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From build...@apache.org
Subject svn commit: r942783 - in /websites/staging/ctakes/trunk: cgi-bin/ content/ content/usedby.html
Date Sat, 07 Mar 2015 20:21:37 GMT
Author: buildbot
Date: Sat Mar  7 20:21:37 2015
New Revision: 942783

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/usedby.html

Propchange: websites/staging/ctakes/trunk/cgi-bin/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Sat Mar  7 20:21:37 2015
@@ -1 +1 @@
-1664859
+1664914

Propchange: websites/staging/ctakes/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Sat Mar  7 20:21:37 2015
@@ -1 +1 @@
-1664859
+1664914

Modified: websites/staging/ctakes/trunk/content/usedby.html
==============================================================================
--- websites/staging/ctakes/trunk/content/usedby.html (original)
+++ websites/staging/ctakes/trunk/content/usedby.html Sat Mar  7 20:21:37 2015
@@ -127,11 +127,7 @@
    </div>
 
    <div class="row">
-      <h2>Academic</h2>
-
-      <p class="lead">
-         Hospitals and Academic Institutions
-      </p>
+      <h2>Hospitals and Academic Institutions</h2>
 
       <p>Boston Children's Hospital</p>
 
@@ -139,6 +135,8 @@
 
       <p>Mayo Clinic</p>
 
+      <p>Massachusetts Institute of Technology</p>
+
       <p>University of Colorado Boulder</p>
 
       <p>University of Pittsburgh</p>
@@ -150,65 +148,35 @@
       <h2>Software Projects</h2>
    </div></p>
 <p><div class="row">
-      <h2>Companies</h2></p>
-<div class="codehilite"><pre>  <span class="nt">&lt;p&gt;&lt;a</span>
<span class="na">href=</span><span class="s">&quot;http://wwww.wiredinformatics.com&quot;</span><span
class="nt">&gt;</span>Wired Informatics<span class="nt">&lt;/a&gt;&lt;/p&gt;</span>
-</pre></div>
-
-
-</div>
-
+      <h2>Companies</h2>
+      <p><a href="http://wwww.wiredinformatics.com">Wired Informatics</a></p>
+   </div></p>
 <p><div class="row">
-      <h2>Publications</h2></p>
-<div class="codehilite"><pre>  <span class="nt">&lt;h3&gt;</span>
If you wish to cite cTAKES in a publication, please use: <span class="nt">&lt;/h3&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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
<span class="nt">&lt;/p&gt;</span>
-
-  <span class="nt">&lt;h3&gt;</span> Other cTAKES publications describing
different components and applications: <span class="nt">&lt;/h3&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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). <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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&#39;s Disease and Ulcerative
Colitis in Electronic Medical Records using Natural Language Processing - A Novel Informatics
Approach. Digestive Disease Week (DDW). <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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.
<span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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.
<span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> Sohn, Sunghwan; Murphy, Sean;
Masanz, James; Kocher, Jean-Pierre; Savova, Guergana. 2010. Classification of medication status
change in clinical narratives. AMIA Fall symposium. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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
<span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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 <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> Sohn, Sunghwan and Savova, Guergana.
2009. Mayo Clinic smoking status classification system. Proc. AMIA, Nov. 2009. <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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 <span class="nt">&lt;/p&gt;</span>
-
-     <span class="nt">&lt;p&gt;</span> 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.
<span class="nt">&lt;/p&gt;</span>
-</pre></div>
-
-
-</div>
-
+      <h2>Publications</h2>
+      <h3> If you wish to cite cTAKES in a publication, please use: </h3>
+         <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>
+      <h3> Other cTAKES publications describing different components and applications:
</h3>
+         <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>
+   </div></p>
 <p><div class="row">
       <div class="col-md-5 col-sm-5 col-padded-top col-center"></p>
 <div class="codehilite"><pre>     <span class="nt">&lt;div</span>
<span class="na">style=</span><span class="s">&quot;width: 100%; max-width:
272px; display: inline-block; text-align: center;&quot;</span><span class="nt">&gt;</span>



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