JohnSnowLabs
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+---
+layout: model
+title: Mapping Phenotype Entities with Corresponding HPO Codes (Pretrained Pipeline)
+author: John Snow Labs
+name: hpo_mapper_pipeline
+date: 2025-05-02
+tags: [licensed, en, clinical, hpo, pipeline, ner, mapper]
+task: [Named Entity Recognition, Chunk Mapping, Pipeline Healthcare]
+language: en
+edition: Healthcare NLP 6.0.0
+spark_version: 3.2
+supported: true
+annotator: PipelineModel
+article_header:
+  type: cover
+use_language_switcher: "Python-Scala-Java"
+---
+
+## Description
+
+This pipeline is designed to map extracted phenotype entities from clinical or biomedical text to their corresponding Human Phenotype Ontology (HPO) codes. It ensures that observed symptoms, signs, and clinical abnormalities are standardized using HPO terminology.
+
+{:.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/hpo_mapper_pipeline_en_6.0.0_3.2_1746195935268.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden}
+[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/hpo_mapper_pipeline_en_6.0.0_3.2_1746195935268.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3}
+
+## How to use
+
+
+
+<div class="tabs-box" markdown="1">
+{% include programmingLanguageSelectScalaPythonNLU.html %}
+  
+```python
+
+from sparknlp.pretrained import PretrainedPipeline
+
+pipeline = PretrainedPipeline("hpo_mapper_pipeline", "en", "clinical/models")
+
+result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
+HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
+1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.""")
+
+```
+
+{:.jsl-block}
+```python
+
+pipeline = nlp.PretrainedPipeline("hpo_mapper_pipeline", "en", "clinical/models")
+
+
+result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
+HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
+1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.""")
+
+```
+```scala
+
+import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
+
+val pipeline = PretrainedPipeline("hpo_mapper_pipeline", "en", "clinical/models")
+
+val result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
+HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
+1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.""")
+
+```
+</div>
+
+## Results
+
+```bash
+
++------------------+-----+---+-----+----------+
+|             chunk|begin|end|label|  hpo_code|
++------------------+-----+---+-----+----------+
+|             APNEA|    0|  4|  HPO|HP:0002104|
+|             apnea|   16| 20|  HPO|HP:0002104|
+|HYPERBILIRUBINEMIA|   66| 83|  HPO|HP:0002904|
+|hyperbilirubinemia|   91|108|  HPO|HP:0002904|
+|            sepsis|  167|172|  HPO|HP:0100806|
++------------------+-----+---+-----+----------+
+
+```
+
+{:.model-param}
+## Model Information
+
+{:.table-model}
+|---|---|
+|Model Name:|hpo_mapper_pipeline|
+|Type:|pipeline|
+|Compatibility:|Healthcare NLP 6.0.0+|
+|License:|Licensed|
+|Edition:|Official|
+|Language:|en|
+|Size:|4.0 MB|
+
+## Included Models
+
+- DocumentAssembler
+- TokenizerModel
+- StopWordsCleaner
+- TokenAssembler
+- SentenceDetectorDLModel
+- TokenizerModel
+- TextMatcherInternalModel
+- ChunkMapperModel
@@ -0,0 +1,110 @@
+---
+layout: model
+title: Mapping Phenotype Entities with Corresponding HPO Codes (Pretrained Pipeline)
+author: John Snow Labs
+name: hpo_mapper_pipeline
+date: 2025-05-02
+tags: [licensed, en, clinical, hpo, pipeline, ner, mapper]
+task: [Named Entity Recognition, Chunk Mapping, Pipeline Healthcare]
+language: en
+edition: Healthcare NLP 6.0.0
+spark_version: 3.0
+supported: true
+annotator: PipelineModel
+article_header:
+  type: cover
+use_language_switcher: "Python-Scala-Java"
+---
+
+## Description
+
+This pipeline is designed to map extracted phenotype entities from clinical or biomedical text to their corresponding Human Phenotype Ontology (HPO) codes. It ensures that observed symptoms, signs, and clinical abnormalities are standardized using HPO terminology.
+
+{:.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/hpo_mapper_pipeline_en_6.0.0_3.0_1746195778533.zip){:.button.button-orange.button-orange-trans.arr.button-icon.hidden}
+[Copy S3 URI](s3://auxdata.johnsnowlabs.com/clinical/models/hpo_mapper_pipeline_en_6.0.0_3.0_1746195778533.zip){:.button.button-orange.button-orange-trans.button-icon.button-copy-s3}
+
+## How to use
+
+
+
+<div class="tabs-box" markdown="1">
+{% include programmingLanguageSelectScalaPythonNLU.html %}
+  
+```python
+
+from sparknlp.pretrained import PretrainedPipeline
+
+pipeline = PretrainedPipeline("hpo_mapper_pipeline", "en", "clinical/models")
+
+result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
+HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
+1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.""")
+
+```
+
+{:.jsl-block}
+```python
+
+pipeline = nlp.PretrainedPipeline("hpo_mapper_pipeline", "en", "clinical/models")
+
+
+result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
+HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
+1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.""")
+
+```
+```scala
+
+import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
+
+val pipeline = PretrainedPipeline("hpo_mapper_pipeline", "en", "clinical/models")
+
+val result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
+HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
+1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.""")
+
+```
+</div>
+
+## Results
+
+```bash
+
++------------------+-----+---+-----+----------+
+|             chunk|begin|end|label|  hpo_code|
++------------------+-----+---+-----+----------+
+|             APNEA|    0|  4|  HPO|HP:0002104|
+|             apnea|   16| 20|  HPO|HP:0002104|
+|HYPERBILIRUBINEMIA|   66| 83|  HPO|HP:0002904|
+|hyperbilirubinemia|   91|108|  HPO|HP:0002904|
+|            sepsis|  167|172|  HPO|HP:0100806|
++------------------+-----+---+-----+----------+
+
+```
+
+{:.model-param}
+## Model Information
+
+{:.table-model}
+|---|---|
+|Model Name:|hpo_mapper_pipeline|
+|Type:|pipeline|
+|Compatibility:|Healthcare NLP 6.0.0+|
+|License:|Licensed|
+|Edition:|Official|
+|Language:|en|
+|Size:|4.0 MB|
+
+## Included Models
+
+- DocumentAssembler
+- TokenizerModel
+- StopWordsCleaner
+- TokenAssembler
+- SentenceDetectorDLModel
+- TokenizerModel
+- TextMatcherInternalModel
+- ChunkMapperModel