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From Stuti Awasthi <stutiawas...@hcl.com>
Subject RE: Integrate cTakes with latest UMLS DB
Date Thu, 31 Mar 2016 11:14:11 GMT
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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi All,
<div>Sorry , I think I got confused with dictionary-gui and dictionary-tool projects.
Jessica mentioned about dictionary tool and its README which I followed along with the previous
mail threads to generate umls dictionary in file format. Im still to use this
 dictionary with cTakes so i might comeback with issues.</div>
<div><br>
</div>
<div>Also I would like to use dictionary-gui posted by Brandon. When I have checkout
the code and imported in eclipse, its showing compilation error in classes due to which even
I have created the jar of the project, it is not running. Any idea about the compilation
 errors or if there is a pre built binary which can be used (similar to dictionary tools jar)
that would be great.</div>
<div><br>
</div>
<div>Thanks for your help and patience.</div>
<div><br>
</div>
<div>Regards</div>
<div>Stuti Awasthi</div>
<div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF932469" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b>
Stuti Awasthi<br>
<b>Sent:</b> Thursday, March 31, 2016 11:58 AM<br>
<b>To:</b> 'user@ctakes.apache.org'<br>
<b>Subject:</b> RE: Integrate cTakes with latest UMLS DB<br>
</font><br>
</div>
<div></div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span style="color:#1F497D">Hi Brandon, Jessica</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">I lookedup at dictionary-gui
utility. &nbsp;Here is what I did : Checkout
</span><span style="color:#1F497D">the source code <a href="https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/"
target="_blank">
https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/</a> and imported in
my eclipse IDE. Now I was not able to find any README with this project. Hence I checked the
code and found that “CreaterGui.java” might be the mail class to launch the GUI.
 My queries are :</span></p>
<p class="MsoListParagraph" style="text-indent:-.25in"><span style="font-family:Symbol;
color:#1F497D"><span style="">·<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span style="color:#1F497D">Is there any README
as Jessica mentioned or simply launching the
</span><span style="color:#1F497D">CreaterGui.java class would be suffice.</span><span
style="color:#1F497D"></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in"><span style="font-family:Symbol;
color:#1F497D"><span style="">·<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span style="color:#1F497D">Is there any commands
to execute tool on linux server (without gnome) . Something like command like options? Im
asking this because Im working on linux machine where I have installed lated UMLS2015.</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Few more questions:</span></p>
<p class="MsoListParagraph" style="text-indent:-.25in"><span style="font-family:Symbol;
color:#1F497D"><span style="">·<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span style="color:#1F497D">As Brandon mentioned
: that I might need to create the tables that will have same information (based on rare /first
word approach). Do we know how to create those tables ?? Any SQL statements or links will
be
 useful.</span></p>
<p class="MsoListParagraph" style="text-indent:-.25in"><span style="font-family:Symbol;
color:#1F497D"><span style="">·<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span style="color:#1F497D">I found the following
link in Ctakes3.1 documentation but looks like broken. Any clue on redirected path/links</span></p>
<ul type="disc">
<ul type="circle">
<li class="MsoNormal" style="color:#333333; line-height:15.0pt; background:white">
<span style="font-size:10.5pt; font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><a
href="https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=423" target="_blank"><span
style="color:#326CA6; text-decoration:none">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=423</span></a></span></li><li
class="MsoNormal" style="color:#333333; line-height:15.0pt; background:white">
<span style="font-size:10.5pt; font-family:&quot;Arial&quot;,&quot;sans-serif&quot;"><a
href="https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=80&amp;start=20#p1459"
target="_blank"><span style="color:#326CA6; text-decoration:none">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=80&amp;start=20#p1459</span></a></span></li></ul>
<li class="MsoNormal" style="color:#1F497D; line-height:15.0pt; background:white">
Can I create full dictionary(not only the fast one) from dictionary tool.</li></ul>
<div>
<p class="MsoNormal"><span style="color:#1F497D">Thanks &amp;Regards</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Stuti Awasthi</span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<div style="border:none; border-top:solid #B5C4DF 1.0pt; padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span
style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
Stuti Awasthi
<br>
<b>Sent:</b> Tuesday, March 29, 2016 5:35 PM<br>
<b>To:</b> 'user@ctakes.apache.org'<br>
<b>Subject:</b> RE: Integrate cTakes with latest UMLS DB</span></p>
</div>
</div>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks Brandon, then I will check
dictionary-gui tool and try to use it and will get back with queries if any.
</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<p class="MsoNormal"><span style="color:#1F497D">Regards</span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D">Stuti Awasthi</span></p>
<div>
<div style="border:none; border-top:solid #B5C4DF 1.0pt; padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span
style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
Geise, Brandon D. [<a href="mailto:bdgeise@geisinger.edu" target="_blank">mailto:bdgeise@geisinger.edu</a>]
<br>
<b>Sent:</b> Tuesday, March 29, 2016 5:32 PM<br>
<b>To:</b> Stuti Awasthi; 'user@ctakes.apache.org'<br>
<b>Subject:</b> RE: Integrate cTakes with latest UMLS DB</span></p>
</div>
</div>
<p class="MsoNormal">&nbsp;</p>
<div>
<p class="MsoNormal">Hi Stuti,</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Unless someone else has created another solution the current Dictionary
Gui tool doesn’t have this support yet.&nbsp; It’s something that I plan to work on
in the future for the GUI tool.&nbsp;
</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Thanks,</p>
<p class="MsoNormal">Brandon</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986"
target="_blank">
Mail</a> for Windows 10</p>
<p class="MsoNormal"><span style="font-size:12.0pt; font-family:&quot;Times New
Roman&quot;,&quot;serif&quot;">&nbsp;</span></p>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From: </b><a href="mailto:stutiawasthi@hcl.com"
target="_blank">Stuti Awasthi</a><br>
<b>Sent: </b>Tuesday, March 29, 2016 7:59 AM<br>
<b>To: </b><a href="mailto:user@ctakes.apache.org" target="_blank">'user@ctakes.apache.org'</a><br>
<b>Subject: </b>RE: Integrate cTakes with latest UMLS DB</p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt; font-family:&quot;Times New
Roman&quot;,&quot;serif&quot;">&nbsp;</span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:#1F497D">Thanks Brandon, Jessica for response.
I will look at dictionary tools as mentioned and will try to figure out how it can be used
for my purpose. I will certainly get back on mailing list with more queries if
 any. </span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">As of now with limited understanding,
I understand that current UMLS2015 database will be converted to hsql format which I can use
in the pipeline by changing configurations in required XMLs.&nbsp; One more query,
 cTakes also provides “<b>DictionaryLookupAnnotatorDB</b>” which is supposed
to be used if we want to connect to required tables in umls database. Please correct my understanding
but do we have similar tool/script to be execute on umls database to generate
 the required format table “umls2015ab” which can be directly included in dictionary lookup.</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks for the help!</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<p class="MsoNormal"><span style="color:#1F497D">Regards</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Stuti Awasthi</span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<div style="border:none; border-top:solid #B5C4DF 1.0pt; padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span
style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
Glover, Jessica [<a href="mailto:Jessica.Glover@ssa.gov" target="_blank">mailto:Jessica.Glover@ssa.gov</a>]
<br>
<b>Sent:</b> Tuesday, March 29, 2016 5:17 PM<br>
<b>To:</b> 'user@ctakes.apache.org'<br>
<b>Subject:</b> RE: Integrate cTakes with latest UMLS DB</span></p>
</div>
</div>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal"><span style="color:#1F497D">Hi Stuti,</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">One thing to note about the dictionary
tool is that it is still in sandbox mode, so there is no official documentation or step-by-step
guide for it. However, it contains a readme, and it has been discussed on
 the mailing list, so you can search the archive for that “documentation.”</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Searchable cTakes mailing list
archive:
<a href="http://ctakes.markmail.org/search/" target="_blank">http://ctakes.markmail.org/search/</a></span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards, </span></p>
<p class="MsoNormal"><span style="color:#1F497D">Jessica</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<div style="border:none; border-top:solid #B5C4DF 1.0pt; padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span
style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
Stuti Awasthi [<a href="mailto:stutiawasthi@hcl.com" target="_blank">mailto:stutiawasthi@hcl.com</a>]
<br>
<b>Sent:</b> Tuesday, March 29, 2016 7:10 AM<br>
<b>To:</b> 'user@ctakes.apache.org'<br>
<b>Subject:</b> RE: Integrate cTakes with latest UMLS DB</span></p>
</div>
</div>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal"><span style="color:#1F497D">Hi All,</span></p>
<p class="MsoNormal"><span style="color:#1F497D">Any help will be good. Im still
waiting for some response.</span></p>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<p class="MsoNormal"><span style="font-size:8.0pt; color:#1F497D">Thanks &amp;Regards</span></p>
<p class="MsoNormal"><span style="font-size:8.0pt; color:#1F497D">Stuti Awasthi</span></p>
<p class="MsoNormal"><span style="font-size:8.0pt; color:#1F497D">&nbsp;</span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D">&nbsp;</span></p>
<div>
<div style="border:none; border-top:solid #B5C4DF 1.0pt; padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span
style="font-size:10.0pt; font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
Stuti Awasthi
<br>
<b>Sent:</b> Monday, March 28, 2016 2:46 PM<br>
<b>To:</b> <a href="mailto:user@ctakes.apache.org" target="_blank">user@ctakes.apache.org</a><br>
<b>Subject:</b> Integrate cTakes with latest UMLS DB</span></p>
</div>
</div>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Hi All,</p>
<p class="MsoNormal">I have been exploring cTakes and wanted to use latest UMLS 2015ab
with it. To achieve the same, I have installed UMLS in mysql database.</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Database Name: umls</p>
<p class="MsoNormal">Numbers of Tables created : 53</p>
<p class="MsoNormal">Eg : mysql&gt; show tables;</p>
<p class="MsoNormal">&#43;--------------------------&#43;</p>
<p class="MsoNormal">| Tables_in_umls&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">&#43;--------------------------&#43;</p>
<p class="MsoNormal">| AMBIGLUI&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">| AMBIGSUI&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">| DELETEDCUI&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">| DELETEDLUI&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">| DELETEDSUI&nbsp;&nbsp; </p>
<p class="MsoNormal">……</p>
<p class="MsoNormal">| SRSTRE1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">| SRSTRE2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Now im not able to find any step by step guide to integrate cTakes
with umls database.</p>
<p class="MsoNormal">Here is what I have done :</p>
<p class="MsoNormal">1) Modified DictionaryLookupAnnotatorDB.xml with jdbc url of my
database along with username and password.</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Now I believe I also need to modify LookupDesc_DB.xml with some
umls tablename which can get cui, tui and text info.
</p>
<p class="MsoNormal">I need some help , which table should I be pointing to lookup ?
Also after is there any other step or I should be good in executing clinical pipeline with
umls database.
</p>
<p class="MsoNormal">Also please point some steps guide/document of available for cTakes
integration with UMLS.</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Thanks &amp;Regards</p>
<p class="MsoNormal">Stuti Awasthi</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal"><span style="color:gray"><br>
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