Description
This pipeline is designed to map extracted phenotype entities from clinical or biomedical text to their corresponding Human Phenotype Ontology (HPO) codes and assign their assertion status. It ensures that observed symptoms, signs, and clinical abnormalities are standardized using HPO terminology.
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("hpo_mapper_pipeline_v2", "en", "clinical/models")
result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.
Mother is A+, GBS unknown, and infant delivered
for decreasing fetal movement and preeclampsia.
Long finger and toes detected.
he has a increased overbite expression.
""")
pipeline = nlp.PretrainedPipeline("hpo_mapper_pipeline_v2", "en", "clinical/models")
result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.
Mother is A+, GBS unknown, and infant delivered
for decreasing fetal movement and preeclampsia.
Long finger and toes detected.
he has a increased overbite expression.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = PretrainedPipeline("hpo_mapper_pipeline_v2", "en", "clinical/models")
val result = pipeline.fullAnnotate("""APNEA: Presumed apnea of prematurity since < 34 wks gestation at birth.
HYPERBILIRUBINEMIA: At risk for hyperbilirubinemia d/t prematurity.
1/25-1/30: Received Amp/Gent while undergoing sepsis evaluation.
Mother is A+, GBS unknown, and infant delivered
for decreasing fetal movement and preeclampsia.
Long finger and toes detected.
he has a increased overbite expression.
""")
Results
+----------+-----------------------+-------------------------+-----+---+--------+
|hpo_code |matched_text |ner_chunk |begin|end|result |
+----------+-----------------------+-------------------------+-----+---+--------+
|HP:0002904|hyperbilirubinemia |hyperbilirubinemia |104 |121|present |
|HP:0002104|Apnea |apnea |16 |20 |possible|
|HP:0034236|apnea prematurity |apnea of prematurity |16 |35 |present |
|HP:0100806|Sepsis |sepsis |186 |191|present |
|HP:0100602|preeclampsia |preeclampsia |287 |298|present |
|HP:0100807|long finger |Long finger |301 |311|present |
|HP:0001558|decrease fetal movement|decreasing fetal movement|257 |281|present |
|HP:0011094|Increased overbite |increased overbite |341 |358|present |
|HP:0011094|overbite |overbite |351 |358|present |
+----------+-----------------------+-------------------------+-----+---+--------+
Model Information
| Model Name: | hpo_mapper_pipeline_v2 |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetector
- TokenizerModel
- InternalDocumentSplitter
- TokenizerModel
- TextMatcherInternalModel
- WordEmbeddingsModel
- ChunkMapperModel
- AssertionDLModel