Hi again: How exactly do you switch to using the cTakes dictionary-lookup-fast. Do I need to go in and alter xml files or is it as simple as adding a certain item to the list of analysis engines?
On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Clayton, > > I don't know how the ytex dictionary lookup works, so I'm afraid that I > can't help you with an answer. Maybe Vijay is the best person to do this. > If you aren't tied to ytex you could try the new cTakes > dictionary-lookup-fast. I tested "Patient came in with a malar rash" and > it found "malar" and "malar rash". > > Vijay, > > At some point the lookup-fast module will be the default for the cTakes > clinical pipeline. In order to synchronize the ytex lookup with cTakes, > would you like to eventually work together on reusing the same code for > ytex? I have no idea what ytex does, but I know the ins and outs of the > cdl-fast module. > > Sean > > > -----Original Message----- > > From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf Of > > Clayton Turner > > Sent: Friday, August 08, 2014 2:08 PM > > To: dev@ctakes.apache.org > > Subject: v_snomed_fword_lookup view > > > > Hi Everyone: > > > > I have a question about how the v_snomed_fword_lookup view works when > > running the CPE. > > > > So my understanding of the view is that it is a view comprised of the > > ytex.umls_aui_fword table, the umls.mrconso table and bits/pieces from > > other umls tables. > > > > I feel like this is not completely correct or my idea of how the join to > > create the view works is off. For example, let's say I want the CPE to > find > > "malar ____" (e.g. malar rash) as a concept in the annotations. It never > > happens after running my CPE descriptor and I cannot find it in my > > v_snomed_fword_lookup view. > > > > select count(*) from umls_aui_fword where fword='malar'; yields 34 > results > > > > select count(*) from umls.mrconso where str='malar'; yields 3 results. > > > > So clearly these two tables know what the cui and context(s) are for > malar > > ____. Yet, whenever I run a gold standard set of notes through the CPE, > > malar is constantly flagged as just a word token and the concept is never > > grabbed. This is recurrent for lots of other concepts, as well, I just > > wanted to use an example to illustrate my issue. > > > > Some troubleshooting I already went through: > > 1) Reinstalled ytex and umls database objects > > 2) Reinstalled a second time after redownloading umls through > > metamorphosys, ensuring that snomed vocabularies were included (also > > checked file sizes and noticed a big difference so I know those > > vocabularies ARE included > > > > Anyone got any ideas as to what the issue could be? > > > > Thank you, > > Clayton Turner > -- -- Clayton Turner email: caturn...@g.cofc.edu phone: (843)-424-3784 web: claytonturner.blogspot.com ------------------------------------------------------------------------------------------------- “When scientifically investigating the natural world, the only thing worse than a blind believer is a seeing denier.” - Neil deGrasse Tyson
