Description
This pipeline is designed to extract oncology-related clinical/medical entities. In this pipeline, 4 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_oncology_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_oncology_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 | Cancer_Surgery |
| 1 | bilateral oophorectomy | 56 | 77 | Cancer_Surgery |
| 2 | omentectomy | 84 | 94 | Cancer_Surgery |
| 3 | total anterior hysterectomy | 98 | 124 | Cancer_Surgery |
| 4 | radical pelvic lymph nodes dissection | 131 | 167 | Cancer_Surgery |
| 5 | ovarian carcinoma | 176 | 192 | Cancer_Dx |
| 6 | mucinous-type carcinoma | 195 | 217 | Cancer_Dx |
| 7 | stage Ic | 220 | 227 | Staging |
| 8 | 1 year ago | 230 | 239 | Relative_Date |
| 9 | chemotherapy | 312 | 323 | Chemotherapy |
| 10 | cyclophosphamide | 326 | 341 | Chemotherapy |
| 11 | 750 mg/m2 | 343 | 351 | Dosage |
| 12 | carboplatin | 354 | 364 | Chemotherapy |
| 13 | 300 mg/m2 | 366 | 374 | Dosage |
| 14 | right | 410 | 414 | Direction |
| 15 | breast | 416 | 421 | Site_Breast |
| 16 | mass | 423 | 426 | Tumor_Finding |
| 17 | 15 cm | 429 | 433 | Tumor_Size |
| 18 | right | 475 | 479 | Direction |
| 19 | breast | 481 | 486 | Site_Breast |
| 20 | in 2 months | 488 | 498 | Relative_Date |
| 21 | Core needle biopsy | 502 | 519 | Pathology_Test |
| 22 | metaplastic carcinoma | 530 | 550 | Cancer_Dx |
| 23 | Neoadjuvant chemotherapy | 554 | 577 | Chemotherapy |
| 24 | Taxotere | 600 | 607 | Chemotherapy |
| 25 | 75 mg/m2 | 610 | 617 | Dosage |
| 26 | Epirubicin | 621 | 630 | Chemotherapy |
| 27 | 75 mg/m2 | 633 | 640 | Dosage |
| 28 | Cyclophosphamide | 648 | 663 | Chemotherapy |
| 29 | 500 mg/m2 | 666 | 674 | Dosage |
| 30 | 6 cycles | 691 | 698 | Cycle_Count |
| 31 | poor response | 705 | 717 | Response_To_Treatment |
| 32 | modified radical mastectomy | 735 | 761 | Cancer_Surgery |
| 33 | MRM | 764 | 766 | Cancer_Surgery |
| 34 | dissection of axillary lymph nodes | 774 | 807 | Cancer_Surgery |
| 35 | skin grafting | 813 | 825 | Cancer_Surgery |
| 36 | radiotherapy | 846 | 857 | Radiotherapy |
| 37 | 5000 cGy | 873 | 880 | Radiation_Dose |
| 38 | 25 fractions | 885 | 896 | Cycle_Count |
| 39 | histopathologic examination | 904 | 930 | Pathology_Test |
| 40 | metaplastic carcinoma | 943 | 963 | Cancer_Dx |
| 41 | squamous differentiation | 970 | 993 | Histological_Type |
| 42 | adenomyoepithelioma | 1011 | 1029 | Cancer_Dx |
| 43 | Immunohistochemistry study | 1033 | 1058 | Pathology_Test |
| 44 | tumor cells | 1076 | 1086 | Pathology_Result |
| 45 | positive | 1092 | 1099 | Biomarker_Result |
| 46 | epithelial markers-cytokeratin | 1105 | 1134 | Biomarker |
| 47 | AE1/AE3 | 1137 | 1143 | Biomarker |
| 48 | myoepithelial markers | 1157 | 1177 | Biomarker |
| 49 | cytokeratin 5/6 | 1190 | 1204 | Biomarker |
| 50 | CK 5/6 | 1207 | 1212 | Biomarker |
| 51 | p63 | 1216 | 1218 | Biomarker |
| 52 | S100 | 1225 | 1228 | Biomarker |
| 53 | hormone receptors | 1254 | 1270 | Biomarker |
| 54 | ER | 1283 | 1284 | Biomarker |
| 55 | PR | 1287 | 1288 | Biomarker |
| 56 | Her-2/Neu | 1295 | 1303 | Oncogene |
| 57 | negative | 1315 | 1322 | Biomarker_Result |
Model Information
| Model Name: | explain_clinical_doc_oncology_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
- TextMatcherInternalModel
- TextMatcherInternalModel
- ChunkMergeModel