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/java/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**** >
