Description
This pipeline can be used to deidentify PHI information from medical texts. The PHI information will be masked and obfuscated in the resulting text.
The pipeline can mask and obfuscate LOCATION, CONTACT, PROFESSION, NAME, DATE, AGE, MEDICALRECORD, ORGANIZATION, HEALTHPLAN, DOCTOR, USERNAME,
LOCATION-OTHER, URL, DEVICE, CITY, ZIP, STATE, PATIENT, COUNTRY, STREET, PHONE, HOSPITAL, EMAIL, IDNUM, BIOID, FAX, LOCATION_OTHER, DLN,
SSN, ACCOUNT, PLATE, VIN, LICENSE, IP entities.
How to use
from sparknlp.pretrained import PretrainedPipeline
deid_pipeline = PretrainedPipeline("ner_deid_subentity_docwise_augmented_pipeline_v2", "en", "clinical/models")
text = """Dr. John Lee, from Royal Medical Clinic in Chicago, attended to the patient on 11/05/2024.
The patient’s medical record number is 56467890.
The patient, Emma Wilson, is 50 years old, her Contact number: 444-456-7890 ."""
deid_result = deid_pipeline.fullAnnotate(text)
from sparknlp.pretrained import PretrainedPipeline
deid_pipeline = nlp.PretrainedPipeline("ner_deid_subentity_docwise_augmented_pipeline_v2", "en", "clinical/models")
text = """Dr. John Lee, from Royal Medical Clinic in Chicago, attended to the patient on 11/05/2024.
The patient’s medical record number is 56467890.
The patient, Emma Wilson, is 50 years old, her Contact number: 444-456-7890 ."""
deid_result = deid_pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val deid_pipeline = PretrainedPipeline("ner_deid_subentity_docwise_augmented_pipeline_v2", "en", "clinical/models")
val text = """Dr. John Lee, from Royal Medical Clinic in Chicago, attended to the patient on 11/05/2024.
The patient’s medical record number is 56467890.
The patient, Emma Wilson, is 50 years old, her Contact number: 444-456-7890 ."""
val deid_result = deid_pipeline.fullAnnotate(text)
Results
+--------------------+-----+---+-------------+
|result |begin|end|entity |
+--------------------+-----+---+-------------+
|John Lee |4 |11 |DOCTOR |
|Royal Medical Clinic|19 |38 |HOSPITAL |
|Chicago |43 |49 |CITY |
|11/05/2024 |80 |89 |DATE |
|56467890 |131 |138|MEDICALRECORD|
|Emma Wilson |154 |164|PATIENT |
|50 |170 |171|AGE |
|444-456-7890 |205 |216|PHONE |
+--------------------+-----+---+-------------+
Model Information
| Model Name: | ner_deid_subentity_docwise_augmented_pipeline_v2 |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.5.3+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.5 GB |
Included Models
- DocumentAssembler
- InternalDocumentSplitter
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- MedicalNerModel
- MedicalNerModel
- NerConverterInternalModel
- NerConverterInternalModel
- NerConverterInternalModel
- PretrainedZeroShotNER
- NerConverterInternalModel
- ChunkMergeModel
- ContextualParserModel
- ContextualParserModel
- ContextualParserModel
- ContextualParserModel
- ContextualParserModel
- ContextualParserModel
- ContextualParserModel
- TextMatcherInternalModel
- TextMatcherInternalModel
- TextMatcherInternalModel
- ContextualParserModel
- RegexMatcherInternalModel
- ContextualParserModel
- ContextualParserModel
- ContextualParserModel
- RegexMatcherInternalModel
- RegexMatcherInternalModel
- RegexMatcherInternalModel
- TextMatcherInternalModel
- ChunkMergeModel
- ChunkMergeModel