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From build...@apache.org
Subject svn commit: r868844 - in /websites/staging/ctakes/trunk: cgi-bin/ content/ content/history.html
Date Mon, 08 Jul 2013 21:14:28 GMT
Author: buildbot
Date: Mon Jul  8 21:14:28 2013
New Revision: 868844

Log:
Staging update by buildbot for ctakes

Modified:
    websites/staging/ctakes/trunk/cgi-bin/   (props changed)
    websites/staging/ctakes/trunk/content/   (props changed)
    websites/staging/ctakes/trunk/content/history.html

Propchange: websites/staging/ctakes/trunk/cgi-bin/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Mon Jul  8 21:14:28 2013
@@ -1 +1 @@
-1500954
+1500955

Propchange: websites/staging/ctakes/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Mon Jul  8 21:14:28 2013
@@ -1 +1 @@
-1500954
+1500955

Modified: websites/staging/ctakes/trunk/content/history.html
==============================================================================
--- websites/staging/ctakes/trunk/content/history.html (original)
+++ websites/staging/ctakes/trunk/content/history.html Mon Jul  8 21:14:28 2013
@@ -87,30 +87,6 @@
 <p>Following Dr. Savova's move to Children's Hospital Boston in early 2010, the core
development team expanded to include Mayo Clinic and Children's Hospital Boston. Additional
collaborations with external groups at University of Colorado, Brandeis University, University
of Pittsburgh, University of California at San Diego continue to extend the capabilities of
cTAKES into areas such Temporal Reasoning, Clinical Question and Answering, and coreference
resolution for the clinical domain. In 2010, cTAKES was adopted by the I2B2 program and is
a central component of the SHARP Area 4. </p>
 <p>On June 11, 2012, cTAKES entered the Apache Incubator.</p>
 <p>On March 20, 2013, cTAKES has graduated into an Apache TLP.</p>
-<h2 id="publications-and-acknowledgments">Publications and Acknowledgments</h2>
-<h4 id="if-you-wish-to-cite-ctakes-in-a-publication-please-use">If you wish to cite
cTAKES in a publication, please use:</h4>
-<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>
-<h4 id="other-ctakes-publications-describing-different-components-and-applications">Other
cTAKES publications describing different components and applications:</h4>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<p>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</p>
-<p>Sohn, Sunghwan and Savova, Guergana. 2009. Mayo Clinic smoking status classification
system. Proc. AMIA, Nov. 2009.</p>
-<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>
-<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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