Description
This pipeline is designed to extract clinical/medical entities. In this pipeline, 4 NER models are used to extract these Clinical Entity Labels: PROBLEM, TEST, TREATMENT
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("explain_clinical_doc_generic_light", "en", "clinical/models")
result = ner_pipeline.annotate("""A 65-year-old woman had a history of debulking surgery, bilateral oophorectomy with omentectomy,
total anterior hysterectomy with radical pelvic lymph nodes dissection due to ovarian carcinoma (mucinous-type carcinoma, stage Ic) 1 year ago.
The patient's medical compliance was poor and failed to complete her chemotherapy (cyclophosphamide 750 mg/m2, carboplatin 300 mg/m2).
Recently, she noted a palpable right breast mass, 15 cm in size which nearly occupied the whole right breast in 2 months.
Core needle biopsy revealed metaplastic carcinoma.
Neoadjuvant chemotherapy with the regimens of Taxotere (75 mg/m2), Epirubicin (75 mg/m2), and Cyclophosphamide (500 mg/m2) was given for 6 cycles with poor response,
followed by a modified radical mastectomy (MRM) with dissection of axillary lymph nodes and skin grafting.
Postoperatively, radiotherapy was done with 5000 cGy in 25 fractions.
The histopathologic examination revealed a metaplastic carcinoma with squamous differentiation associated with adenomyoepithelioma.
Immunohistochemistry study showed that the tumor cells are positive for epithelial markers-cytokeratin (AE1/AE3) stain, and myoepithelial markers, including cytokeratin 5/6 (CK 5/6), p63, and S100 stains.
Expressions of hormone receptors, including ER, PR, and Her-2/Neu, were all negative.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("explain_clinical_doc_generic_light", "en", "clinical/models")
val result = ner_pipeline.annotate("""A 65-year-old woman had a history of debulking surgery, bilateral oophorectomy with omentectomy,
total anterior hysterectomy with radical pelvic lymph nodes dissection due to ovarian carcinoma (mucinous-type carcinoma, stage Ic) 1 year ago.
The patient's medical compliance was poor and failed to complete her chemotherapy (cyclophosphamide 750 mg/m2, carboplatin 300 mg/m2).
Recently, she noted a palpable right breast mass, 15 cm in size which nearly occupied the whole right breast in 2 months.
Core needle biopsy revealed metaplastic carcinoma.
Neoadjuvant chemotherapy with the regimens of Taxotere (75 mg/m2), Epirubicin (75 mg/m2), and Cyclophosphamide (500 mg/m2) was given for 6 cycles with poor response,
followed by a modified radical mastectomy (MRM) with dissection of axillary lymph nodes and skin grafting.
Postoperatively, radiotherapy was done with 5000 cGy in 25 fractions.
The histopathologic examination revealed a metaplastic carcinoma with squamous differentiation associated with adenomyoepithelioma.
Immunohistochemistry study showed that the tumor cells are positive for epithelial markers-cytokeratin (AE1/AE3) stain, and myoepithelial markers, including cytokeratin 5/6 (CK 5/6), p63, and S100 stains.
Expressions of hormone receptors, including ER, PR, and Her-2/Neu, were all negative.
""")
Results
| | chunks | begin | end | entities |
|---:|:--------------------------------------|--------:|------:|:---------------|
| 0 | debulking surgery | 37 | 53 | TREATMENT |
| 1 | bilateral oophorectomy | 56 | 77 | CANCER_SURGERY |
| 2 | omentectomy | 84 | 94 | TREATMENT |
| 3 | total anterior hysterectomy | 98 | 124 | TREATMENT |
| 4 | radical pelvic lymph nodes dissection | 131 | 167 | TREATMENT |
| 5 | ovarian carcinoma | 176 | 192 | PROBLEM |
| 6 | mucinous-type carcinoma | 195 | 217 | PROBLEM |
| 7 | stage Ic | 220 | 227 | PROBLEM |
| 8 | her chemotherapy | 308 | 323 | TREATMENT |
| 9 | cyclophosphamide | 326 | 341 | TREATMENT |
| 10 | carboplatin | 354 | 364 | TREATMENT |
| 11 | a palpable right breast mass | 400 | 427 | PROBLEM |
| 12 | Core needle biopsy | 504 | 521 | TREATMENT |
| 13 | metaplastic carcinoma | 532 | 552 | PROBLEM |
| 14 | Neoadjuvant chemotherapy | 557 | 580 | TREATMENT |
| 15 | the regimens | 587 | 598 | TREATMENT |
| 16 | Taxotere | 603 | 610 | TREATMENT |
| 17 | Epirubicin | 624 | 633 | TREATMENT |
| 18 | Cyclophosphamide | 651 | 666 | TREATMENT |
| 19 | poor response | 708 | 720 | PROBLEM |
| 20 | a modified radical mastectomy | 737 | 765 | TREATMENT |
| 21 | MRM | 768 | 770 | TEST |
| 22 | dissection of axillary lymph nodes | 778 | 811 | TREATMENT |
| 23 | skin grafting | 817 | 829 | TREATMENT |
| 24 | radiotherapy | 851 | 862 | TREATMENT |
| 25 | The histopathologic examination | 906 | 936 | TEST |
| 26 | a metaplastic carcinoma | 947 | 969 | PROBLEM |
| 27 | squamous differentiation | 976 | 999 | PROBLEM |
| 28 | adenomyoepithelioma | 1017 | 1035 | PROBLEM |
| 29 | Immunohistochemistry study | 1040 | 1065 | TEST |
| 30 | the tumor cells | 1079 | 1093 | PROBLEM |
| 31 | epithelial markers-cytokeratin | 1112 | 1141 | PROBLEM |
| 32 | AE1/AE3 | 1144 | 1150 | TEST |
| 33 | stain | 1153 | 1157 | TEST |
| 34 | myoepithelial markers | 1164 | 1184 | TEST |
| 35 | cytokeratin | 1197 | 1207 | TEST |
| 36 | CK | 1214 | 1215 | TEST |
| 37 | p63 | 1223 | 1225 | TEST |
| 38 | S100 stains | 1232 | 1242 | TEST |
| 39 | hormone receptors | 1261 | 1277 | TEST |
| 40 | ER | 1290 | 1291 | TEST |
| 41 | PR | 1294 | 1295 | TEST |
| 42 | Her-2/Neu | 1302 | 1310 | TEST |
Model Information
| Model Name: | explain_clinical_doc_generic_light |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.8 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel