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
