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From Stuti Awasthi <stutiawas...@hcl.com>
Subject RE: Integrate cTakes with latest UMLS DB
Date Tue, 05 Apr 2016 07:32:18 GMT
Hi Brandon,

Sorry for coming late on this as I was stuck with some other task. Ok so I have used Dictionary_Gui
with Java 8 and compiled successfully. After that used the tool to create the hsql data files
for my current UMLS2015 and it generates all the relevant files as described in your post

After generating the dictionary, I wanted to use it with cTakes , so I have modified "UmlsLookupAnnotator.xml"

And selected "AggregatePlaintextFastUMLSProcessor" as analysis engine for clinicalpipeline.
Following is the error which Im getting:
Error Trace:
05 Apr 2016 11:52:55  INFO JdbcConnectionFactory - Connecting to jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/umls2015aa/umls2015aa:

.................................................. 50
.................................................. 100
.................................................. 150
05 Apr 2016 11:53:52  INFO JdbcConnectionFactory -  Database connected
05 Apr 2016 11:53:53 ERROR JdbcConceptFactory - Could not create Concept Data Selection Call
java.sql.SQLException: Table not found in statement [SELECT * FROM long WHERE CUI = ?]
        at org.hsqldb.jdbc.Util.throwError(Unknown Source)
        at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source)
        at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source)
        at org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.createSelectCall(JdbcConceptFactory.java:204)
        at org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.<init>(JdbcConceptFactory.java:83)
        at org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.<init>(JdbcConceptFactory.java:57)
        at org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory.<init>(UmlsJdbcConceptFactory.java:30)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)

Please find attached "umls2015aa.xml" file generated by dictionary_gui tool. Why Im getting
the above mentioned error.. Any ideas/suggestions will be helpful.

Thanks &Regards
Stuti Awasthi

From: Stuti Awasthi
Sent: Thursday, March 31, 2016 5:17 PM
To: user@ctakes.apache.org
Subject: RE: Integrate cTakes with latest UMLS DB

Ya I have read the long conversation between you and Sean on how to use dictionary tool utility
and that really helped. Thanks to Sean.
Thanks for java 8 pointer. Presently Im using Java7 and already added libraries in build path.
Let me try with Java8 and Il come back.

Example of error : org.apache.ctakes.dictionary.creator.gui.umls.Concept.java

concept.getTuis().stream().forEach( this::addTui );

The method stream() is undefined for the type Collection<Tui>

This is just an example, similarly Im getting more errors in different classes.

Stuti Awasthi

From: Geise, Brandon D. [bdgeise@geisinger.edu]
Sent: Thursday, March 31, 2016 5:02 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: RE: Integrate cTakes with latest UMLS DB
Hi Stuti,

All credit for the dictionary work goes to Sean Finan.  What errors are you getting?  I'm
not aware of a precompiled jar.  I do remember that I needed to switch to Java 8, if you aren't
already to compile the project.  You also may need to reference the lib folder or move those
jars to the project library path in order to compile.


From: Stuti Awasthi [mailto:stutiawasthi@hcl.com]
Sent: Thursday, March 31, 2016 7:14 AM
To: 'user@ctakes.apache.org' <user@ctakes.apache.org<mailto:user@ctakes.apache.org>>
Subject: RE: Integrate cTakes with latest UMLS DB

Hi All,
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.

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.

Thanks for your help and patience.

Stuti Awasthi
From: Stuti Awasthi
Sent: Thursday, March 31, 2016 11:58 AM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB
Hi Brandon, Jessica

I lookedup at dictionary-gui utility.  Here is what I did : Checkout the source code https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/
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 :

*         Is there any README as Jessica mentioned or simply launching the CreaterGui.java
class would be suffice.

*         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.

Few more questions:

*         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.

*         I found the following link in Ctakes3.1 documentation but looks like broken. Any
clue on redirected path/links

     *   https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=423
     *   https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80&start=20#p1459

  *   Can I create full dictionary(not only the fast one) from dictionary tool.
Thanks &Regards
Stuti Awasthi

From: Stuti Awasthi
Sent: Tuesday, March 29, 2016 5:35 PM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB

Thanks Brandon, then I will check dictionary-gui tool and try to use it and will get back
with queries if any.

Stuti Awasthi
From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu]
Sent: Tuesday, March 29, 2016 5:32 PM
To: Stuti Awasthi; 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Stuti,

Unless someone else has created another solution the current Dictionary Gui tool doesn't have
this support yet.  It's something that I plan to work on in the future for the GUI tool.


Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Stuti Awasthi<mailto:stutiawasthi@hcl.com>
Sent: Tuesday, March 29, 2016 7:59 AM
To: 'user@ctakes.apache.org'<mailto:user@ctakes.apache.org>
Subject: RE: Integrate cTakes with latest UMLS DB

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.

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.  One more query, cTakes also provides "DictionaryLookupAnnotatorDB" 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.

Thanks for the help!

Stuti Awasthi

From: Glover, Jessica [mailto:Jessica.Glover@ssa.gov]
Sent: Tuesday, March 29, 2016 5:17 PM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Stuti,

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."

Searchable cTakes mailing list archive: http://ctakes.markmail.org/search/


From: Stuti Awasthi [mailto:stutiawasthi@hcl.com]
Sent: Tuesday, March 29, 2016 7:10 AM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi All,
Any help will be good. Im still waiting for some response.

Thanks &Regards
Stuti Awasthi

From: Stuti Awasthi
Sent: Monday, March 28, 2016 2:46 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Integrate cTakes with latest UMLS DB

Hi All,
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.

Database Name: umls
Numbers of Tables created : 53
Eg : mysql> show tables;
| Tables_in_umls           |
| AMBIGLUI                 |
| AMBIGSUI                 |
| DELETEDCUI               |
| DELETEDLUI               |
| SRSTRE1                  |
| SRSTRE2                  |

Now im not able to find any step by step guide to integrate cTakes with umls database.
Here is what I have done :
1) Modified DictionaryLookupAnnotatorDB.xml with jdbc url of my database along with username
and password.

Now I believe I also need to modify LookupDesc_DB.xml with some umls tablename which can get
cui, tui and text info.
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.
Also please point some steps guide/document of available for cTakes integration with UMLS.

Thanks &Regards
Stuti Awasthi

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