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: [email protected] [mailto:[email protected]] On Behalf Of Karthik Sarma Sent: Monday, September 16, 2013 3:25 PM To: [email protected] 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 [email protected] gchat: [email protected] linkedin: www.linkedin.com/in/ksarma On Mon, Sep 16, 2013 at 3:11 PM, Chen, Pei <[email protected]>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:[email protected]] > *Sent:* Monday, September 16, 2013 5:13 PM > *To:* [email protected] > *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**** > ________________________________ GHC Confidentiality Statement This message and any attached files might contain confidential information protected by federal and state law. The information is intended only for the use of the individual(s) or entities originally named as addressees. The improper disclosure of such information may be subject to civil or criminal penalties. If this message reached you in error, please contact the sender and destroy this message. Disclosing, copying, forwarding, or distributing the information by unauthorized individuals or entities is strictly prohibited by law.
