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(r)
NDAs: NDA 20-634 LEVAQUIN(r) (levofloxacin) Tablets, NDA 20-635
LEVAQUIN(r) (levofloxacin) Injection, NDA 21-721 LEVAQUIN(r)
(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.
