I edited the wiki paragraph that describes the ctakes properties configuration file as requested...
On Thu, 11 Oct 2018 at 18:57, Chris Mattmann <[email protected]> wrote: > I’ve granted your permissions to edit the wiki. > > Can you edit this page: > > > > https://wiki.apache.org/tika/cTAKESParser > > > > With a note on if you want to use a different engine and how? > > > > > > > > *From: *Patrick Young <[email protected]> > *Reply-To: *"[email protected]" <[email protected]> > *Date: *Wednesday, October 10, 2018 at 1:16 PM > *To: *"[email protected]" <[email protected]> > *Subject: *Re: missing medication mentions (tika cTAKESParser) Inbox x > > > > Chris, I've registered as Patrick Young and gone to > > HelpContents <https://wiki.apache.org/tika/HelpContents> » > HelpMiscellaneous <https://wiki.apache.org/tika/HelpMiscellaneous> » > cTAKESParser <https://wiki.apache.org/tika/cTAKESParser> » > FrequentlyAskedQuestions > <https://wiki.apache.org/tika/HelpMiscellaneous/FrequentlyAskedQuestions> > > > > Is this what you meant? > > > > > > > > > > On Wed, 10 Oct 2018 at 21:03, Chris Mattmann <[email protected]> wrote: > > 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 > > > > -- > > Dr Patrick M Young > -- Dr Patrick M Young
