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Posted to user@ctakes.apache.org by Vlad Valtchinov <vl...@gmail.com> on 2013/09/16 23:10:38 UTC
configuring cTakes for getting input from a db table and persisting output to i2b2 and/or flat db table
Hello cTakes Users-
we're relatively new to cTakes (even though not to NLP)
and are currently evaluating cTakes 3.0 for moving some of
our clinical radiology DSS pipeline to Apache cTakes.
We have an evaluation install under Linux, and would like to start
with configuring cTakes to a) take input from a ms sql db table, and b)
configure it so that it writes NLP results back to the db, in i2b2 format as
well
as in a flat table format. Somebody out there has probably implemented this
already -
can you point us to an online resource where this is detailed, or even
better
share binary implementation with us? cTakes is supposedly very similar to
another
Apache project, Solr, and yet we could not find a clear documentation of
DataHandler configuration under cTakes... maybe not looking at the right
place...
Thanks much in advance.
Vlad Valtchinov
Brigham Radiology, CEBI
RE: configuring cTakes for getting input from a db table and persisting output to i2b2 and/or flat db table
Posted by Vlad Valtchinov <vl...@gmail.com>.
Thanks for the responses, Pei.
So what seems to be the prevailing and most mature deployment mode out there
-
deposit xml formatted input files in a given directory and cTakes write the
results back in a similar format? Any idea how this compares in speed and
scalability to
the db input/db output option?
Regarding JdbcCollectionReader (input) and CasConsumer (output) enabling -
are there ways to add and configure those from the visual tool, CVD (as it
is done in the
ctakes i2b2 tool on the i2b2 wiki)? Also, where do you
specify the mapping of the db columns to the internal filed names so cTakes
knows
what to process (like i.e. in the DataHandler's section of the
solrconfig.xml file)?
If somebody has implemented a similar cTakes config and would be willing to
share the details and the wisdom we will appreciate tremendously.
Regards,
vlad
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Monday, September 16, 2013 6:12 PM
To: user@ctakes.apache.org; vlad.valtchinov@gmail.com
Subject: RE: configuring cTakes for getting input from a db table and
persisting output to i2b2 and/or flat db table
> to a) take input from a ms sql db table
Something like a JdbcCollectionReader?
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/a
pache/ctakes/core/cr/JdbcCollectionReader.java
>b) configure it so that it writes NLP results back to the db
Something like a CasConsumer?
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/a
pache/ctakes/core/cc/CasConsumer.java
>, in i2b2 format as well as in a flat table format.
There was some early/prelim work done in sandbox on the i2b2 formats, but
never really made it to mainstream ctakes (yet.).
http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/java/org/
chboston/cnlp/ctakes/gui/runtime/result/
--Pei
From: Vlad Valtchinov [mailto:vlad.valtchinov@gmail.com]
Sent: Monday, September 16, 2013 5:13 PM
To: user@ctakes.apache.org
Subject: configuring cTakes for getting input from a db table and persisting
output to i2b2 and/or flat db table
Hello cTakes Users-
we're relatively new to cTakes (even though not to NLP)
and are currently evaluating cTakes 3.0 for moving some of
our clinical radiology DSS pipeline to Apache cTakes.
We have an evaluation install under Linux, and would like to start
with configuring cTakes to a) take input from a ms sql db table, and b)
configure it so that it writes NLP results back to the db, in i2b2 format as
well
as in a flat table format. Somebody out there has probably implemented this
already -
can you point us to an online resource where this is detailed, or even
better
share binary implementation with us? cTakes is supposedly very similar to
another
Apache project, Solr, and yet we could not find a clear documentation of
DataHandler configuration under cTakes... maybe not looking at the right
place...
Thanks much in advance.
Vlad Valtchinov
Brigham Radiology, CEBI
RE: configuring cTakes for getting input from a db table and
persisting output to i2b2 and/or flat db table
Posted by "Carrell, David" <ca...@ghc.org>.
Our NLP developers have created components that can be called in the collection processing engine's (CPE) configurator to read from a relational database (via ODBC) and to either write the structured data to a relational database or to a flat (CSV) file. It is very useful. I think a wizard to allow non-developers to implement the same locally would be greatly appreciated.
-David Carrell
Group Health
-----Original Message-----
From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik Sarma
Sent: Monday, September 16, 2013 3:25 PM
To: dev@ctakes.apache.org
Subject: Re: configuring cTakes for getting input from a db table and persisting output to i2b2 and/or flat db table
I was actually thinking about this use case earlier today -- it is not particularly easy to set cTAKES up to work with a local database (either for lookup or for data, though the latter is certainly easier). Setting up the appropriate database for a local UMLS installation is also inconvenient for the non-developer. I have been thinking about putting together a wizard or some such to help folks through the process -- do you think it'd be worthwhile? I'm not really sure what proportion of users use a local UMLS install; personally I've found the web API to be far too slow for my workflows.
--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to the House of Delegates of the American Medical Association ksarma@ksarma.com
gchat: ksarma@gmail.com
linkedin: www.linkedin.com/in/ksarma
On Mon, Sep 16, 2013 at 3:11 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> > to a) take input from a ms sql db table****
>
> Something like a JdbcCollectionReader?****
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java
> /org/apache/ctakes/core/cr/JdbcCollectionReader.java
> ****
>
> ** **
>
> >b) configure it so that it writes NLP results back to the db****
>
> Something like a CasConsumer?****
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java
> /org/apache/ctakes/core/cc/CasConsumer.java
> ****
>
> ** **
>
> >, in i2b2 format as well as in a flat table format.****
>
> There was some early/prelim work done in sandbox on the i2b2 formats,
> but never really made it to mainstream ctakes (yet...). ****
>
>
> http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/jav
> a/org/chboston/cnlp/ctakes/gui/runtime/result/
> ****
>
> ** **
>
> --Pei****
>
> ** **
>
> *From:* Vlad Valtchinov [mailto:vlad.valtchinov@gmail.com]
> *Sent:* Monday, September 16, 2013 5:13 PM
> *To:* user@ctakes.apache.org
> *Subject:* configuring cTakes for getting input from a db table and
> persisting output to i2b2 and/or flat db table****
>
> ** **
>
> Hello cTakes Users-****
>
> ** **
>
> we're relatively new to cTakes (even though not to NLP)****
>
> and are currently evaluating cTakes 3.0 for moving some of****
>
> our clinical radiology DSS pipeline to Apache cTakes.****
>
> ** **
>
> We have an evaluation install under Linux, and would like to start****
>
> with configuring cTakes to a) take input from a ms sql db table, and
> b)***
> *
>
> configure it so that it writes NLP results back to the db, in i2b2
> format as well****
>
> as in a flat table format. Somebody out there has probably implemented
> this already -****
>
> can you point us to an online resource where this is detailed, or even
> better ****
>
> share binary implementation with us? cTakes is supposedly very similar
> to another ****
>
> Apache project, Solr, and yet we could not find a clear documentation
> of**
> **
>
> DataHandler configuration under cTakes... maybe not looking at the
> right
> place...****
>
> ** **
>
> Thanks much in advance.****
>
> ** **
>
> Vlad Valtchinov****
>
> Brigham Radiology, CEBI****
>
________________________________
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Re: configuring cTakes for getting input from a db table and
persisting output to i2b2 and/or flat db table
Posted by Karthik Sarma <ks...@ksarma.com>.
I was actually thinking about this use case earlier today -- it is not
particularly easy to set cTAKES up to work with a local database (either
for lookup or for data, though the latter is certainly easier). Setting up
the appropriate database for a local UMLS installation is also inconvenient
for the non-developer. I have been thinking about putting together a wizard
or some such to help folks through the process -- do you think it'd be
worthwhile? I'm not really sure what proportion of users use a local UMLS
install; personally I've found the web API to be far too slow for my
workflows.
--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical
Association
ksarma@ksarma.com
gchat: ksarma@gmail.com
linkedin: www.linkedin.com/in/ksarma
On Mon, Sep 16, 2013 at 3:11 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> > to a) take input from a ms sql db table****
>
> Something like a JdbcCollectionReader?****
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
> ****
>
> ** **
>
> >b) configure it so that it writes NLP results back to the db****
>
> Something like a CasConsumer?****
>
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
> ****
>
> ** **
>
> >, in i2b2 format as well as in a flat table format.****
>
> There was some early/prelim work done in sandbox on the i2b2 formats, but
> never really made it to mainstream ctakes (yet…). ****
>
>
> http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/java/org/chboston/cnlp/ctakes/gui/runtime/result/
> ****
>
> ** **
>
> --Pei****
>
> ** **
>
> *From:* Vlad Valtchinov [mailto:vlad.valtchinov@gmail.com]
> *Sent:* Monday, September 16, 2013 5:13 PM
> *To:* user@ctakes.apache.org
> *Subject:* configuring cTakes for getting input from a db table and
> persisting output to i2b2 and/or flat db table****
>
> ** **
>
> Hello cTakes Users-****
>
> ** **
>
> we’re relatively new to cTakes (even though not to NLP)****
>
> and are currently evaluating cTakes 3.0 for moving some of****
>
> our clinical radiology DSS pipeline to Apache cTakes.****
>
> ** **
>
> We have an evaluation install under Linux, and would like to start****
>
> with configuring cTakes to a) take input from a ms sql db table, and b)***
> *
>
> configure it so that it writes NLP results back to the db, in i2b2 format
> as well****
>
> as in a flat table format. Somebody out there has probably implemented
> this already –****
>
> can you point us to an online resource where this is detailed, or even
> better ****
>
> share binary implementation with us? cTakes is supposedly very similar to
> another ****
>
> Apache project, Solr, and yet we could not find a clear documentation of**
> **
>
> DataHandler configuration under cTakes... maybe not looking at the right
> place...****
>
> ** **
>
> Thanks much in advance.****
>
> ** **
>
> Vlad Valtchinov****
>
> Brigham Radiology, CEBI****
>
RE: configuring cTakes for getting input from a db table and
persisting output to i2b2 and/or flat db table
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
> to a) take input from a ms sql db table
Something like a JdbcCollectionReader?
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
>b) configure it so that it writes NLP results back to the db
Something like a CasConsumer?
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
>, in i2b2 format as well as in a flat table format.
There was some early/prelim work done in sandbox on the i2b2 formats, but never really made it to mainstream ctakes (yet...).
http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/java/org/chboston/cnlp/ctakes/gui/runtime/result/
--Pei
From: Vlad Valtchinov [mailto:vlad.valtchinov@gmail.com]
Sent: Monday, September 16, 2013 5:13 PM
To: user@ctakes.apache.org
Subject: configuring cTakes for getting input from a db table and persisting output to i2b2 and/or flat db table
Hello cTakes Users-
we're relatively new to cTakes (even though not to NLP)
and are currently evaluating cTakes 3.0 for moving some of
our clinical radiology DSS pipeline to Apache cTakes.
We have an evaluation install under Linux, and would like to start
with configuring cTakes to a) take input from a ms sql db table, and b)
configure it so that it writes NLP results back to the db, in i2b2 format as well
as in a flat table format. Somebody out there has probably implemented this already -
can you point us to an online resource where this is detailed, or even better
share binary implementation with us? cTakes is supposedly very similar to another
Apache project, Solr, and yet we could not find a clear documentation of
DataHandler configuration under cTakes... maybe not looking at the right place...
Thanks much in advance.
Vlad Valtchinov
Brigham Radiology, CEBI