Description
This pretrained model maps UMLS codes to corresponding HPO codes. It also returns all the possible HPO 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("umls_code")
mapperModel = ChunkMapperModel.pretrained("umls_hpo_mapper", "en", "clinical/models")\
.setInputCols(["umls_code"])\
.setOutputCol("mappings")\
.setRels(["hpo_code"])
mapper_pipeline = Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["C2973529"],["C0000731"],["C0008035"]]).toDF("text")
result = mapper_pipeline.fit(data).transform(data)
document_assembler = nlp.DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = nlp.Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("umls_code")
mapperModel = medical.ChunkMapperModel.pretrained("umls_hpo_mapper", "en", "clinical/models")\
.setInputCols(["umls_code"])\
.setOutputCol("mappings")\
.setRels(["hpo_code"])
mapper_pipeline = nlp.Pipeline(stages=[
document_assembler,
chunk_assembler,
mapperModel
])
data = spark.createDataFrame([["C2973529"],["C0000731"],["C0008035"]]).toDF("text")
result = mapper_pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val chunk_assembler = new Doc2Chunk()
.setInputCols("document")
.setOutputCol("umls_code")
val mapperModel = ChunkMapperModel.pretrained("umls_hpo_mapper", "en", "clinical/models")
.setInputCols("umls_code")
.setOutputCol("mappings")
.setRels(Array("hpo_code"))
val mapper_pipeline = new Pipeline().setStages(Array(
document_assembler,
chunk_assembler,
mapperModel
))
val data = Seq("C2973529", "C0000731", "C0008035").toDF("text")
val result = mapper_pipeline.fit(data).transform(data)
Results
+---------+----------+-----------------+
|umls_code| hpo_code|all_k_resolutions|
+---------+----------+-----------------+
| C2973529|HP:0011944| HP:0011944:::|
| C0000731|HP:0003270| HP:0003270:::|
| C0008035|HP:0006649| HP:0006649:::|
+---------+----------+-----------------+
Model Information
Model Name: | umls_hpo_mapper |
Compatibility: | Healthcare NLP 6.0.4+ |
License: | Licensed |
Edition: | Official |
Input Labels: | [ner_chunk] |
Output Labels: | [mappings] |
Language: | en |
Size: | 35.4 KB |