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2023-04-11-umls_clinical_findings_resolver_pipeline_en (#89)
* Add model 2023-04-11-umls_clinical_findings_resolver_pipeline_en * Add model 2023-04-11-umls_drug_substance_resolver_pipeline_en --------- Co-authored-by: Cabir40 <cabir4006@gmail.com>
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docs/_posts/Cabir40/2023-04-11-umls_clinical_findings_resolver_pipeline_en.md
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--- | ||
layout: model | ||
title: Clinical Findings to UMLS Code Pipeline | ||
author: John Snow Labs | ||
name: umls_clinical_findings_resolver_pipeline | ||
date: 2023-04-11 | ||
tags: [licensed, clinical, en, umls, pipeline] | ||
task: Chunk Mapping | ||
language: en | ||
edition: Healthcare NLP 4.3.2 | ||
spark_version: 3.0 | ||
supported: true | ||
annotator: PipelineModel | ||
article_header: | ||
type: cover | ||
use_language_switcher: "Python-Scala-Java" | ||
--- | ||
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## Description | ||
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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. | ||
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{:.btn-box} | ||
<button class="button button-orange" disabled>Live Demo</button> | ||
<button class="button button-orange" disabled>Open in Colab</button> | ||
[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_clinical_findings_resolver_pipeline_en_4.3.2_3.0_1681216655167.zip){:.button.button-orange} | ||
[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_clinical_findings_resolver_pipeline_en_4.3.2_3.0_1681216655167.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} | ||
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## How to use | ||
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<div class="tabs-box" markdown="1"> | ||
{% include programmingLanguageSelectScalaPythonNLU.html %} | ||
```python | ||
from sparknlp.pretrained import PretrainedPipeline | ||
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pipeline = PretrainedPipeline("umls_clinical_findings_resolver_pipeline", "en", "clinical/models") | ||
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text = 'HTG-induced pancreatitis associated with an acute hepatitis, and obesity' | ||
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result = pipeline.annotate(text) | ||
``` | ||
```scala | ||
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline | ||
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val pipeline = new PretrainedPipeline("umls_clinical_findings_resolver_pipeline", "en", "clinical/models") | ||
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val text = "HTG-induced pancreatitis associated with an acute hepatitis, and obesity" | ||
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val result = pipeline.annotate(text) | ||
``` | ||
</div> | ||
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## Results | ||
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```bash | ||
+------------------------+---------+---------+ | ||
|chunk |ner_label|umls_code| | ||
+------------------------+---------+---------+ | ||
|HTG-induced pancreatitis|PROBLEM |C1963198 | | ||
|an acute hepatitis |PROBLEM |C4750596 | | ||
|obesity |PROBLEM |C1963185 | | ||
+------------------------+---------+---------+ | ||
``` | ||
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{:.model-param} | ||
## Model Information | ||
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{:.table-model} | ||
|---|---| | ||
|Model Name:|umls_clinical_findings_resolver_pipeline| | ||
|Type:|pipeline| | ||
|Compatibility:|Healthcare NLP 4.3.2+| | ||
|License:|Licensed| | ||
|Edition:|Official| | ||
|Language:|en| | ||
|Size:|4.3 GB| | ||
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## Included Models | ||
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- DocumentAssembler | ||
- SentenceDetectorDLModel | ||
- TokenizerModel | ||
- WordEmbeddingsModel | ||
- MedicalNerModel | ||
- NerConverterInternalModel | ||
- ChunkMapperModel | ||
- ChunkMapperModel | ||
- ChunkMapperFilterer | ||
- Chunk2Doc | ||
- BertSentenceEmbeddings | ||
- SentenceEntityResolverModel | ||
- ResolverMerger |
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docs/_posts/Cabir40/2023-04-11-umls_drug_substance_resolver_pipeline_en.md
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--- | ||
layout: model | ||
title: Drug Substance to UMLS Code Pipeline | ||
author: John Snow Labs | ||
name: umls_drug_substance_resolver_pipeline | ||
date: 2023-04-11 | ||
tags: [licensed, clinical, en, umls, pipeline, drug, subtance] | ||
task: Chunk Mapping | ||
language: en | ||
edition: Healthcare NLP 4.3.2 | ||
spark_version: 3.0 | ||
supported: true | ||
annotator: PipelineModel | ||
article_header: | ||
type: cover | ||
use_language_switcher: "Python-Scala-Java" | ||
--- | ||
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## Description | ||
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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. | ||
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{:.btn-box} | ||
<button class="button button-orange" disabled>Live Demo</button> | ||
<button class="button button-orange" disabled>Open in Colab</button> | ||
[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/umls_drug_substance_resolver_pipeline_en_4.3.2_3.0_1681217098344.zip){:.button.button-orange} | ||
[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/umls_drug_substance_resolver_pipeline_en_4.3.2_3.0_1681217098344.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3} | ||
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## How to use | ||
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<div class="tabs-box" markdown="1"> | ||
{% include programmingLanguageSelectScalaPythonNLU.html %} | ||
```python | ||
from sparknlp.pretrained import PretrainedPipeline | ||
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pipeline = PretrainedPipeline("umls_drug_substance_resolver_pipeline", "en", "clinical/models") | ||
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result = pipeline.annotate("The patient was given metformin, lenvatinib and Magnesium hydroxide 100mg/1ml") | ||
``` | ||
```scala | ||
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline | ||
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val pipeline = PretrainedPipeline("umls_drug_substance_resolver_pipeline", "en", "clinical/models") | ||
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val result = pipeline.annotate("The patient was given metformin, lenvatinib and Magnesium hydroxide 100mg/1ml") | ||
``` | ||
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{:.nlu-block} | ||
```python | ||
+-----------------------------+---------+---------+ | ||
|chunk |ner_label|umls_code| | ||
+-----------------------------+---------+---------+ | ||
|metformin |DRUG |C0025598 | | ||
|lenvatinib |DRUG |C2986924 | | ||
|Magnesium hydroxide 100mg/1ml|DRUG |C1134402 | | ||
+-----------------------------+---------+---------+ | ||
``` | ||
</div> | ||
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{:.model-param} | ||
## Model Information | ||
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{:.table-model} | ||
|---|---| | ||
|Model Name:|umls_drug_substance_resolver_pipeline| | ||
|Type:|pipeline| | ||
|Compatibility:|Healthcare NLP 4.3.2+| | ||
|License:|Licensed| | ||
|Edition:|Official| | ||
|Language:|en| | ||
|Size:|5.1 GB| | ||
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## Included Models | ||
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- DocumentAssembler | ||
- SentenceDetector | ||
- TokenizerModel | ||
- WordEmbeddingsModel | ||
- MedicalNerModel | ||
- NerConverter | ||
- ChunkMapperModel | ||
- ChunkMapperModel | ||
- ChunkMapperFilterer | ||
- Chunk2Doc | ||
- BertSentenceEmbeddings | ||
- SentenceEntityResolverModel | ||
- ResolverMerger |