Hi Sekhar,
Do you use the CAS Visual Debugger (CVD), or even a text editor that will
show you the character positions of the document text?
I can see from your output that the evidence spans for each RxNorm code are
annotated.
Code Evidence span offsets
10311 793-797
3256 1152-1155
450530 576-584
217992 452-460
3639 2454-2457
Look in those places in your document to find out what language is
triggering these codes.
Other things to note:
A common abbreviation of Deoxycorticosterone is "DOC". I bolded where I see
DOC and 3256 in your output. Similarly, "ADR" is another way to express
Doxorubicin, and I've bolded that in your output as well. See below.
{'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': {}}
Hope this helps,
Jessica
On Tue, Jun 4, 2019 at 1:40 PM gandhi rajan <[email protected]> wrote:
> 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
> !!!"
>
>
