uimaFIT][2]: uimaFIT provides Java annotations for describing UIMA components which can be used to directly describe the UIMA components in the code. 3. [Knowtator][3]: Knowtator is a general-purpose text annotation tool that is integrated with the Protégé knowledge representation system. 4. [Anafora][4]: Anafora is a browser-based annotation tool. #Videos cTAKES description by Guergana: [https://vimeo.com/24829353][5] #Awards [cTAKES paper received the highest number of citations][6] contributing to the [JAMIA][7] 2012 impact factor. ![cTAKES paper received the highest number of citations][8] #Publications ####If you wish to cite cTAKES in a publication, please use: 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 ####Other cTAKES publications describing different components and applications: 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. 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. 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). 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). 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. 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. 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. 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. 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. 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. 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. 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. 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. Sohn, Sunghwan; Murphy, Sean; Masanz, James; Kocher, Jean-Pierre; Savova, Guergana. 2010. Classification of medication status change in clinical narratives. AMIA Fall symposium. 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. 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 Cheng, Lionel; Zheng, Jiaping; Savova, Guergana and Erickson, Bradley. 2010. Discerning tumor status from unstructured MRI reports – 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 Sohn, Sunghwan and Savova, Guergana. 2009. Mayo Clinic smoking status classification system. Proc. AMIA, Nov. 2009. 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 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. [1]: http://uima.apache.org/ [2]: http://uima.apache.org/uimafit.html [3]: http://knowtator.sourceforge.net/quickstart.shtml [4]: https://github.com/weitechen/anafora#README [5]: https://vimeo.com/24829353 [6]: images/jamia_award_2013.jpg [7]: http://jamia.bmj.com/ [8]: images/jamia_award_2013_small.jpg