Description
This pipeline extracts Test entities from clinical texts and maps them to their corresponding Logical Observation Identifiers Names and Codes (LOINC) codes using sbiobert_base_cased_mli Sentence Bert Embeddings.
Trained on the official LOINC 2.83 dataset.
This pipeline may also resolve to non-numeric LOINC codes, including LOINC’s own internal Part codes (prefixed “LP”). If you only need numeric, directly orderable/reportable LOINC codes, use sbiobertresolve_loinc_numeric_pipeline_2_83 instead.
It also provides the official resolution of the codes within the brackets.
Live Demo Open in Colab Copy S3 URI
How to use
from sparknlp.pretrained import PretrainedPipeline
loinc_pipeline = PretrainedPipeline("sbiobertresolve_loinc_pipeline_2_83", "en", "clinical/models")
data = spark.createDataFrame([["The patient's glucose and hemoglobin A1c levels were checked, along with a basic metabolic panel including sodium and potassium, and a complete blood count."]]).toDF("text")
result = loinc_pipeline.transform(data)
from johnsnowlabs import nlp, medical
loinc_pipeline = nlp.PretrainedPipeline("sbiobertresolve_loinc_pipeline_2_83", "en", "clinical/models")
data = spark.createDataFrame([["The patient's glucose and hemoglobin A1c levels were checked, along with a basic metabolic panel including sodium and potassium, and a complete blood count."]]).toDF("text")
result = loinc_pipeline.transform(data)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val loinc_pipeline = PretrainedPipeline("sbiobertresolve_loinc_pipeline_2_83", "en", "clinical/models")
val data = Seq("The patient's glucose and hemoglobin A1c levels were checked, along with a basic metabolic panel including sodium and potassium, and a complete blood count.").toDF("text")
val result = loinc_pipeline.transform(data)
Results
| chunk | label | loinc_code | resolution | all_codes | all_resolutions |
|:----------------------|:--------|:-------------|:----------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| glucose | Test | 2345-7 | glucose [Glucose [Mass/volume] in Serum or Plasma] | 2345-7:::74790-7:::51419-0:::81637-1:::47621-8:::104638-2:::50016-5:::72648-9:::27353-2:::6248-9:::41653-7:::LP69206-8:::4269-7:::95720-9:::41896-2:::26682-5:::50667-5:::97506-0:::80093-8:::20643-3 | glucose [Glucose [Mass/volume] in Serum or Plasma]:::Glucose HBT [Glucose challenge (hydrogen breath test) panel - Exhaled gas]:::Glucose cor [Sodium [Moles/volume] corrected for glucose in Serum or Plasma]:::Glucose correlation [Glucose meter to reference method correlation [Ratio] in Serum, Plasma or Blood by calculation]:::glucose.iv [Glucose.IV [Mass] of Dose]:::Glucose SD [Glucose standard deviation/Glucose mean in Reporting Period Interstitial fluid by calculation]:::sugar [Sugar [Type] of Dose]:::glucose gradient [Glucose in serum - glucose in synovial fluid [Molar concentration difference]]:::Glucose mean value [Glucose mean value [Mass/volume] in Blood Estimated from glycated hemoglobin]:::Gly [Soybean IgE Ab [Units/volume] in Serum]:::Glucomtr [Glucose [Mass/volume] in Capillary blood by Glucometer]:::glucose csf [Glucose in CSF]:::glucose.po [Glucose.PO [Mass] of Dose]:::GlyR [Glycine receptor Ab [Titer] in Serum or Plasma by Immunoassay]:::Glucose Mtr Dev [Type of Glucose meter device]:::glycolate [Glycolate [Presence] in Urine]:::glucose tolerance [Glucose tolerance [Interpretation] in Serum or Plasma Narrative]:::Glucose management indicator [Glucose management indicator]:::glucosamine [Glucosamine [Moles/volume] in Serum or Plasma]:::Gln [Glutamine [Moles/volume] in Serum or Plasma] |
| hemoglobin A1c levels | Test | 41995-2 | hemoglobin a1c [Hemoglobin A1c [Mass/volume] in Blood] | 41995-2:::LP16412-6:::43150-2:::4548-4:::10486-9:::21687-9:::112870-1:::LP16430-8:::51196-4:::10346-5:::50319-3:::17871-5:::4593-0:::LP94632-4:::50385-4:::6864-3:::72914-5:::LP94633-2:::14563-1:::96595-4:::2030-5 | hemoglobin a1c [Hemoglobin A1c [Mass/volume] in Blood]:::hemoglobin a1 [Hemoglobin A1]:::Hemoglobin A1c measurement device panel [Hemoglobin A1c measurement device panel]:::hemoglobin a1c/hemoglobin.total [Hemoglobin A1c/Hemoglobin.total in Blood]:::hemoglobin ag [Hemoglobin Ag [Presence] in Tissue by Immune stain]:::Hemoglobin, alpha 1 [HBA1 gene mutations found [Identifier] in Blood or Tissue by Targeted gene mutation analysis Nominal]:::hemoglobin a1c & estimated average glucose panel [Hemoglobin A1c and estimated average glucose panel - Blood]:::hemoglobin f1 [Hemoglobin F1]:::hemoglobin a1/hemoglobin.total [Hemoglobin A1/Hemoglobin.total in Blood by Electrophoresis]:::hemoglobin a [Hemoglobin A [Units/volume] in Blood by Electrophoresis]:::hbme-1 ag [HBME-1 Ag [Presence] in Tissue by Immune stain]:::hemoglobin h [Hemoglobin H [Presence] in Blood by Heat denaturation]:::hemoglobin i [Hemoglobin I [Presence] in Blood by Electrophoresis acid (pH 6.3)]:::hemoglobin d+g [Hemoglobin D+G]:::A1 Microglob [Alpha-1-Microglobulin.placental [Presence] in Vaginal fluid]:::hemoglobin s [Hemoglobin S [Presence] in Blood by Solubility test]:::hna 1c ab [HNA 1c Ab [Presence] in Serum by Immunoassay]:::hemoglobin n+i [Hemoglobin N+I]:::hemoglobin^1st specimen [Hemoglobin [Presence] in Stool from gastrointestinal --1st specimen]:::Hemoglobin A1c/Hemoglobin.total in DBS [Hemoglobin A1c/Hemoglobin.total in DBS]:::CO Hemoglobin [Carboxyhemoglobin/Hemoglobin.total in Arterial blood] |
| basic metabolic panel | Test | 51990-0 | basic metabolic panel [Basic metabolic panel - Blood] | 51990-0:::101655-9:::89044-2:::9350-0:::50042-1:::79531-0:::43147-8:::24321-2:::79529-4:::104076-5:::79530-2:::112034-4:::81578-7:::LP76085-7:::LP35945-2:::1547-9:::107464-0:::41966-3 | basic metabolic panel [Basic metabolic panel - Blood]:::basic metabolic & hematocrit panel [Basic metabolic and hematocrit panel - Blood]:::basic metabolic & albumin panel [Basic metabolic and albumin panel - Serum or Plasma]:::Metabolic screen [Sulfhydryls [Presence] in Urine]:::Basal metabolic rate index [Basal metabolic rate index]:::basic mobility items [Basic mobility items number [Activity Measure for Post-Acute Care]]:::Metabolism measurement device panel [Metabolism measurement device panel]:::basic metabolic 2000 panel [Basic metabolic 2000 panel - Serum or Plasma]:::basic mobility score [Basic mobility score [AM-PAC]]:::basic metabolic & hemoglobin & hematocrit panel [Basic metabolic with hemoglobin and hematocrit panel - Blood]:::Basic mobility score SE [Basic mobility score standard error [AM-PAC]]:::Basic information [Basic information]:::PT Brain metabolic [PT Brain metabolic]:::mds.basic [MDS.basic]:::metabolism measurement device [Metabolism measurement device]:::glucose^baseline [Glucose [Mass/volume] in Serum or Plasma --baseline]:::metabolic disease screening [Metabolic disease screening Newborn]:::Name of Metabolism measurement device [Name of Metabolism measurement device] |
| sodium | Test | 2951-2 | sodium [Sodium [Moles/volume] in Serum or Plasma] | 2951-2:::81011-9:::9086-0:::16527-4:::9087-8:::2957-9:::43423-3:::87451-1:::50912-5:::87452-9:::14055-8:::28003-2:::74993-7:::51205-3:::23611-7:::2954-6:::2950-4:::32340-2:::43223-7:::49135-7:::54437-9 | sodium [Sodium [Moles/volume] in Serum or Plasma]:::sodium intake [Sodium intake 24 hour Estimated]:::Sodium intake Est [Sodium intake Estimated]:::calcium/sodium [Calcium/Sodium [Mass Ratio] in Serum or Plasma]:::Sodium intake Measured [Sodium intake Measured]:::sodium renal clearance [Sodium renal clearance in 24 hour Urine and Serum or Plasma]:::sodium urate [Sodium urate [Saturation Fraction] in 24 hour Urine]:::Sodium [Mass/volume] in Specimen [Sodium [Mass/volume] in Specimen]:::Sodium Hair-sCnt [Sodium [Moles/mass] in Hair]:::Sodium [Mass/mass] in Specimen [Sodium [Mass/mass] in Specimen]:::Sodium Stl-sCnt [Sodium [Moles/mass] in Stool]:::sodium/potassium [Sodium/Potassium [Molar ratio] in Serum or Plasma]:::Chloride+sodium Pnl [Chloride and sodium panel [Moles/volume] - Sweat]:::Sodium Hair-mCnt [Sodium [Mass/mass] in Hair]:::Nemasol sodium [Para aminosalicylate [Susceptibility] by Method for Slow-growing mycobacteria]:::Sodium Sweat-sCnc [Sodium [Moles/volume] in Sweat]:::Sodium [Moles/volume] in Body fluid [Sodium [Moles/volume] in Body fluid]:::Sodium Spec-sCnc [Sodium [Moles/volume] in Specimen]:::Sodium/Creat Ur-Rto [Sodium/Creatinine [Ratio] in Urine]:::fractional excretion of sodium [Fractional excretion of sodium [Ratio] in Urine and Serum or Plasma]:::sodium urate/total [Sodium urate/Total in Stone by Infrared spectroscopy] |
| potassium | Test | 2823-3 | potassium [Potassium [Moles/volume] in Serum or Plasma] | 2823-3:::10322-6:::9073-8:::28003-2:::2830-8:::59733-6:::9074-6:::25506-7:::87455-2:::50902-6:::32336-0:::49788-3:::59010-9:::32713-0:::79710-0:::87454-5:::9482-1:::12814-0:::2828-2:::34548-8:::6940-1 | potassium [Potassium [Moles/volume] in Serum or Plasma]:::potassium intake [Potassium intake 24 hour]:::Potassium intake Est [Potassium intake Estimated]:::sodium/potassium [Sodium/Potassium [Molar ratio] in Serum or Plasma]:::potassium renal clearance [Potassium renal clearance in 24 hour Urine and Serum or Plasma]:::Potassium Tiss-mCnt [Potassium [Mass/mass] in Tissue]:::Potassium intake Measured [Potassium intake Measured]:::Potassium Stl-sCnt [Potassium [Moles/mass] in Stool]:::Potassium Spec-mCnt [Potassium [Mass/mass] in Specimen]:::Potassium Hair-sCnt [Potassium [Moles/mass] in Hair]:::Potassium Spec-sCnc [Potassium [Moles/volume] in Specimen]:::Potassium Amn-sCnc [Potassium [Moles/volume] in Amniotic fluid]:::fractional excretion of potassium [Fractional excretion of potassium [Ratio] in Urine and Serum or Plasma collected for unspecified duration]:::Potassium BldA-sCnc [Potassium [Moles/volume] in Arterial blood]:::Potassium Hair-mCnt [Potassium [Mass/mass] in Hair]:::Potassium [Mass/volume] in Specimen [Potassium [Mass/volume] in Specimen]:::Potassium Wat-mCnc [Potassium [Mass/volume] in Water]:::Potassium Vitf-sCnc [Potassium [Moles/volume] in Vitreous fluid]:::Potassium Ur-sCnc [Potassium [Moles/volume] in Urine]:::Sodium + Potassium Pnl [Sodium and Potassium panel [Moles/volume] - Serum or Plasma]:::Potassium ?Tm Stl-sRate [Potassium [Moles/time] in unspecified time Stool] |
| complete blood count | Test | 24358-4 | Complete Blood Count [Hemogram without Platelets panel - Blood] | 24358-4:::58410-2:::74412-8:::47288-6:::1335-9:::789-8:::51876-1:::LP71083-7:::786-4:::777-3:::39227-4:::41986-1:::LP15101-6:::57022-6:::57021-8:::51637-7:::53963-5:::111533-6:::34556-1:::24360-0 | Complete Blood Count [Hemogram without Platelets panel - Blood]:::complete blood count panel [CBC panel - Blood by Automated count]:::complete blood count w differential panel [CBC W Differential panel - Cord blood]:::complete blood count wo differential panel [CBC WO Differential panel - Cord blood]:::whole blood given [Whole blood given [Volume]]:::Whole blood [Erythrocytes [#/volume] in Blood by Automated count]:::whole blood units given [Whole blood units given [#]]:::whole blood units [Whole blood units]:::HEMATOLOGY/CELL COUNTS [MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count]:::Platelet count [Platelets [#/volume] in Blood by Automated count]:::hematocrit test status [Hematocrit test status CPHS]:::Hematocrit Test Status/Results [Hematocrit test status/results Set CPHS]:::hematocrit [Hematocrit]:::complete blood count w reflex manual differential panel [CBC W Reflex Manual Differential panel - Blood]:::complete blood count w auto differential panel [CBC W Auto Differential panel - Blood]:::plateletocrit [Plateletcrit [Volume Fraction] in Blood]:::blood [Blood [Presence] in Urine by Visual]:::specimen count [Specimen Count [#] by calculation]:::Cell count panel - Body fluid [Cell count panel - Body fluid]:::hemoglobin & hematocrit panel [Hemoglobin and Hematocrit panel - Blood] |
Model Information
| Model Name: | sbiobertresolve_loinc_pipeline_2_83 |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 3.0 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel