Description
This pipeline extracts Procedure and measurement (Test) entities and maps them to their corresponding SNOMED codes using sbiobert_base_cased_mli Sentence Bert Embeddings.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("snomed_procedures_measurements_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""Based on the severity of her abdominal examination and the persistence of her symptoms,
it has been determined that she requires a laparoscopic jejunectomy, possible appendectomy, and
cholecystectomy.Laboratory values indicate a white blood cell count of 15.3,
hemoglobin level of 12.8, and normal platelet count. Alkaline phosphatase is elevated at 184,
while liver function tests are otherwise normal. Electrolyte levels are within the normal range.
Glucose levels are at 134, BUN is 4, and creatinine is 0.7.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("snomed_procedures_measurements_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""Based on the severity of her abdominal examination and the persistence of her symptoms,
it has been determined that she requires a laparoscopic jejunectomy, possible appendectomy, and
cholecystectomy.Laboratory values indicate a white blood cell count of 15.3,
hemoglobin level of 12.8, and normal platelet count. Alkaline phosphatase is elevated at 184,
while liver function tests are otherwise normal. Electrolyte levels are within the normal range.
Glucose levels are at 134, BUN is 4, and creatinine is 0.7.""")
Results
+------------------------+-----+---+---------+-----------+--------------------------------+------------------------------------------------------------+------------------------------------------------------------+
| chunk|begin|end|ner_label|snomed_code| resolution| all_k_resolutions| all_k_codes|
+------------------------+-----+---+---------+-----------+--------------------------------+------------------------------------------------------------+------------------------------------------------------------+
|laparoscopic jejunectomy| 143|166|Procedure| 1220546008|laparoscopic excision of jejunum|laparoscopic excision of jejunum:::laparoscopic appendice...|1220546008:::6025007:::307195003:::1220549001:::708627007...|
| appendectomy| 178|189|Procedure| 80146002| appendectomy|appendectomy:::appendicotomy:::appendicectomy:::secondary...|80146002:::17041004:::149412002:::82730006:::174045003:::...|
| cholecystectomy| 208|222|Procedure| 38102005| cholecystectomy|cholecystectomy:::choledochectomy:::cholecystotomy:::endo...|38102005:::6402000:::44337006:::45595009:::34130000:::899...|
| white blood cell count| 253|274| Test| 767002| white blood cell count|white blood cell count:::white blood cell test:::differen...|767002:::252305002:::142922003:::44190001:::391558003:::4...|
| hemoglobin level| 297|312| Test| 313995005| hemoglobin a level|hemoglobin a level:::plasma hemoglobin level:::hemoglobin...|313995005:::104142005:::407705000:::143073002:::35170002:...|
| platelet count| 334|347| Test| 61928009| platelet count|platelet count:::plateletcrit:::platelet estimate:::mean ...|61928009:::250314004:::8574009:::75672003:::80329005:::40...|
| Alkaline phosphatase| 350|369| Test| 88810008|alkaline phosphatase measurement|alkaline phosphatase measurement:::alkaline phosphatase s...|88810008:::45745006:::143948004:::166625007:::271234008::...|
| liver function tests| 409|428| Test| 143927001| liver function tests|liver function tests:::liver function test:::liver functi...|143927001:::26958001:::166601004:::269992001:::736164009:...|
| Electrolyte levels| 452|469| Test| 79301008| electrolytes measurement|electrolytes measurement:::electrolyte regulation:::blood...|79301008:::276025008:::144342002:::401142008:::386275008:...|
| Glucose levels| 512|525| Test| 144323001| serum glucose level|serum glucose level:::plasma glucose level:::blood glucos...|144323001:::167094009:::144184004:::36048009:::72191006::...|
| BUN| 539|541| Test| 105011006| bun measurement|bun measurement:::cinching:::bost operation:::pexy:::blou...|105011006:::16227009:::85651007:::1431002:::46747009:::45...|
| creatinine| 553|562| Test| 70901006| creatinine measurement|creatinine measurement:::plasma creatinine level:::serum ...|70901006:::166729007:::166713004:::144658009:::313936008:...|
+------------------------+-----+---+---------+-----------+--------------------------------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | snomed_procedures_measurements_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.4 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel