Description
This dedicated pipeline utilizes sbiobert_base_cased_mli Sentence Bert Embeddings to extract clinical terms and link them to their corresponding MedDRA LLT (Lowest Level Term) codes. Additionally, it provides the MedDRA Preferred Term codes for each MedDRA LLT code within the meddra_llt_code metadata’s all_k_aux_labels. Furthermore, it conducts mappings of MedDRA LLT codes to MedDRA Preferred Term (PT) codes using the meddra_llt_pt_mapper model and to ICD-10 codes using the meddra_llt_icd10_mapper model.
This pipeline can extract the following clincial entities:
Procedure, Kidney_Disease, Cerebrovascular_Disease, Heart_Disease, Disease_Syndrome_Disorder, ImagingFindings, Symptom, VS_Finding, EKG_Findings, Communicable_Disease, Substance, Internal_organ_or_component, External_body_part_or_region, Modifier, Triglycerides, Alcohol, Smoking, Pregnancy, Hypertension, Obesity, Injury_or_Poisoning, Test, Hyperlipidemia, BMI, Oncological, Psychological_Condition, LDL, Diabetes, PROBLEM
How to use
from sparknlp.pretrained import PretrainedPipeline
meddra_llt_pipeline = PretrainedPipeline.from_disk("meddra_llt_resolver_pipeline")
result = meddra_llt_pipeline.fullAnnotate("""This is an 82-year-old male with a history of prior tobacco use, benign hypertension, chronic renal insufficiency, chronic bronchitis, gastritis, and ischemic attack. He initially presented to Braintree with ST elevation and was transferred to St. Margaret’s Center. He underwent cardiac catheterization because of the left main coronary artery stenosis, which was complicated by hypotension and bradycardia. We describe the side effects of 5-FU in a colon cancer patient who suffered mucositis and dermatitis."""')
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val meddra_llt_pipeline = PretrainedPipeline.from_disk("meddra_llt_resolver_pipeline")
val result = meddra_llt_pipeline.fullAnnotate("""This is an 82-year-old male with a history of prior tobacco use, benign hypertension, chronic renal insufficiency, chronic bronchitis, gastritis, and ischemic attack. He initially presented to Braintree with ST elevation and was transferred to St. Margaret’s Center. He underwent cardiac catheterization because of the left main coronary artery stenosis, which was complicated by hypotension and bradycardia. We describe the side effects of 5-FU in a colon cancer patient who suffered mucositis and dermatitis.""")
Results
+--------------------------------------+-------------------------+---------------+----------------------------------+-------------------------------------------------+-----------------------------------------------+
|chunk |label |meddra_llt_code|resolution |icd10_code |meddra_pt_code |
+--------------------------------------+-------------------------+---------------+----------------------------------+-------------------------------------------------+-----------------------------------------------+
|tobacco |Smoking |10067622 |tobacco interaction |NONE |10067622:Tobacco interaction |
|benign hypertension |PROBLEM |10004455 |benign secondary hypertension |NONE |10039834:Secondary hypertension |
|chronic renal insufficiency |Kidney_Disease |10050441 |chronic renal insufficiency |NONE |10064848:Chronic kidney disease |
|chronic bronchitis |PROBLEM |10008841 |chronic bronchitis |NONE |10006458:Bronchitis chronic |
|gastritis |Disease_Syndrome_Disorder|10017853 |gastritis |K29.6:Other gastritis |10017853:Gastritis |
|ischemic attack |Cerebrovascular_Disease |10072760 |transient ischemic attack |NONE |10044390:Transient ischaemic attack |
|ST elevation |PROBLEM |10041887 |st elevated |NONE |10014392:Electrocardiogram ST segment elevation|
|cardiac catheterization |Procedure |10048606 |cardiac catheterization |NONE |10007815:Catheterisation cardiac |
|the left main coronary artery stenosis|PROBLEM |10090240 |left main coronary artery stenosis|NONE |10011089:Coronary artery stenosis |
|hypotension |VS_Finding |10021097 |hypotension |I95:Hypotension |10021097:Hypotension |
|bradycardia |VS_Finding |10006093 |bradycardia |R00.1:Bradycardia, unspecified |10006093:Bradycardia |
|the side effects |PROBLEM |10044252 |toxic symptom |NONE |10070863:Toxicity to various agents |
|a colon cancer |PROBLEM |10009944 |colon cancer |NONE |10009944:Colon cancer |
|mucositis |Disease_Syndrome_Disorder|10028127 |mucositis |NONE |10028116:Mucosal inflammation |
|dermatitis |Disease_Syndrome_Disorder|10012431 |dermatitis |L27:Dermatitis due to substances taken internally|10012431:Dermatitis |
+--------------------------------------+-------------------------+---------------+----------------------------------+-------------------------------------------------+-----------------------------------------------+
Model Information
| Model Name: | meddra_llt_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.4 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel
- Resolution2Chunk
- ChunkMapperModel
- ChunkMapperModel
References
This pipeline is prepared using the models that are trained with the September 2024 (v27.1) of MedDRA dataset. To utilize this pipeline, possession of a valid MedDRA license is requisite. If you possess one and wish to use this model, kindly contact us at support@johnsnowlabs.com.