Description
This pipeline extracts oncological entities from clinical texts and map them to their corresponding ICD-O codes using sbiobert_base_cased_mli Sentence Bert Embeddings.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("icdo_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""TRAF6 is a putative oncogene in a variety of cancers including
bladder cancer and skin cancer . WWP2 appears to regulate the expression of the well characterized
tumor suppressor phosphatase and tensin homolog (PTEN) in endometrial cancer and squamous cell carcinoma.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("icdo_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""TRAF6 is a putative oncogene in a variety of cancers including
bladder cancer and skin cancer . WWP2 appears to regulate the expression of the well characterized
tumor suppressor phosphatase and tensin homolog (PTEN) in endometrial cancer and squamous cell carcinoma.""")
Results
+------------------+-----------------+------------+-----------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
| chunk| label| icdO_code| resolution| all_codes| all_resolutions|
+------------------+-----------------+------------+-----------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
| cancers| Oncological| 8000/3| cancer|8000/3:::8010/3:::8010/9:::800:::8420/3:::8140/3:::8010/3-C76.0:::8...|cancer:::carcinoma:::carcinomatosis:::neoplasms:::ceruminous carcin...|
| bladder cancer| Oncological|8010/3-C67.9| carcinoma, of bladder|8010/3-C67.9:::8010/3-C67.5:::8230/3-C67.9:::8140/3-C67.9:::8441/3-...|carcinoma, of bladder:::carcinoma, of bladder neck:::solid carcinom...|
| skin cancer| Oncological|8010/3-C44.9| carcinoma, of skin|8010/3-C44.9:::8010/9-C44.9:::8070/3-C44.9:::8140/3-C44.9:::8980/3-...|carcinoma, of skin:::carcinomatosis of skin:::squamous cell carcino...|
| tumor| Oncological| 8000/1| tumor|8000/1:::8040/1:::8001/1:::9365/3:::8000/6:::8103/0:::9364/3:::8940...|tumor:::tumorlet:::tumor cells:::askin tumor:::tumor, secondary:::p...|
|endometrial cancer| Oncological| 8380/3| endometrioid carcinoma|8380/3:::8010/3-C54.1:::8380/3-C57.9:::8575/3-C54.1:::8560/3-C54.1:...|endometrioid carcinoma:::carcinoma, of endometrium:::endometrioid a...|
| squamous cell|Histological_Type| 805-808|squamous cell neoplasms|805-808:::8070/3:::C08.1:::C32.2:::9084/0:::C09.1:::8075/3:::C44.0:...|squamous cell neoplasms:::squamous carcinoma:::sublingual gland:::s...|
| carcinoma| Cancer_Dx| 8010/3| carcinoma|8010/3:::8010/9:::8420/3:::8480/3:::8240/3:::8550/3:::8140/3:::8010...|carcinoma:::carcinomatosis:::ceruminous carcinoma:::mucous carcinom...|
+------------------+-----------------+------------+-----------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
Model Information
| Model Name: | icdo_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.3 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel