Description
This pipeline extracts anatomical structure entities and maps them to their corresponding SNOMED (body structure version) codes using sbiobert_base_cased_mli Sentence Bert Embeddings.
How to use
from sparknlp.pretrained import PretrainedPipeline
snomed_pipeline = PretrainedPipeline("snomed_body_structure_resolver_pipeline", "en", "clinical/models")
result = snomed_pipeline.annotate("""The patient is a 30-year-old female with a long history of insulin-dependent diabetes, type 2; coronary artery disease; chronic renal insufficiency; peripheral vascular disease, also secondary to diabetes; who was originally admitted to an outside hospital for what appeared to be acute paraplegia, lower extremities. She did receive a course of Bactrim for 14 days for UTI.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val snomed_pipeline = PretrainedPipeline("snomed_body_structure_resolver_pipeline", "en", "clinical/models")
val result = snomed_pipeline.annotate("""The patient is a 30-year-old female with a long history of insulin-dependent diabetes, type 2; coronary artery disease; chronic renal insufficiency; peripheral vascular disease, also secondary to diabetes; who was originally admitted to an outside hospital for what appeared to be acute paraplegia, lower extremities. She did receive a course of Bactrim for 14 days for UTI.""")
Results
+-------------------+-----+---+---------+-----------+--------------------------+------------------------------------------------------------+------------------------------------------------------------+
| chunk|begin|end|ner_label|snomed_code| resolution| all_k_resolutions| all_k_codes|
+-------------------+-----+---+---------+-----------+--------------------------+------------------------------------------------------------+------------------------------------------------------------+
| coronary artery| 95|109| BodyPart| 181294004| coronary artery|coronary artery:::coronary artery part:::segment of coron...|181294004:::119204004:::360487004:::55537005:::41801008::...|
| renal| 128|132| BodyPart| 64033007| renal structure|renal structure:::renal area:::renal segment:::renal vess...|64033007:::243968009:::84924000:::303402001:::361332007::...|
|peripheral vascular| 149|167| BodyPart| 51833009|peripheral vascular system|peripheral vascular system:::peripheral artery:::peripher...|51833009:::840581000:::3058005:::300054001:::281828002:::...|
| lower extremities| 299|315| BodyPart| 61685007| lower extremity|lower extremity:::lower extremity region:::lower extremit...|61685007:::127951001:::120575009:::182281004:::276744008:...|
+-------------------+-----+---+---------+-----------+--------------------------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | snomed_body_structure_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.3.0+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.4 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel