diff --git a/docs/_posts/akrztrk/2024-12-19-medication_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-12-19-medication_resolver_pipeline_en.md new file mode 100644 index 0000000000..35a61acbe1 --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-19-medication_resolver_pipeline_en.md @@ -0,0 +1,132 @@ +--- +layout: model +title: Pipeline to Resolve Medication Codes +author: John Snow Labs +name: medication_resolver_pipeline +date: 2024-12-19 +tags: [licensed, en, resolver, snomed, umls, rxnorm, ndc, ade, pipeline] +task: [Pipeline Healthcare, Named Entity Recognition] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +A pretrained resolver pipeline to extract medications and resolve their adverse reactions (ADE), RxNorm, UMLS, NDC, SNOMED CT codes, and action/treatments in clinical text. + +Action/treatments are available for branded medication, and SNOMED codes are available for non-branded medication. + +This pipeline can be used as Lightpipeline (with `annotate/fullAnnotate`). You can use `medication_resolver_transform_pipeline` for Spark transform. + +## Predicted Entities + +`DRUG` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/medication_resolver_pipeline_en_5.5.1_3.0_1734639447518.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/medication_resolver_pipeline_en_5.5.1_3.0_1734639447518.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +ner_pipeline = PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models") + +result = ner_pipeline.annotate("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. +The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet. +""") + +``` + +{:.jsl-block} +```python + +ner_pipeline = nlp.PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models") + +result = ner_pipeline.annotate("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. +The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet. +""") + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val ner_pipeline = PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models") + +val result = ner_pipeline.annotate("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. +The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet. +""") + +``` +
+ +## Results + +```bash + + ++----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+----------------+-----------+-------------+ +|chunk |ner_label|ADE |RxNorm |Action |Treatment |UMLS |SNOMED_CT |NDC_Product|NDC_Package | ++----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+----------------+-----------+-------------+ +|Amlodopine Vallarta 10-320mg|DRUG |Gynaecomastia |722131 |NONE |NONE |C1949334|1153435009 |00093-7693 |00093-7693-56| +|Eviplera |DRUG |Anxiety |217010 |Inhibitory Bone Resorption|Osteoporosis |C0720318|NONE |NONE |NONE | +|Lescol 40 MG |DRUG |NONE |103919 |Hypocholesterolemic |Heterozygous Familial Hypercholesterolemia|C0353573|NONE |00078-0234 |00078-0234-05| +|Everolimus 1.5 mg tablet |DRUG |Acute myocardial infarction|2056895|NONE |NONE |C4723581|1029521000202102|00054-0604 |00054-0604-21| ++----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+----------------+-----------+-------------+ + + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|medication_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|3.3 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetectorDLModel +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverterInternalModel +- TextMatcherInternalModel +- ChunkMergeModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- Finisher diff --git a/docs/_posts/akrztrk/2024-12-19-medication_resolver_transform_pipeline_en.md b/docs/_posts/akrztrk/2024-12-19-medication_resolver_transform_pipeline_en.md new file mode 100644 index 0000000000..54780365ea --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-19-medication_resolver_transform_pipeline_en.md @@ -0,0 +1,142 @@ +--- +layout: model +title: Pipeline to Resolve Medication Codes(Transform) +author: John Snow Labs +name: medication_resolver_transform_pipeline +date: 2024-12-19 +tags: [licensed, en, resolver, snomed, umls, rxnorm, ndc, ade, pipeline] +task: [Pipeline Healthcare, Named Entity Recognition] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +A pretrained resolver pipeline to extract medications and resolve their adverse reactions (ADE), RxNorm, UMLS, NDC, SNOMED CT codes, and action/treatments in clinical text. + +Action/treatments are available for branded medication, and SNOMED codes are available for non-branded medication. + +This pipeline can be used with Spark transform. You can use `medication_resolver_pipeline` as Lightpipeline (with `annotate/fullAnnotate`). + +## Predicted Entities + +`DRUG` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/medication_resolver_transform_pipeline_en_5.5.1_3.0_1734635642246.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/medication_resolver_transform_pipeline_en_5.5.1_3.0_1734635642246.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +medication_resolver_pipeline = PretrainedPipeline("medication_resolver_transform_pipeline", "en", "clinical/models") + +text = """The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. +The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""" + +data = spark.createDataFrame([[text]]).toDF("text") + +result = medication_resolver_pipeline.transform(data) + +``` + +{:.jsl-block} +```python + +medication_resolver_pipeline = nlp.PretrainedPipeline("medication_resolver_transform_pipeline", "en", "clinical/models") + +text = """The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. +The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""" + +data = spark.createDataFrame([[text]]).toDF("text") + +result = medication_resolver_pipeline.transform(data) + + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val medication_resolver_pipeline = new PretrainedPipeline("medication_resolver_transform_pipeline", "en", "clinical/models") + +val data = Seq("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. +The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""").toDS.toDF("text") + +val result = medication_resolver_pipeline.fit(data).transform(data) + +``` +
+ +## Results + +```bash + + ++----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+----------------+-----------+-------------+ +|chunk |ner_label|ADE |RxNorm |Action |Treatment |UMLS |SNOMED_CT |NDC_Product|NDC_Package | ++----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+----------------+-----------+-------------+ +|Amlodopine Vallarta 10-320mg|DRUG |Gynaecomastia |722131 |NONE |NONE |C1949334|1153435009 |00093-7693 |00093-7693-56| +|Eviplera |DRUG |Anxiety |217010 |Inhibitory Bone Resorption|Osteoporosis |C0720318|NONE |NONE |NONE | +|Lescol 40 MG |DRUG |NONE |103919 |Hypocholesterolemic |Heterozygous Familial Hypercholesterolemia|C0353573|NONE |00078-0234 |00078-0234-05| +|Everolimus 1.5 mg tablet |DRUG |Acute myocardial infarction|2056895|NONE |NONE |C4723581|1029521000202102|00054-0604 |00054-0604-21| ++----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+----------------+-----------+-------------+ + + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|medication_resolver_transform_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|3.3 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetectorDLModel +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverterInternalModel +- TextMatcherInternalModel +- ChunkMergeModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger +- Doc2Chunk +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperModel +- Doc2Chunk +- ChunkMapperModel +- Finisher diff --git a/docs/_posts/akrztrk/2024-12-23-snomed_multi_mapper_pipeline_en.md b/docs/_posts/akrztrk/2024-12-23-snomed_multi_mapper_pipeline_en.md new file mode 100644 index 0000000000..43bd86fd9a --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-23-snomed_multi_mapper_pipeline_en.md @@ -0,0 +1,100 @@ +--- +layout: model +title: SNOMED Code Mapping Pipeline +author: John Snow Labs +name: snomed_multi_mapper_pipeline +date: 2024-12-23 +tags: [licensed, en, snomed, pipeline] +task: Pipeline Healthcare +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +This pretrained pipeline maps SNOMED codes to their corresponding ICD-10, ICD-O, and UMLS codes. + +## Predicted Entities + +`snomed_code` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/snomed_multi_mapper_pipeline_en_5.5.1_3.0_1734953947952.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/snomed_multi_mapper_pipeline_en_5.5.1_3.0_1734953947952.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +mapper_pipeline = PretrainedPipeline("snomed_multi_mapper_pipeline", "en", "clinical/models") + +result = mapper_pipeline.fullAnnotate(["10000006", "128501000"]) + +``` + +{:.jsl-block} +```python + +mapper_pipeline = nlp.PretrainedPipeline("snomed_multi_mapper_pipeline", "en", "clinical/models") + +result = mapper_pipeline.fullAnnotate(["10000006", "128501000"]) + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val mapper_pipeline = PretrainedPipeline("snomed_multi_mapper_pipeline", "en", "clinical/models") + +val result = mapper_pipeline.fullAnnotate(["10000006", "128501000"]) + +``` +
+ +## Results + +```bash + ++-----------+------------+---------+---------+ +|snomed_code|icd10cm_code|icdo_code|umls_code| ++-----------+------------+---------+---------+ +| 10000006| R07.9| NONE| C0232289| +| 128501000| NONE| C49.5| C0448606| ++-----------+------------+---------+---------+ + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|snomed_multi_mapper_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|9.4 MB| + +## Included Models + +- DocumentAssembler +- DocMapperModel +- DocMapperModel +- DocMapperModel diff --git a/docs/_posts/akrztrk/2024-12-23-umls_clinical_findings_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-12-23-umls_clinical_findings_resolver_pipeline_en.md new file mode 100644 index 0000000000..5b55014ef9 --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-23-umls_clinical_findings_resolver_pipeline_en.md @@ -0,0 +1,109 @@ +--- +layout: model +title: Clinical Findings to UMLS Code Pipeline +author: John Snow Labs +name: umls_clinical_findings_resolver_pipeline +date: 2024-12-23 +tags: [licensed, en, resolver, clinical, umls, pipeline] +task: [Pipeline Healthcare, Chunk Mapping] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +This pretrained pipeline maps entities (Clinical Findings) with their corresponding UMLS CUI codes. You’ll just feed your text and it will return the corresponding UMLS codes. + +## Predicted Entities + +`PROBLEM` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_clinical_findings_resolver_pipeline_en_5.5.1_3.0_1734985321381.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_clinical_findings_resolver_pipeline_en_5.5.1_3.0_1734985321381.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +resolver_pipeline = PretrainedPipeline("umls_clinical_findings_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""HTG-induced pancreatitis associated with an acute hepatitis, and obesity""") + +``` + +{:.jsl-block} +```python + +resolver_pipeline = nlp.PretrainedPipeline("umls_clinical_findings_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""HTG-induced pancreatitis associated with an acute hepatitis, and obesity""") + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val resolver_pipeline = PretrainedPipeline("umls_clinical_findings_resolver_pipeline", "en", "clinical/models") + +val result = resolver_pipeline.annotate("""HTG-induced pancreatitis associated with an acute hepatitis, and obesity""") + +``` +
+ +## Results + +```bash + ++------------------------+---------+---------+ +|chunk |ner_label|umls_code| ++------------------------+---------+---------+ +|HTG-induced pancreatitis|PROBLEM |C3808945 | +|an acute hepatitis |PROBLEM |C4750596 | +|obesity |PROBLEM |C4759928 | ++------------------------+---------+---------+ + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|umls_clinical_findings_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|4.4 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetector +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverter +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger diff --git a/docs/_posts/akrztrk/2024-12-23-umls_drug_substance_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-12-23-umls_drug_substance_resolver_pipeline_en.md new file mode 100644 index 0000000000..69a318ca8b --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-23-umls_drug_substance_resolver_pipeline_en.md @@ -0,0 +1,110 @@ +--- +layout: model +title: Drug Substance to UMLS Code Pipeline +author: John Snow Labs +name: umls_drug_substance_resolver_pipeline +date: 2024-12-23 +tags: [licensed, en, resolver, clinical, umls, drug, subtance, pipeline] +task: [Pipeline Healthcare, Chunk Mapping] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +This pretrained pipeline maps entities (Drug Substances) with their corresponding UMLS CUI codes. You’ll just feed your text and it will return the corresponding UMLS codes. + +## Predicted Entities + +`DRUG` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_drug_substance_resolver_pipeline_en_5.5.1_3.0_1734963236674.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_drug_substance_resolver_pipeline_en_5.5.1_3.0_1734963236674.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +resolver_pipeline = PretrainedPipeline("umls_drug_substance_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""The patient was given metformin, lenvatinib and Magnesium hydroxide 100mg/1ml""") + +``` + +{:.jsl-block} +```python + +resolver_pipeline = nlp.PretrainedPipeline("umls_drug_substance_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""The patient was given metformin, lenvatinib and Magnesium hydroxide 100mg/1ml""") + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val resolver_pipeline = PretrainedPipeline("umls_drug_substance_resolver_pipeline", "en", "clinical/models") + +val result = resolver_pipeline.annotate("""The patient was given metformin, lenvatinib and Magnesium hydroxide 100mg/1ml""") + +``` +
+ +## Results + +```bash + ++-----------------------------+---------+---------+ +|chunk |ner_label|umls_code| ++-----------------------------+---------+---------+ +|metformin |DRUG |C0025598 | +|lenvatinib |DRUG |C2986924 | +|Magnesium hydroxide 100mg/1ml|DRUG |C1134402 | ++-----------------------------+---------+---------+ + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|umls_drug_substance_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|5.1 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetector +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverter +- ChunkMapperModel +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger diff --git a/docs/_posts/akrztrk/2024-12-24-umls_disease_syndrome_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-12-24-umls_disease_syndrome_resolver_pipeline_en.md new file mode 100644 index 0000000000..176bd758a5 --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-24-umls_disease_syndrome_resolver_pipeline_en.md @@ -0,0 +1,113 @@ +--- +layout: model +title: Diseases and Syndromes to UMLS Code Pipeline +author: John Snow Labs +name: umls_disease_syndrome_resolver_pipeline +date: 2024-12-24 +tags: [licensed, en, resolver, clinical, umls, pipeline] +task: [Pipeline Healthcare, Chunk Mapping] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +This pretrained pipeline maps entities (Diseases and Syndromes) with their corresponding UMLS CUI codes. You’ll just feed your text and it will return the corresponding UMLS codes. + +## Predicted Entities + +`PROBLEM` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_disease_syndrome_resolver_pipeline_en_5.5.1_3.0_1735043968113.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_disease_syndrome_resolver_pipeline_en_5.5.1_3.0_1735043968113.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +resolver_pipeline = PretrainedPipeline("umls_disease_syndrome_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""A 34-year-old female with a history of poor appetite, gestational diabetes mellitus, acyclovir allergy and polyuria.""") + +``` + +{:.jsl-block} +```python + +resolver_pipeline = nlp.PretrainedPipeline("umls_disease_syndrome_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""A 34-year-old female with a history of poor appetite, gestational diabetes mellitus, acyclovir allergy and polyuria.""") + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val resolver_pipeline = PretrainedPipeline("umls_disease_syndrome_resolver_pipeline", "en", "clinical/models") + +val result = resolver_pipeline.annotate("""A 34-year-old female with a history of poor appetite, gestational diabetes mellitus, acyclovir allergy and polyuria.""") + +``` +
+ +## Results + +```bash + ++-----------------------------+---------+---------+ +|chunk |ner_label|umls_code| ++-----------------------------+---------+---------+ +|poor appetite |PROBLEM |C0003123 | +|gestational diabetes mellitus|PROBLEM |C0085207 | +|acyclovir allergy |PROBLEM |C0571297 | +|polyuria |PROBLEM |C0011848 | ++-----------------------------+---------+---------+ + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|umls_disease_syndrome_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|3.4 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetector +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverter +- MedicalNerModel +- NerConverter +- ChunkMergeModel +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger diff --git a/docs/_posts/akrztrk/2024-12-24-umls_drug_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-12-24-umls_drug_resolver_pipeline_en.md new file mode 100644 index 0000000000..1f737a6b9a --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-24-umls_drug_resolver_pipeline_en.md @@ -0,0 +1,108 @@ +--- +layout: model +title: Clinical Drugs to UMLS Code Mapping +author: John Snow Labs +name: umls_drug_resolver_pipeline +date: 2024-12-24 +tags: [licensed, en, resolver, clinical, umls, pipeline] +task: [Pipeline Healthcare, Chunk Mapping] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +This pretrained pipeline maps entities (Clinical Drugs) with their corresponding UMLS CUI codes. You’ll just feed your text and it will return the corresponding UMLS codes. + +## Predicted Entities + +`DRUG` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_drug_resolver_pipeline_en_5.5.1_3.0_1735036946079.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_drug_resolver_pipeline_en_5.5.1_3.0_1735036946079.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +resolver_pipeline = PretrainedPipeline("umls_drug_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""The patient was given Adapin 10 MG, coumadn 5 mg.""") + +``` + +{:.jsl-block} +```python + +resolver_pipeline = nlp.PretrainedPipeline("umls_drug_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""The patient was given Adapin 10 MG, coumadn 5 mg.""") + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val resolver_pipeline = PretrainedPipeline("umls_drug_resolver_pipeline", "en", "clinical/models") + +val result = resolver_pipeline.annotate("""The patient was given Adapin 10 MG, coumadn 5 mg.""") + +``` +
+ +## Results + +```bash + ++------------+---------+---------+ +|chunk |ner_label|umls_code| ++------------+---------+---------+ +|Adapin 10 MG|DRUG |C1382178 | +|coumadn 5 mg|DRUG |C1368171 | ++------------+---------+---------+ + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|umls_drug_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|4.0 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetector +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverter +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger diff --git a/docs/_posts/akrztrk/2024-12-24-umls_major_concepts_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-12-24-umls_major_concepts_resolver_pipeline_en.md new file mode 100644 index 0000000000..65e0e6f6b4 --- /dev/null +++ b/docs/_posts/akrztrk/2024-12-24-umls_major_concepts_resolver_pipeline_en.md @@ -0,0 +1,110 @@ +--- +layout: model +title: Clinical Major Concepts to UMLS Code Pipeline +author: John Snow Labs +name: umls_major_concepts_resolver_pipeline +date: 2024-12-24 +tags: [licensed, en, resolver, clinical, umls, pipeline] +task: [Pipeline Healthcare, Chunk Mapping] +language: en +edition: Healthcare NLP 5.5.1 +spark_version: 3.0 +supported: true +annotator: PipelineModel +article_header: + type: cover +use_language_switcher: "Python-Scala-Java" +--- + +## Description + +This pretrained pipeline maps entities (Clinical Major Concepts) with their corresponding UMLS CUI codes. You’ll just feed your text and it will return the corresponding UMLS codes. + +## Predicted Entities + +`Qualitative_Concept`, `Mental_Process`, `Health_Care_Activity`, `Professional_or_Occupational_Group`, `Population_Group`, `Group`, `Pharmacologic_Substance`, `Research_Activity`, `Medical_Device`, `Diagnostic_Procedure`, `Molecular_Function`, `Spatial_Concept`, `Organic_Chemical`, `Amino_Acid`, `Peptide_or_Protein`, `Disease_or_Syndrome`, `Daily_or_Recreational_Activity`, `Quantitative_Concept`, `Biologic_Function`, `Organism_Attribute`, `Clinical_Attribute`, `Pathologic_Function`, `Eukaryote`, `Body_Part`, `Organ_or_Organ_Component`, `Anatomical_Structure`, `Cell_Component`, `Geographic_Area`, `Manufactured_Object`, `Tissue`, `Plant`, `Nucleic_Acid`, `Nucleoside_or_Nucleotide`, `Indicator`, `Reagent_or_Diagnostic_Aid`, `Prokaryote`, `Chemical`, `Therapeutic_or_Preventive_Procedure`, `Gene_or_Genome`, `Mammal`, `Laboratory_Procedure`, `Substance`, `Molecular_Biology_Research_Technique`, `Neoplastic_Process`, `Cell`, `Food`, `Genetic_Function`, `Mental_or_Behavioral_Dysfunction`, `Body_Substance`, `Sign_or_Symptom`, `Injury_or_Poisoning`, `Body_Location_or_Region`, `Organization`, `Body_System`, `Fungus`, `Virus`, `Nucleotide_Sequence`, `Biomedical_or_Dental_Material` + +{:.btn-box} + + +[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_major_concepts_resolver_pipeline_en_5.5.1_3.0_1735048229500.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden} +[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_major_concepts_resolver_pipeline_en_5.5.1_3.0_1735048229500.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} + +## How to use + + + +
+{% include programmingLanguageSelectScalaPythonNLU.html %} + +```python + +from sparknlp.pretrained import PretrainedPipeline + +resolver_pipeline = PretrainedPipeline("umls_major_concepts_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""The patient complains of pustules after falling from stairs. She has been advised Arthroscopy by her primary care pyhsician""") + +``` + +{:.jsl-block} +```python + +resolver_pipeline = nlp.PretrainedPipeline("umls_major_concepts_resolver_pipeline", "en", "clinical/models") + +result = resolver_pipeline.annotate("""The patient complains of pustules after falling from stairs. She has been advised Arthroscopy by her primary care pyhsician""") + +``` +```scala + +import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline + +val resolver_pipeline = PretrainedPipeline("umls_major_concepts_resolver_pipeline", "en", "clinical/models") + +val result = resolver_pipeline.annotate("""The patient complains of pustules after falling from stairs. She has been advised Arthroscopy by her primary care pyhsician""") + +``` +
+ +## Results + +```bash + ++----------------------+-----------------------------------+---------+ +|chunk |ner_label |umls_code| ++----------------------+-----------------------------------+---------+ +|pustules |Sign_or_Symptom |C0241157 | +|stairs |Daily_or_Recreational_Activity |C4300351 | +|Arthroscopy |Therapeutic_or_Preventive_Procedure|C0179144 | +|primary care pyhsician|Health_Care_Activity |C3266804 | ++----------------------+-----------------------------------+---------+ + +``` + +{:.model-param} +## Model Information + +{:.table-model} +|---|---| +|Model Name:|umls_major_concepts_resolver_pipeline| +|Type:|pipeline| +|Compatibility:|Healthcare NLP 5.5.1+| +|License:|Licensed| +|Edition:|Official| +|Language:|en| +|Size:|6.4 GB| + +## Included Models + +- DocumentAssembler +- SentenceDetector +- TokenizerModel +- WordEmbeddingsModel +- MedicalNerModel +- NerConverter +- ChunkMapperModel +- ChunkMapperFilterer +- Chunk2Doc +- BertSentenceEmbeddings +- SentenceEntityResolverModel +- ResolverMerger