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From build...@apache.org
Subject svn commit: r942756 - in /websites/staging/ctakes/trunk: cgi-bin/ content/ content/usedby.html
Date Sat, 07 Mar 2015 14:42:45 GMT
Author: buildbot
Date: Sat Mar  7 14:42:44 2015
New Revision: 942756

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 14:42:44 2015
@@ -1 +1 @@
-1664748
+1664859

Propchange: websites/staging/ctakes/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Sat Mar  7 14:42:44 2015
@@ -1 +1 @@
-1664748
+1664859

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 14:42:44 2015
@@ -123,45 +123,107 @@
 <!--- BEGIN MAIN CONTENT -->
     <div class="container">
    <div class="row">
-      <h1> Who's using cTAKES? </h1>
-      <p> There are a variety of different organizations using and working on cTAKES.</p>
+      <h1> Users of cTAKES </h1>
    </div>
+
    <div class="row">
       <h2>Academic</h2>
+
       <p class="lead">
          Hospitals and Academic Institutions
       </p>
-      <p> Insert images for the different institutions </p>
+
       <p>Boston Children's Hospital</p>
+
       <p>Cincinnati Children’s Hospital</p>
+
       <p>Mayo Clinic</p>
+
       <p>University of Colorado Boulder</p>
+
       <p>University of Pittsburgh</p>
+
       <p>University of California, San Diego</p>
    </div>
-   <div class="row">
+
+<p><div class="row">
       <h2>Software Projects</h2>
-   </div>
-   <div class="row">
-      <h2>Companies</h2>
-      <p><a href="http://wwww.wiredinformatics.com">Wired Informatics</a></p>
-   </div>
-   <div class="row">
-      <h2>Publications</h2>
-   </div>
-   <div class="row">
-      <div class="col-md-5 col-sm-5 col-padded-top col-center">
-         <div style="width: 100%; max-width: 272px; display: inline-block; text-align:
center;">
-            <img src="images/pb-ctakes.jpg" style="margin-top: 15px; width: 100%; max-width:
200px;"/>
-            <div class="caption" style="min-width: 272px;">Click <a href="mailto:dev@ctakes.apache.org">
here</a> to add
-               your name/organization.
-            </div>
-         </div>
-      </div>
-   </div>
+   </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>
 
+<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>
+
+<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>
+        <span class="nt">&lt;img</span> <span class="na">src=</span><span
class="s">&quot;images/pb-ctakes.jpg&quot;</span> <span class="na">style=</span><span
class="s">&quot;margin-top: 15px; width: 100%; max-width: 200px;&quot;</span><span
class="nt">/&gt;</span>
+
+        <span class="nt">&lt;div</span> <span class="na">class=</span><span
class="s">&quot;caption&quot;</span> <span class="na">style=</span><span
class="s">&quot;min-width: 272px;&quot;</span><span class="nt">&gt;</span>Click
<span class="nt">&lt;a</span> <span class="na">href=</span><span
class="s">&quot;mailto:dev@ctakes.apache.org&quot;</span><span class="nt">&gt;</span>
here<span class="nt">&lt;/a&gt;</span> to add
+           your name/organization.
+        <span class="nt">&lt;/div&gt;</span>
+     <span class="nt">&lt;/div&gt;</span>
+  <span class="nt">&lt;/div&gt;</span>
+</pre></div>
+
+
+<p></div>
+</div></p>
 <!--- END MAIN CONTENT --> 
 
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