Description
This model maps HGNC identifiers to their current approved gene symbol. 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_code_symbol_mapper_2026","en","clinical/models")\
.setInputCols(["ner_chunk"])\
.setOutputCol("mappings")\
.setRels(["symbol"])
pipeline = Pipeline(stages=[document_assembler, chunk_assembler, code_mapper])
data = spark.createDataFrame([[c] for c in ['HGNC:11998', 'HGNC:1100', 'HGNC:3236', 'HGNC:6407', 'HGNC:583', 'HGNC:7989', 'HGNC:9588', 'HGNC:12805']]).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_code_symbol_mapper_2026","en","clinical/models")\
.setInputCols(["ner_chunk"])\
.setOutputCol("mappings")\
.setRels(["symbol"])
pipeline = nlp.Pipeline(stages=[document_assembler, chunk_assembler, code_mapper])
data = spark.createDataFrame([[c] for c in ['HGNC:11998', 'HGNC:1100', 'HGNC:3236', 'HGNC:6407', 'HGNC:583', 'HGNC:7989', 'HGNC:9588', 'HGNC:12805']]).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_code_symbol_mapper_2026", "en", "clinical/models")
.setInputCols(Array("ner_chunk"))
.setOutputCol("mappings")
.setRels(Array("symbol"))
val pipeline = new Pipeline().setStages(Array(documentAssembler, chunkAssembler, codeMapper))
val data = Seq("HGNC:11998", "HGNC:1100", "HGNC:3236", "HGNC:6407", "HGNC:583", "HGNC:7989", "HGNC:9588", "HGNC:12805").toDF("text")
val result = pipeline.fit(data).transform(data)
Results
| HGNC Code | symbol |
|:------------|:---------|
| HGNC:11998 | TP53 |
| HGNC:1100 | BRCA1 |
| HGNC:3236 | EGFR |
| HGNC:6407 | KRAS |
| HGNC:583 | APC |
| HGNC:7989 | NRAS |
| HGNC:9588 | PTEN |
| HGNC:12805 | XDH |
Model Information
| Model Name: | hgnc_code_symbol_mapper_2026 |
| Compatibility: | Healthcare NLP 6.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [ner_chunk] |
| Output Labels: | [mappings] |
| Language: | en |
| Size: | 637.5 KB |