Description
This pipeline includes Named-Entity Recognition, Assertion Status and Relation Extraction models to extract information from oncology texts. This pipeline focuses on entities related to biomarkers.
Live Demo Open in Colab Download Copy S3 URI
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("oncology_biomarker_pipeline", "en", "clinical/models")
text = '''Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2.'''
result = pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = new PretrainedPipeline("oncology_biomarker_pipeline", "en", "clinical/models")
val text = "Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2."
val result = pipeline.fullAnnotate(text)
import nlu
nlu.load("en.oncology_biomarker.pipeline").predict("""Immunohistochemistry was negative for thyroid transcription factor-1 and napsin A. The test was positive for ER and PR, and negative for HER2.""")
Results
******************** ner_oncology_wip results ********************
| chunk | ner_label |
|:-------------------------------|:-----------------|
| negative | Biomarker_Result |
| thyroid transcription factor-1 | Biomarker |
| napsin | Biomarker |
| positive | Biomarker_Result |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Result |
| HER2 | Oncogene |
******************** ner_oncology_biomarker_wip results ********************
| chunk | ner_label |
|:-------------------------------|:-----------------|
| negative | Biomarker_Result |
| thyroid transcription factor-1 | Biomarker |
| napsin A | Biomarker |
| positive | Biomarker_Result |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Result |
| HER2 | Biomarker |
******************** ner_oncology_test_wip results ********************
| chunk | ner_label |
|:-------------------------------|:-----------------|
| Immunohistochemistry | Pathology_Test |
| negative | Biomarker_Result |
| thyroid transcription factor-1 | Biomarker |
| napsin A | Biomarker |
| positive | Biomarker_Result |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Result |
| HER2 | Oncogene |
******************** ner_biomarker results ********************
| chunk | ner_label |
|:-------------------------------|:----------------------|
| Immunohistochemistry | Test |
| negative | Biomarker_Measurement |
| thyroid transcription factor-1 | Biomarker |
| napsin A | Biomarker |
| positive | Biomarker_Measurement |
| ER | Biomarker |
| PR | Biomarker |
| negative | Biomarker_Measurement |
| HER2 | Biomarker |
******************** assertion_oncology_wip results ********************
| chunk | ner_label | assertion |
|:-------------------------------|:---------------|:------------|
| Immunohistochemistry | Pathology_Test | Past |
| thyroid transcription factor-1 | Biomarker | Present |
| napsin A | Biomarker | Present |
| ER | Biomarker | Present |
| PR | Biomarker | Present |
| HER2 | Oncogene | Present |
******************** assertion_oncology_test_binary_wip results ********************
| chunk | ner_label | assertion |
|:-------------------------------|:---------------|:----------------|
| Immunohistochemistry | Pathology_Test | Medical_History |
| thyroid transcription factor-1 | Biomarker | Medical_History |
| napsin A | Biomarker | Medical_History |
| ER | Biomarker | Medical_History |
| PR | Biomarker | Medical_History |
| HER2 | Oncogene | Medical_History |
******************** re_oncology_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------------------|:-----------------|:-------------------------------|:-----------------|:--------------|
| Immunohistochemistry | Pathology_Test | negative | Biomarker_Result | O |
| negative | Biomarker_Result | thyroid transcription factor-1 | Biomarker | is_related_to |
| negative | Biomarker_Result | napsin A | Biomarker | is_related_to |
| positive | Biomarker_Result | ER | Biomarker | is_related_to |
| positive | Biomarker_Result | PR | Biomarker | is_related_to |
| positive | Biomarker_Result | HER2 | Oncogene | O |
| ER | Biomarker | negative | Biomarker_Result | O |
| PR | Biomarker | negative | Biomarker_Result | O |
| negative | Biomarker_Result | HER2 | Oncogene | is_related_to |
******************** re_oncology_granular_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------------------|:-----------------|:-------------------------------|:-----------------|:--------------|
| Immunohistochemistry | Pathology_Test | negative | Biomarker_Result | O |
| negative | Biomarker_Result | thyroid transcription factor-1 | Biomarker | is_finding_of |
| negative | Biomarker_Result | napsin A | Biomarker | is_finding_of |
| positive | Biomarker_Result | ER | Biomarker | is_finding_of |
| positive | Biomarker_Result | PR | Biomarker | is_finding_of |
| positive | Biomarker_Result | HER2 | Oncogene | is_finding_of |
| ER | Biomarker | negative | Biomarker_Result | O |
| PR | Biomarker | negative | Biomarker_Result | O |
| negative | Biomarker_Result | HER2 | Oncogene | is_finding_of |
******************** re_oncology_biomarker_result_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------------------|:-----------------|:-------------------------------|:-----------------|:--------------|
| Immunohistochemistry | Pathology_Test | negative | Biomarker_Result | is_finding_of |
| negative | Biomarker_Result | thyroid transcription factor-1 | Biomarker | is_finding_of |
| negative | Biomarker_Result | napsin A | Biomarker | is_finding_of |
| positive | Biomarker_Result | ER | Biomarker | is_finding_of |
| positive | Biomarker_Result | PR | Biomarker | is_finding_of |
| positive | Biomarker_Result | HER2 | Oncogene | O |
| ER | Biomarker | negative | Biomarker_Result | O |
| PR | Biomarker | negative | Biomarker_Result | O |
| negative | Biomarker_Result | HER2 | Oncogene | is_finding_of |
Model Information
| Model Name: | oncology_biomarker_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 4.3.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- ChunkMergeModel
- ChunkMergeModel
- AssertionDLModel
- AssertionDLModel
- PerceptronModel
- DependencyParserModel
- RelationExtractionModel
- RelationExtractionModel
- RelationExtractionModel