Description
This advanced pipeline extracts clinical conditions from clinical texts and utilizes the sbiobert_base_cased_mli Sentence Bert Embeddings to map these entities to their corresponding SNOMED codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("snomed_conditions_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""Medical professionals rushed in the bustling emergency room to attend to the patient with distressed breathing.
The attending physician immediately noted signs of respiratory distress, including stridor, a high-pitched sound indicative of upper respiratory tract obstruction.
The patient, struggling to breathe, exhibited dyspnea. Concern raised when they began experiencing syncope,
a sudden loss of consciousness likely stemming from inadequate oxygenation. Further examination revealed a respiratory tract hemorrhage.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("snomed_conditions_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""Medical professionals rushed in the bustling emergency room to attend to the patient with distressed breathing.
The attending physician immediately noted signs of respiratory distress, including stridor, a high-pitched sound indicative of upper respiratory tract obstruction.
The patient, struggling to breathe, exhibited dyspnea. Concern raised when they began experiencing syncope,
a sudden loss of consciousness likely stemming from inadequate oxygenation. Further examination revealed a respiratory tract hemorrhage.""")
Results
+-----------------------------------+-----+---+-------------------------+---------+-----------------------------------+------------------------------------------------------------+------------------------------------------------------------+
| chunk|begin|end| ner_label| code| description| all_codes| resolutions|
+-----------------------------------+-----+---+-------------------------+---------+-----------------------------------+------------------------------------------------------------+------------------------------------------------------------+
| distressed breathing| 90|109| Symptom|271825005| distressed breathing|271825005:::230145002:::386813002:::248585001:::47653008:...|distressed breathing:::difficulty breathing:::breathing a...|
| respiratory distress| 173|192| VS_Finding|271825005| respiratory distress|271825005:::418092006:::75483001:::373895009:::230145002:...|respiratory distress:::respiratory tract congestion:::pai...|
| stridor| 205|211| Symptom| 70407001| stridor|70407001:::301826004:::58596002:::301287002:::307487006::...|stridor:::intermittent stridor:::inhalatory stridor:::exp...|
| a high-pitched sound| 214|233| PROBLEM| 51406002| high pitched voice|51406002:::300211002:::271661003:::405495005:::23292001::...|high pitched voice:::responds to high frequency sounds:::...|
|upper respiratory tract obstruction| 249|283|Disease_Syndrome_Disorder| 68372009|upper respiratory tract obstruction|68372009:::79688008:::73342002:::301252002:::201060008:::...|upper respiratory tract obstruction:::respiratory obstruc...|
| struggling to breathe| 309|329| Symptom|289105003| difficulty controlling breathing|289105003:::230145002:::289116005:::386813002:::271825005...|difficulty controlling breathing:::difficulty breathing::...|
| dyspnea| 342|348| Symptom|267036007| dyspnea|267036007:::60845006:::25209001:::34560001:::59265000:::8...|dyspnea:::exertional dyspnea:::inspiratory dyspnea:::expi...|
| syncope| 395|401| Symptom|271594007| syncope|271594007:::234167006:::90129003:::445535007:::31457007::...|syncope:::situational syncope:::tussive syncope:::witness...|
| a sudden loss of consciousness| 414|443| PROBLEM| 32834005| brief loss of consciousness|32834005:::40863000:::7862002:::15203004:::419045004:::27...|brief loss of consciousness:::moderate loss of consciousn...|
| inadequate oxygenation| 466|487| Symptom|238161004| impaired oxygen delivery|238161004:::70944005:::238162006:::123826004:::238160003:...|impaired oxygen delivery:::impaired gas exchange:::impair...|
| a respiratory tract hemorrhage| 519|548| PROBLEM| 95431003| respiratory tract hemorrhage|95431003:::233783005:::405541003:::78144005:::276543004::...|respiratory tract hemorrhage:::tracheal hemorrhage:::bron...|
+-----------------------------------+-----+---+-------------------------+---------+-----------------------------------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | snomed_conditions_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.3.0+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel