Detect Medical Conditions, Disorders, Diseases, and Injuries Entities (MEDICAL_CONDITION_DISORDER)

Description

This pipeline can be used to extracts medical condition disorder information in medical text.

Predicted Entities

MEDICAL_CONDITION_DISORDER

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How to use

from sparknlp.pretrained import PretrainedPipeline

ner_pipeline = PretrainedPipeline("ner_medical_condition_disorder_benchmark_pipeline", "en", "clinical/models")

text = """IDENTIFYING DATA AND CHIEF COMPLAINT :
Mrs. Saujule T. Neathe is a 73 year old Gravida 6 Para 4 abortions 2 with a background history of stage IIIC papillary serous adenocarcinoma of the ovary who presents on 5/30/94 for failure to thrive , right lower lobe pneumonia and obstructive uropathy .
This course of chemotherapy was complicated only by persistent diarrhea and some nausea and vomiting .
An abdominopelvic computerized tomography scan during that admission showed recurrent disease in the pelvis with bilateral hydronephrosis .
Two days following discharge , however , the patient was admitted to Sephsandpot Center because of a decreased urinary output and persistent nausea and vomiting and anorexia .
PHYSICAL EXAMINATION :
( on admission ) showed the patient to be low-grade febrile with temperature of 99.6. She was noted to be a thin , cachectic woman in no apparent distress . Head and neck examination remarkable only for extreme dry mucous membranes consistent with dehydration .
Abdomen :
showed well healed midline scar , non-distended , non-tender , bowel sounds were good , multiple small nodules were palpated subcutaneously in the upper abdomen which was non-tender , there was no costovertebral angle tenderness .
Pelvic and rectal examinations confirmed recurrence of tumor mass in the pelvis .
The patient was occult blood negative .
Extremities : showed no evidence of acute deep venous thrombosis . However , left leg had two plus pitting edema to the knee whereas the right leg had minimal edema .
"""

result = ner_pipeline.fullAnnotate(text)
from sparknlp.pretrained import PretrainedPipeline

ner_pipeline = nlp.PretrainedPipeline("ner_medical_condition_disorder_benchmark_pipeline", "en", "clinical/models")

text = """IDENTIFYING DATA AND CHIEF COMPLAINT :
Mrs. Saujule T. Neathe is a 73 year old Gravida 6 Para 4 abortions 2 with a background history of stage IIIC papillary serous adenocarcinoma of the ovary who presents on 5/30/94 for failure to thrive , right lower lobe pneumonia and obstructive uropathy .
This course of chemotherapy was complicated only by persistent diarrhea and some nausea and vomiting .
An abdominopelvic computerized tomography scan during that admission showed recurrent disease in the pelvis with bilateral hydronephrosis .
Two days following discharge , however , the patient was admitted to Sephsandpot Center because of a decreased urinary output and persistent nausea and vomiting and anorexia .
PHYSICAL EXAMINATION :
( on admission ) showed the patient to be low-grade febrile with temperature of 99.6. She was noted to be a thin , cachectic woman in no apparent distress . Head and neck examination remarkable only for extreme dry mucous membranes consistent with dehydration .
Abdomen :
showed well healed midline scar , non-distended , non-tender , bowel sounds were good , multiple small nodules were palpated subcutaneously in the upper abdomen which was non-tender , there was no costovertebral angle tenderness .
Pelvic and rectal examinations confirmed recurrence of tumor mass in the pelvis .
The patient was occult blood negative .
Extremities : showed no evidence of acute deep venous thrombosis . However , left leg had two plus pitting edema to the knee whereas the right leg had minimal edema .
"""

result = ner_pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val ner_pipeline = PretrainedPipeline("ner_medical_condition_disorder_benchmark_pipeline", "en", "clinical/models")

val text = """IDENTIFYING DATA AND CHIEF COMPLAINT :
Mrs. Saujule T. Neathe is a 73 year old Gravida 6 Para 4 abortions 2 with a background history of stage IIIC papillary serous adenocarcinoma of the ovary who presents on 5/30/94 for failure to thrive , right lower lobe pneumonia and obstructive uropathy .
This course of chemotherapy was complicated only by persistent diarrhea and some nausea and vomiting .
An abdominopelvic computerized tomography scan during that admission showed recurrent disease in the pelvis with bilateral hydronephrosis .
Two days following discharge , however , the patient was admitted to Sephsandpot Center because of a decreased urinary output and persistent nausea and vomiting and anorexia .
PHYSICAL EXAMINATION :
( on admission ) showed the patient to be low-grade febrile with temperature of 99.6. She was noted to be a thin , cachectic woman in no apparent distress . Head and neck examination remarkable only for extreme dry mucous membranes consistent with dehydration .
Abdomen :
showed well healed midline scar , non-distended , non-tender , bowel sounds were good , multiple small nodules were palpated subcutaneously in the upper abdomen which was non-tender , there was no costovertebral angle tenderness .
Pelvic and rectal examinations confirmed recurrence of tumor mass in the pelvis .
The patient was occult blood negative .
Extremities : showed no evidence of acute deep venous thrombosis . However , left leg had two plus pitting edema to the knee whereas the right leg had minimal edema .
"""

val result = ner_pipeline.fullAnnotate(text)

Results

|    | chunk                           |   begin |   end | ner_label                  |
|---:|:--------------------------------|--------:|------:|:---------------------------|
|  0 | papillary serous adenocarcinoma |     148 |   178 | MEDICAL_CONDITION_DISORDER |
|  1 | pneumonia                       |     258 |   266 | MEDICAL_CONDITION_DISORDER |
|  2 | obstructive uropathy            |     272 |   291 | MEDICAL_CONDITION_DISORDER |
|  3 | disease                         |     484 |   490 | MEDICAL_CONDITION_DISORDER |
|  4 | hydronephrosis                  |     521 |   534 | MEDICAL_CONDITION_DISORDER |
|  5 | anorexia                        |     703 |   710 | MEDICAL_CONDITION_DISORDER |
|  6 | dehydration                     |     985 |   995 | MEDICAL_CONDITION_DISORDER |
|  7 | tumor                           |    1295 |  1299 | MEDICAL_CONDITION_DISORDER |
|  8 | deep venous thrombosis          |    1404 |  1425 | MEDICAL_CONDITION_DISORDER |

Model Information

Model Name: ner_medical_condition_disorder_benchmark_pipeline
Type: pipeline
Compatibility: Healthcare NLP 5.5.3+
License: Licensed
Edition: Official
Language: en
Size: 1.7 GB

Included Models

  • DocumentAssembler
  • SentenceDetector
  • TokenizerModel
  • WordEmbeddingsModel
  • TextMatcherInternalModel
  • TextMatcherInternalModel
  • MedicalNerModel
  • NerConverterInternalModel
  • MedicalNerModel
  • NerConverterInternalModel
  • ChunkMergeModel
  • ChunkMergeModel

Benchmarking


                     label  precision    recall  f1-score   support
MEDICAL_CONDITION_DISORDER      0.936     0.834     0.882      3439
                         O      0.993     0.998     0.995     79132
                  accuracy      -         -         0.991     82571
                 macro-avg      0.964     0.916     0.939     82571
              weighted-avg      0.990     0.991     0.990     82571