Thanks Patrick, would you consider updating this in an FAQ on the wiki page I referenced below?
If you register for an account there and tell me the name I can grant you permissions to edit the page. thanks! Cheers, Chris From: Patrick Young <[email protected]> Reply-To: "[email protected]" <[email protected]> Date: Wednesday, October 10, 2018 at 12:59 PM To: "[email protected]" <[email protected]> Subject: Re: missing medication mentions (tika cTAKESParser) Inbox x Steph, the cTakes GUI is the default CVD I mentioned above & it does find the relevant medications. What are RRF files? Chris, ***good shout***. Made me realise what the issue was: the analysis engine... I altered CTakesConfig.properties file to point at AggregatePlaintextFastUMLSProcessor.xml rather than AggregatePlaintextUMLSProcessor.xml by editing this line aeDescriptorPath=/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml For the benefit of future travellers, I also had to reboot my computer afterwards... the database gets locked otherwise & it won't work. Thank you all for responding to me so promptly. I'm most happy. On Wed, 10 Oct 2018 at 16:35, Chris Mattmann <[email protected]> wrote: Hmm, perhaps Patrick take a look at the CTAKESContentHandler code here [1] and the wiki here: https://wiki.apache.org/tika/cTAKESParser We may be pinned to an older version of cTAKES and/or we may not be flowing it out properly (we take CTAKES output and then format it for TIka). Cheers, Chris [1] https://github.com/apache/tika/blob/master/tika-parsers/src/main/java/org/apache/tika/parser/ctakes/CTAKESContentHandler.java From: Tim Allison <[email protected]> Reply-To: "[email protected]" <[email protected]> Date: Wednesday, October 10, 2018 at 8:05 AM To: "[email protected]" <[email protected]> Subject: Re: missing medication mentions (tika cTAKESParser) Inbox x Chris, I know nothing about ctakes...any ideas? On Wed, Oct 10, 2018 at 4:33 AM Patrick Young <[email protected]> wrote: I am using tika-app-1.19.jar & ctakes4.0.0 to populate neo4j with ctakes event mentions extracted from biomedical articles. However, I've noticed some medication mentions e.g., indinavir, zidovudine are missed while other antiretrovirals such as lamivudine are detected. The default CVD spots these meds properly though... any ideas why this might be happening? Many thanks, Paddy Young -- Dr Patrick M Young -- Dr Patrick M Young
