Hi Sekhar, To answer your first question, As per my knowledge, I don't think there are any config change to filter output. You gotta pick and choose the desired output as per your requirement by parsing the output XML.
On Tuesday, June 4, 2019, Hari, Sekhar <[email protected]> wrote: > Hi All – > > > > I see something that is not correct in the cTAKES output for the text > below. I sincerely hope somebody can guide me here with my questions at the > end. Not sure if I’m doing anything wrong with the cTAKES configuration. > > > > *Content:* > > “Since the last approved labeling, there has been no submission > to LEVAQUIN® > > NDAs: NDA 20-634 LEVAQUIN® (levofloxacin) Tablets, NDA 20-635 > > LEVAQUIN® (levofloxacin) Injection, NDA 21-721 LEVAQUIN® > > (levofloxacin) Oral Solution.” > > > > There are several lines after this. But the only brand name of the drug > that is mentioned in the whole document is ‘LEVAQUIN’ and generic name > mentioned is ‘levofloxacin’. These names appear at a couple of places in > the document, and then there are some disease names mentioned too. > > > > *Objective:* > > Retrieve the generic name and brand name from the text using the cTAKES > returned RXNORM codes. > > > > We do a POST of the full text to the API - http://XX.XX.XX.XX/ctakes-web- > rest/service/analyze. > > > > *…following is the output from API:* > > {'ANATOMICALSITEMENTION': {'ORAL': ['START: 793', 'END: 797', 'POLARITY: > 1', '[CODINGSCHEME: SNOMEDCT_US, CODE: 74262004, CUI: C0226896, TUI: > T030]']}, 'MEDICATIONMENTION': {'TABLETS': ['START: 474', 'END: 481', > 'POLARITY: 1', '[CODINGSCHEME: SNOMEDCT_US, CODE: 46992007, CUI: C0039225, > TUI: T122]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 385055001, CUI: C0039225, > TUI: T122]', '[CODINGSCHEME: RXNORM, CODE: 10311, CUI: C0039225, TUI: > T122]'], 'INJECTION': ['START: 817', 'END: 826', 'POLARITY: 1', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 129326001, CUI: C1533685, TUI: T061]', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 28289002, CUI: C1533685, TUI: T061]', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 59108006, CUI: C1533685, TUI: T061]'], > 'DOC': ['START: 1152', 'END: 1155', 'POLARITY: 1', '[CODINGSCHEME: RXNORM, > CODE: 3256, CUI: C0011710, TUI: T109]', '[CODINGSCHEME: RXNORM, CODE: 3256, > CUI: C0011710, TUI: T121]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 56156001, > CUI: C0011710, TUI: T125]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 1336006, > CUI: C0011710, TUI: T109]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 1336006, > CUI: C0011710, TUI: T121]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 75029008, > CUI: C0011710, TUI: T125]', '[CODINGSCHEME: RXNORM, CODE: 3256, CUI: > C0011710, TUI: T125]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 56156001, CUI: > C0011710, TUI: T109]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 56156001, CUI: > C0011710, TUI: T121]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 1336006, CUI: > C0011710, TUI: T125]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 75029008, CUI: > C0011710, TUI: T109]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 75029008, CUI: > C0011710, TUI: T121]'], 'SOLUTION': ['START: 576', 'END: 584', 'POLARITY: > 1', '[CODINGSCHEME: RXNORM, CODE: 450530, CUI: C1382100, TUI: T122]'], > 'ORAL': ['START: 793', 'END: 797', 'POLARITY: 1', '[CODINGSCHEME: > SNOMEDCT_US, CODE: 74262004, CUI: C0226896, TUI: T030]'], 'LEVAQUIN': > ['START: 452', 'END: 460', 'POLARITY: 1', '[CODINGSCHEME: RXNORM, CODE: > 217992, CUI: C0721336, TUI: T121]', '[CODINGSCHEME: RXNORM, CODE: 217992, > CUI: C0721336, TUI: T109]'], 'ADR': ['START: 2454', 'END: 2457', 'POLARITY: > 1', '[CODINGSCHEME: SNOMEDCT_US, CODE: 68444001, CUI: C0013089, TUI: > T195]', '[CODINGSCHEME: SNOMEDCT_US, CODE: 68444001, CUI: C0013089, TUI: > T109]', '[CODINGSCHEME: RXNORM, CODE: 3639, CUI: C0013089, TUI: T195]', > '[CODINGSCHEME: RXNORM, CODE: 3639, CUI: C0013089, TUI: T109]', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 372817009, CUI: C0013089, TUI: T195]', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 372817009, CUI: C0013089, TUI: T109]']}, > 'DRUGCHANGESTATUSANNOTATION': {}, 'STRENGTHANNOTATION': {}, > 'FRACTIONSTRENGTHANNOTATION': {}, 'FREQUENCYUNITANNOTATION': {}, > 'DISEASEDISORDERMENTION': {'RUPTURE': ['START: 1579', 'END: 1586', > 'POLARITY: 1', '[CODINGSCHEME: SNOMEDCT_US, CODE: 125671007, CUI: C3203359, > TUI: T037]']}, 'SIGNSYMPTOMMENTION': {'RED': ['START: 1081', 'END: 1084', > 'POLARITY: 1', '[CODINGSCHEME: SNOMEDCT_US, CODE: 386713009, CUI: C0332575, > TUI: T033]'], 'CONTENT': ['START: 2992', 'END: 2999', 'POLARITY: 1', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 271599002, CUI: C0423896, TUI: T041]'], > 'HISTORY': ['START: 34', 'END: 41', 'POLARITY: 1', '[CODINGSCHEME: > SNOMEDCT_US, CODE: 392521001, CUI: C0262926, TUI: T033]']}, > 'ROUTEANNOTATION': {}, 'DATEANNOTATION': {}, 'MEASUREMENTANNOTATION': {}, > 'PROCEDUREMENTION': {'INJECTION': ['START: 817', 'END: 826', 'POLARITY: 1', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 129326001, CUI: C1533685, TUI: T061]', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 28289002, CUI: C1533685, TUI: T061]', > '[CODINGSCHEME: SNOMEDCT_US, CODE: 59108006, CUI: C1533685, TUI: T061]']}, > 'TIMEMENTION': {}, 'STRENGTHUNITANNOTATION': {}} > > > > *Questions:* > > 1. How do we restrict the output to show only RXNORM coding scheme? > Please describe with any config change example, if possible. > > 2. These are the unique RXNORM codes from the above output: > '10311', '3256', '450530', '217992', '3639'. These codes map to the drug > names: ‘DESOXYCORTICOSTERONE', 'LEVAQUIN', 'DOXORUBICIN’ > > a. The text do not mention anything about ‘DESOXYCORTICOSTERONE' > and 'DOXORUBICIN’. How is cTAKES reporting that? > > b. The text has ‘levofloxacin’, and an RXNORM code is not returned > for this name. Any idea? > > 3. How do we enable cTAKES so that it returns only those codes that > are available in RxTerms dictionary? None of the RXNORM codes reported > above are available in RxTerms. > > > > Thanks > > Sekhar H. > > > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
