Description
This model maps current approved gene symbols to their corresponding HGNC identifier. Trained on the HGNC monthly release dated 2026-08-04.
Live Demo Open in Colab Copy S3 URI
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("ner_chunk")
code_mapper = ChunkMapperModel.pretrained("hgnc_symbol_code_mapper_2026","en","clinical/models")\
.setInputCols(["ner_chunk"])\
.setOutputCol("mappings")\
.setRels(["hgnc_id"])
pipeline = Pipeline(stages=[document_assembler, chunk_assembler, code_mapper])
data = spark.createDataFrame([[s] for s in ['TP53', 'BRCA1', 'EGFR', 'KRAS', 'APC', 'NRAS', 'PTEN', 'XDH']]).toDF("text")
result = pipeline.fit(data).transform(data)
document_assembler = nlp.DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
chunk_assembler = nlp.Doc2Chunk()\
.setInputCols(["document"])\
.setOutputCol("ner_chunk")
code_mapper = medical.ChunkMapperModel.pretrained("hgnc_symbol_code_mapper_2026","en","clinical/models")\
.setInputCols(["ner_chunk"])\
.setOutputCol("mappings")\
.setRels(["hgnc_id"])
pipeline = nlp.Pipeline(stages=[document_assembler, chunk_assembler, code_mapper])
data = spark.createDataFrame([[s] for s in ['TP53', 'BRCA1', 'EGFR', 'KRAS', 'APC', 'NRAS', 'PTEN', 'XDH']]).toDF("text")
result = pipeline.fit(data).transform(data)
val documentAssembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val chunkAssembler = new Doc2Chunk()
.setInputCols("document")
.setOutputCol("ner_chunk")
val codeMapper = ChunkMapperModel
.pretrained("hgnc_symbol_code_mapper_2026", "en", "clinical/models")
.setInputCols(Array("ner_chunk"))
.setOutputCol("mappings")
.setRels(Array("hgnc_id"))
val pipeline = new Pipeline().setStages(Array(documentAssembler, chunkAssembler, codeMapper))
val data = Seq("TP53", "BRCA1", "EGFR", "KRAS", "APC", "NRAS", "PTEN", "XDH").toDF("text")
val result = pipeline.fit(data).transform(data)
Results
| symbol | HGNC Code |
|:---------|:------------|
| TP53 | HGNC:11998 |
| BRCA1 | HGNC:1100 |
| EGFR | HGNC:3236 |
| KRAS | HGNC:6407 |
| APC | HGNC:583 |
| NRAS | HGNC:7989 |
| PTEN | HGNC:9588 |
| XDH | HGNC:12805 |
Model Information
| Model Name: | hgnc_symbol_code_mapper_2026 |
| Compatibility: | Healthcare NLP 6.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [ner_chunk] |
| Output Labels: | [mappings] |
| Language: | en |
| Size: | 618.4 KB |