Hi As i checkout the ctakes from svn repo and followed the dev install guide. I found ctakes using umls2011. How can update that to umls2016. i have umls on my local as well.
On Thu, Jan 19, 2017 at 2:31 PM, pratik agarwal <pratikagarwal2...@gmail.com > wrote: > Hi Sean > > I have 2 problems here that I need help with: > > *Problem 1:* > I added a custom dictionary using the dictionary-gui module that you built. > I downloaded the complete rxnorm files from UMLS website: > RxNorm_full_prescribe_01032017.zip > <https://download.nlm.nih.gov/rxnorm/RxNorm_full_prescribe_01032017.zip>, > You mentioned in the dictionary-gui thread that the module parses > "MRCONSO.RRF" to create the dictionary in .script format. I found a file > "RXNCONSO.RRF" in the zip directory I downloaded, and changed every mention > of "RXNORM" to "RXNORM_16AA_160906F" and appended it to "MRCONSO.RRF" > thinking that the codes will get added to the dictionary, but when I passed > a query to the database using .rc file created: > > > *SELECT * FROM RXNORM_16AA_160906F WHERE RXNORM_16AA_160906F = 997422; * > > it returned 0 matches. > > Note that 997422 was present in the modified "MRCONSO.RRF" as: > *997422|ENG||||||1358127|1358127|997422||RXNORM_16AA_160906F > |SY|997422|Allegra > 180 MG Oral Tablet||N|4096|* > > This din't seem to work, so I opened "MrconsoParser.java" in the > dictionary-gui module and I found a line: > > *static private final String[] RXNORM_EXCLUSIONS = { "SY" };* > > So I removed *"SY"* from the set and made it empty: *RXNORM_EXCLUSIONS = { > }; *thinking maybe the lines having *SY *are being excluded, but even after > this it was no use. > > It would be great if you could help me understand what's going on here. > > > *Problem 2: * > When I query the database with the code: *309035,* it returns a match > where *CUI > = 975312*. > This is the code for *Castor Oil 793MG. * > > Since it exists in the dictionary, when I pass *"Castor Oil 793 MG", *I > should ideally get: > Castor Oil 793 MG --> codes:[309035] > > Instead, I still get: > Castor --> codes:[2129] > Oil --> codes:[1021284] > 793 MG --> codes:[] > > Please help me understand how this is actually picking out the covered > text, and if there's a way I can modify the pattern so that it gives me the > required output. > > Thanks and Best Regards > Pratik Agarwal > > On Tue, Jan 3, 2017 at 7:42 PM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Pratik, > > > > Because combinations of strength, route, form, etc. for medications > amount > > to an enormous number of unique terms, the possible combinations are not > > included in the default ctakes dictionary. > > > > You can: > > 1. Add a custom dictionary with your fully-defined terms of interest, or > > 2. Create a post-process module that maps [drug, strength, route, form] > > to rxnorm codes based upon coded drug and following text or other codes. > > 3. Use something like the drug-ner module to identify drug attributes > and > > use them instead of fully-specifying drug, strength, route, form codes. > > > > There may be other possibilities, or maybe somebody out there has already > > done this and can be of further assistance. > > > > Sean > > > > -----Original Message----- > > From: pratik agarwal [mailto:pratikagarwal2...@gmail.com] > > Sent: Monday, December 26, 2016 4:57 AM > > To: dev@ctakes.apache.org > > Subject: Getting specific RXNORM and ICD codes instead of class codes > > > > Hi Everyone > > > > I am using cTAKES from the svn repository in IntelliJ IDEA. I wrote a > > small script calling the *getFastPipeline()* function from the > > *ClinicalPipelineFactory* class. > > > > On passing the string: > > *"clonazePAM 0.5 mg oral tablet* > > *clopidogrel 75 mg oral tablet"* > > > > I'm getting the annotated RXNORM tokens as: > > > > *clonazePAM --> codes: [2598]* > > *0.5 mg --> codes: []* > > *0.5 --> codes: []* > > *oral tablet --> codes: [317541]* > > > > > > *clopidogrel --> codes: [32968]* > > *75mg --> codes:[]* > > > > *oral tablet ---> codes: [317541]* > > > > where actually I need something like: > > > > *clonazePAM 0.5 mg oral tablet --> codes: [197527]* *clopidogrel 75 mg > > oral tablet --> codes:[309362]* > > > > Can you please suggest if there's a way I can get these specific codes > > instead of the class codes? > > > > Thanks and Best Regards. > > Pratik Agarwal > > > -- with Regards Shahid Ashraf
