Description
This pretrained model maps HPO codes to corresponding UMLS codes. It also returns all the possible UMLS codes in the all_k_resolutions
in the metadata.
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("hpo_code")
mapperModel = ChunkMapperModel.pretrained("hpo_umls_mapper", "en", "clinical/models")\
.setInputCols(["hpo_code"])\
.setOutputCol("mappings")\
.setRels(["umls_code"])
mapper_pipeline = Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["HP:0000010"],["HP:0200039"],["HP:0000951"]]).toDF("text")
result = mapper_pipeline.fit(data).transform(data)
document_assembler = nlp.DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = nlp.Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("hpo_code")
mapperModel = medical.ChunkMapperModel.pretrained("hpo_umls_mapper", "en", "clinical/models")\
.setInputCols(["hpo_code"])\
.setOutputCol("mappings")\
.setRels(["umls_code"])
mapper_pipeline = nlp.Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["HP:0000010"],["HP:0200039"],["HP:0000951"]]).toDF("text")
result = mapper_pipeline.fit(data).transform(data)
val ocument_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val chunk_assembler = new Doc2Chunk()
.setInputCols("document")
.setOutputCol("hpo_code")
val mapperModel = ChunkMapperModel.pretrained("hpo_umls_mapper", "en", "clinical/models")
.setInputCols("hpo_code")
.setOutputCol("mappings")
.setRels(Array("umls_code"))
val mapper_pipeline = new Pipeline().setStages(Array(
document_assembler,
chunk_assembler,
mapperModel
))
val data = Seq("HP:0000010", "HP:0200039", "HP:0000951").toDF("text")
val result = mapper_pipeline.fit(data).transform(data)
Results
+----------+---------+-----------------------------------------+
| hpo_code|umls_code| all_k_resolutions|
+----------+---------+-----------------------------------------+
|HP:0000010| C0262421|C0262421:::C0262655:::C0034186:::C0520575|
|HP:0200039| C0877055| C0877055:::C0152081:::C0241157|
|HP:0000951| C0037268|C0037268:::C0241164:::C0043345:::C0038325|
+----------+---------+-----------------------------------------+
Model Information
Model Name: | hpo_umls_mapper |
Compatibility: | Healthcare NLP 6.0.4+ |
License: | Licensed |
Edition: | Official |
Input Labels: | [ner_chunk] |
Output Labels: | [mappings] |
Language: | en |
Size: | 27.7 KB |