Description
This pipeline is designed to extract clinical/medical entities from texts written by non-healthcare professionals. In this pipeline, 3 NER models and 2 text matchers are used to extract the clinical entity labels.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("explain_clinical_doc_vop_light", "en", "clinical/models")
result = ner_pipeline.annotate("""I am 60 years old and my health problems started around 5 years ago when I began getting constant headaches and feeling dizzy all the time.
I went to my regular doctor, and they told me I had high blood pressure. They put me on amlodipine, 5 mg a day, to help lower it.
About 2 years ago, I had an MRI, and they found I had something called an acoustic neuroma — it’s a non-cancerous tumor in the brain. That probably explained why my headaches were getting so bad.
I went through the surgery, and thankfully there weren’t any big problems. After the surgery, I did lose some hearing on that side and developed ringing in my ear that hasn't gone away.
Last year, I started having chest pain and ended up going to the emergency room. They said I had heart disease and had to put a stent in one of the arteries in my heart (the LAD artery).
Now I take aspirin 81 mg every day, metoprolol 25 mg twice a day, and atorvastatin 40 mg at night.
Lately, I’ve been having more pain and stiffness in my joints. Blood tests showed inflammation, and I was diagnosed with rheumatoid arthritis.
Now I take methotrexate once a week (15 mg) and also folic acid every day.
On top of all that, my blood sugar has been running high, so my doctors are watching me for type 2 diabetes.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("explain_clinical_doc_vop_light", "en", "clinical/models")
val result = ner_pipeline.annotate("""I am 60 years old and my health problems started around 5 years ago when I began getting constant headaches and feeling dizzy all the time.
I went to my regular doctor, and they told me I had high blood pressure. They put me on amlodipine, 5 mg a day, to help lower it.
About 2 years ago, I had an MRI, and they found I had something called an acoustic neuroma — it’s a non-cancerous tumor in the brain. That probably explained why my headaches were getting so bad.
I went through the surgery, and thankfully there weren’t any big problems. After the surgery, I did lose some hearing on that side and developed ringing in my ear that hasn't gone away.
Last year, I started having chest pain and ended up going to the emergency room. They said I had heart disease and had to put a stent in one of the arteries in my heart (the LAD artery).
Now I take aspirin 81 mg every day, metoprolol 25 mg twice a day, and atorvastatin 40 mg at night.
Lately, I’ve been having more pain and stiffness in my joints. Blood tests showed inflammation, and I was diagnosed with rheumatoid arthritis.
Now I take methotrexate once a week (15 mg) and also folic acid every day.
On top of all that, my blood sugar has been running high, so my doctors are watching me for type 2 diabetes.
""")
Results
| | chunks | begin | end | entities |
|---:|:---------------------------------|--------:|------:|:--------------------------|
| 0 | 60 years old | 5 | 16 | Age |
| 1 | around 5 years ago | 49 | 66 | DateTime |
| 2 | constant | 89 | 96 | Modifier |
| 3 | headaches | 98 | 106 | Symptom |
| 4 | dizzy | 120 | 124 | Symptom |
| 5 | all the time | 126 | 137 | Duration |
| 6 | doctor | 162 | 167 | Employment |
| 7 | high blood pressure | 193 | 211 | TestResult |
| 8 | amlodipine | 229 | 238 | Drug |
| 9 | 5 mg | 241 | 244 | Dosage |
| 10 | a day | 246 | 250 | Frequency |
| 11 | About 2 years ago | 272 | 288 | DateTime |
| 12 | MRI | 300 | 302 | Test |
| 13 | acoustic neuroma | 346 | 361 | Disease_Syndrome_Disorder |
| 14 | non-cancerous tumor in the brain | 372 | 403 | Disease_Syndrome_Disorder |
| 15 | headaches | 437 | 445 | Symptom |
| 16 | lose some hearing | 569 | 585 | Symptom |
| 17 | ringing in my ear | 614 | 630 | Symptom |
| 18 | Last year | 655 | 663 | DateTime |
| 19 | chest pain | 683 | 692 | Symptom |
| 20 | emergency room | 720 | 733 | ClinicalDept |
| 21 | heart disease | 752 | 764 | Disease_Syndrome_Disorder |
| 22 | stent | 783 | 787 | MedicalDevice |
| 23 | arteries | 803 | 810 | BodyPart |
| 24 | heart | 818 | 822 | BodyPart |
| 25 | LAD artery | 829 | 838 | BodyPart |
| 26 | Now | 843 | 845 | DateTime |
| 27 | aspirin | 854 | 860 | Drug |
| 28 | 81 mg | 862 | 866 | Dosage |
| 29 | every day | 868 | 876 | Frequency |
| 30 | metoprolol | 879 | 888 | Drug |
| 31 | 25 mg | 890 | 894 | Dosage |
| 32 | twice a day | 896 | 906 | Frequency |
| 33 | atorvastatin | 913 | 924 | Drug |
| 34 | 40 mg | 926 | 930 | Dosage |
| 35 | at night | 932 | 939 | Frequency |
| 36 | pain | 973 | 976 | Symptom |
| 37 | stiffness in my joints | 982 | 1003 | Symptom |
| 38 | Blood tests | 1006 | 1016 | Test |
| 39 | inflammation | 1025 | 1036 | Symptom |
| 40 | rheumatoid arthritis | 1064 | 1083 | Disease_Syndrome_Disorder |
| 41 | Now | 1087 | 1089 | DateTime |
| 42 | methotrexate | 1098 | 1109 | Drug |
| 43 | once a week | 1111 | 1121 | Frequency |
| 44 | 15 mg | 1124 | 1128 | Dosage |
| 45 | folic acid | 1140 | 1149 | Drug |
| 46 | every day | 1151 | 1159 | Frequency |
| 47 | blood sugar | 1186 | 1196 | Test |
| 48 | high | 1215 | 1218 | TestResult |
| 49 | doctors | 1227 | 1233 | Employment |
| 50 | type 2 diabetes | 1255 | 1269 | Disease_Syndrome_Disorder |
Model Information
| Model Name: | explain_clinical_doc_vop_light |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- RegexMatcherInternalModel
- ContextualParserModel
- ChunkConverter
- ChunkMergeModel