James, If you could share some examples, I'll take a closer look. But in the meantime, in your LookupDesc_Db.xml [1], I believe you can just use the NamedEntityLookupConsumerImpl instead of the UmlsToSnomedDbConsumerImpl. While you're there, you may also consider expanding the Lookup Window or Parts Of Speech exclusions...
[1] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml On Mon, Sep 22, 2014 at 2:17 AM, EM Gladiators <[email protected]> wrote: > Pei, I am not seeing anything being filtered in the logs. I checked both > the output in the terminal and also I set the log in the software to log > everything. How do I go about suppressing the OrangeBook filter and use > only Rxnorm? I'm still not sure the filtering is the problem, because > aspirin is also found in OrangeBook. But, removing the OrgangeBook filter > would be a good place to start to see if it improves the medication name > recognition. > > Thank you, > > James > > On Sun, Sep 21, 2014 at 10:30 PM, Pei Chen <[email protected]> wrote: >> >> In the logs, do you see something like "Filtered out xyz"? >> I think the default configuration has a OrangeBook Filter consumer >> applied. That is only RxNorm concepts that also exist in the >> OrangeBook are returned. I'm not sure if this is causing some of your >> drugs to be missed, but worth taking out OrangeBook filter out to >> confirm. >> We should probably default all RxNorm to be returned and make the >> OrangeBook filter optional in the future release. >> >> On Sun, Sep 21, 2014 at 5:53 PM, EM Gladiators <[email protected]> >> wrote: >> > I have recently installed ctakes. I am using the >> > AggregatePlaintextUMLSProcessor. When running the CVD, it is not >> > accurately >> > annotating all medication names. Specific medication names that it >> > annotates correctly are metformin and nifedipine. Specific medications >> > it >> > fails to annotate are aspirin and simvastatin. It is unclear why some >> > names >> > would be annotated correctly and some not, even though all medication >> > names >> > are found in rxnorm. I am afraid that it is not correctly using the >> > rxnorm >> > files. Is there a way to check to see if the full rxnorm is being >> > searched? >> > >> > I have not had a problem with snomed CT terms, ctakes does appear to be >> > capturing these correctly. >> > >> > Thank you, >> > >> > James Foster >> > >> > My setup is as follows... >> > >> > Mac OS 10.9.4 >> > Java version 1.8.0_20 >> > ctakes version 3.2.0 with optional resources package > >
