Dosage strength is not returned in the response #69
Description
Hello,
While trying to get the structured clinical data from the text, we have noticed that the drug strength is not parsed by the ctakes. I see that there is the component in the codebase "ctakes-drug-ner".
Is this component enabled by default? or do we have to enable it manually.
Here is the sample snapshot for same text from the CLAMP and CTAKES-REST-SERVICE:
CLAMP
ctakes-response:
{ "AnatomicalSiteMention": [ { "begin": 93, "end": 98, "text": "brain", "polarity": 1, "conceptAttributes": [ { "code": "12738006", "cui": "C0006104", "codingScheme": "SNOMEDCT_US", "tui": "T023" } ] }, { "begin": 160, "end": 164, "text": "hand", "polarity": 1, "conceptAttributes": [ { "code": "85562004", "cui": "C0018563", "codingScheme": "SNOMEDCT_US", "tui": "T023" } ] }, { "begin": 571, "end": 574, "text": "log", "polarity": 1, "conceptAttributes": [ { "code": "22735005", "cui": "C0228228", "codingScheme": "SNOMEDCT_US", "tui": "T023" } ] } ], "MedicationMention": [ { "begin": 175, "end": 180, "text": "today", "polarity": 1, "conceptAttributes": [ { "code": null, "cui": "C0310367", "codingScheme": "customDictionary", "tui": "T109" }, { "code": null, "cui": "C0310367", "codingScheme": "customDictionary", "tui": "T195" } ] }, { "begin": 218, "end": 225, "text": "namenda", "polarity": 1, "conceptAttributes": [ { "code": "405206", "cui": "C1330412", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "405206", "cui": "C1330412", "codingScheme": "RXNORM", "tui": "T109" } ] }, { "begin": 349, "end": 359, "text": "citalopram", "polarity": 1, "conceptAttributes": [ { "code": "321986007", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T109" }, { "code": "2556", "cui": "C0008845", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "2556", "cui": "C0008845", "codingScheme": "RXNORM", "tui": "T109" }, { "code": "372596005", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T121" }, { "code": "372596005", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T109" }, { "code": "321986007", "cui": "C0008845", "codingScheme": "SNOMEDCT_US", "tui": "T121" } ] }, { "begin": 482, "end": 487, "text": "lasix", "polarity": 1, "conceptAttributes": [ { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T109" } ] }, { "begin": 597, "end": 602, "text": "lasix", "polarity": 1, "conceptAttributes": [ { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T121" }, { "code": "202991", "cui": "C0699992", "codingScheme": "RXNORM", "tui": "T109" } ] } ], "DrugChangeStatusAnnotation": [], "StrengthAnnotation": [], "FractionStrengthAnnotation": [], "FrequencyUnitAnnotation": [], "DiseaseDisorderMention": [ { "begin": 3, "end": 23, "text": "Alzheimer's dementia", "polarity": 1, "conceptAttributes": [ { "code": "26929004", "cui": "C0002395", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 15, "end": 23, "text": "dementia", "polarity": 1, "conceptAttributes": [ { "code": "52448006", "cui": "C0497327", "codingScheme": "SNOMEDCT_US", "tui": "T048" } ] }, { "begin": 366, "end": 385, "text": "Alzheimers dementia", "polarity": 1, "conceptAttributes": [ { "code": "26929004", "cui": "C0002395", "codingScheme": "SNOMEDCT_US", "tui": "T047" }, { "code": "142811000119104", "cui": "C3665464", "codingScheme": "SNOMEDCT_US", "tui": "T048" } ] }, { "begin": 377, "end": 385, "text": "dementia", "polarity": 1, "conceptAttributes": [ { "code": "52448006", "cui": "C0497327", "codingScheme": "SNOMEDCT_US", "tui": "T048" } ] }, { "begin": 467, "end": 470, "text": "CHF", "polarity": 1, "conceptAttributes": [ { "code": "42343007", "cui": "C0018802", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 934, "end": 943, "text": "infection", "polarity": 1, "conceptAttributes": [ { "code": "40733004", "cui": "C0009450", "codingScheme": "SNOMEDCT_US", "tui": "T047" }, { "code": "189822004", "cui": "C0009450", "codingScheme": "SNOMEDCT_US", "tui": "T047" }, { "code": "191415002", "cui": "C0009450", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 947, "end": 950, "text": "CHF", "polarity": 1, "conceptAttributes": [ { "code": "42343007", "cui": "C0018802", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] }, { "begin": 1073, "end": 1076, "text": "CHF", "polarity": 1, "conceptAttributes": [ { "code": "42343007", "cui": "C0018802", "codingScheme": "SNOMEDCT_US", "tui": "T047" } ] } ], "SignSymptomMention": [ { "begin": 228, "end": 232, "text": "mild", "polarity": 1, "conceptAttributes": [ { "code": "446411000124101", "cui": "C1513302", "codingScheme": "SNOMEDCT_US", "tui": "T033" } ] }, { "begin": 323, "end": 333, "text": "motivation", "polarity": 1, "conceptAttributes": [ { "code": "106121005", "cui": "C0026605", "codingScheme": "SNOMEDCT_US", "tui": "T041" }, { "code": "363882003", "cui": "C0026605", "codingScheme": "SNOMEDCT_US", "tui": "T041" } ] }, { "begin": 338, "end": 346, "text": "appetite", "polarity": 1, "conceptAttributes": [ { "code": "33911006", "cui": "C0003618", "codingScheme": "SNOMEDCT_US", "tui": "T040" } ] }, { "begin": 904, "end": 910, "text": "likely", "polarity": 1, "conceptAttributes": [ { "code": "2931005", "cui": "C0332148", "codingScheme": "SNOMEDCT_US", "tui": "T033" } ] }, { "begin": 911, "end": 925, "text": "cause of death", "polarity": 1, "conceptAttributes": [ { "code": "16100001", "cui": "C0007465", "codingScheme": "SNOMEDCT_US", "tui": "T033" }, { "code": "184305005", "cui": "C0007465", "codingScheme": "SNOMEDCT_US", "tui": "T033" } ] }, { "begin": 920, "end": 925, "text": "death", "polarity": 1, "conceptAttributes": [ { "code": "419620001", "cui": "C0011065", "codingScheme": "SNOMEDCT_US", "tui": "T040" } ] } ], "DateAnnotation": [ { "begin": 45, "end": 57, "text": "Apr 11, 2018", "polarity": 0, "conceptAttributes": [] }, { "begin": 67, "end": 79, "text": "Nov 04, 2015", "polarity": 0, "conceptAttributes": [] } ], "RouteAnnotation": [], "MeasurementAnnotation": [ { "begin": 255, "end": 260, "text": "23 mg", "polarity": 0, "conceptAttributes": [] }, { "begin": 621, "end": 626, "text": "2 lbs", "polarity": 0, "conceptAttributes": [] } ], "ProcedureMention": [ { "begin": 45, "end": 48, "text": "Apr", "polarity": 1, "conceptAttributes": [ { "code": "265414003", "cui": "C2004459", "codingScheme": "SNOMEDCT_US", "tui": "T061" } ] }, { "begin": 58, "end": 62, "text": "MMSE", "polarity": 1, "conceptAttributes": [ { "code": "273617000", "cui": "C0451306", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 80, "end": 84, "text": "MMSE", "polarity": 1, "conceptAttributes": [ { "code": "273617000", "cui": "C0451306", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 89, "end": 98, "text": "mri brain", "polarity": 1, "conceptAttributes": [ { "code": "29567006", "cui": "C0412675", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 89, "end": 92, "text": "mri", "polarity": 1, "conceptAttributes": [ { "code": "312250003", "cui": "C0024485", "codingScheme": "SNOMEDCT_US", "tui": "T060" }, { "code": "113091000", "cui": "C0024485", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 115, "end": 124, "text": "TREATMENT", "polarity": 1, "conceptAttributes": [ { "code": "277132007", "cui": "C0087111", "codingScheme": "SNOMEDCT_US", "tui": "T061" }, { "code": "276239002", "cui": "C0087111", "codingScheme": "SNOMEDCT_US", "tui": "T061" } ] }, { "begin": 564, "end": 570, "text": "weight", "polarity": 1, "conceptAttributes": [ { "code": "39857003", "cui": "C1305866", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] }, { "begin": 606, "end": 612, "text": "weight", "polarity": 1, "conceptAttributes": [ { "code": "39857003", "cui": "C1305866", "codingScheme": "SNOMEDCT_US", "tui": "T060" } ] } ], "TimeMention": [], "StrengthUnitAnnotation": [] }
StrengthAnnotation and FractionStrengthAnnotation are received empty.
Can you please point me in the right direction.
Thanks.