Description
This pretrained pipeline is built on the top of ner_bionlp model.
Predicted Entities
Available as Private API Endpoint
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("ner_bionlp_pipeline", "en", "clinical/models")
text = '''The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family. Here we describe the genomicorganization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene forType II diabetes mellitus in the Pima Indian population. The gene spansapproximately 7.6 kb and contains one noncoding and two coding exons separated byapproximately 2.2 and approximately 2.6 kb introns, respectively. We identified14 single nucleotide polymorphisms (SNPs), including one that predicts aVal366Ala substitution, and an 8 base-pair (bp) insertion/deletion. Ourexpression studies revealed the presence of the transcript in various humantissues including pancreas, and two major insulin-responsive tissues: fat andskeletal muscle. The characterization of the KCNJ9 gene should facilitate furtherstudies on the function of the KCNJ9 protein and allow evaluation of thepotential role of the locus in Type II diabetes.'''
result = pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = new PretrainedPipeline("ner_bionlp_pipeline", "en", "clinical/models")
val text = "The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family. Here we describe the genomicorganization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene forType II diabetes mellitus in the Pima Indian population. The gene spansapproximately 7.6 kb and contains one noncoding and two coding exons separated byapproximately 2.2 and approximately 2.6 kb introns, respectively. We identified14 single nucleotide polymorphisms (SNPs), including one that predicts aVal366Ala substitution, and an 8 base-pair (bp) insertion/deletion. Ourexpression studies revealed the presence of the transcript in various humantissues including pancreas, and two major insulin-responsive tissues: fat andskeletal muscle. The characterization of the KCNJ9 gene should facilitate furtherstudies on the function of the KCNJ9 protein and allow evaluation of thepotential role of the locus in Type II diabetes."
val result = pipeline.fullAnnotate(text)
import nlu
nlu.load("en.med_ner.bionlp.pipeline").predict("""The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family. Here we describe the genomicorganization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene forType II diabetes mellitus in the Pima Indian population. The gene spansapproximately 7.6 kb and contains one noncoding and two coding exons separated byapproximately 2.2 and approximately 2.6 kb introns, respectively. We identified14 single nucleotide polymorphisms (SNPs), including one that predicts aVal366Ala substitution, and an 8 base-pair (bp) insertion/deletion. Ourexpression studies revealed the presence of the transcript in various humantissues including pancreas, and two major insulin-responsive tissues: fat andskeletal muscle. The characterization of the KCNJ9 gene should facilitate furtherstudies on the function of the KCNJ9 protein and allow evaluation of thepotential role of the locus in Type II diabetes.""")
Results
| | ner_chunk | begin | end | ner_label | confidence |
|---:|:-----------------------|--------:|------:|:---------------------|-------------:|
| 0 | human | 4 | 8 | Organism | 0.9996 |
| 1 | Kir 3.3 | 17 | 23 | Gene_or_gene_product | 0.99635 |
| 2 | GIRK3 | 26 | 30 | Gene_or_gene_product | 1 |
| 3 | potassium | 92 | 100 | Simple_chemical | 0.9452 |
| 4 | GIRK | 103 | 106 | Gene_or_gene_product | 0.998 |
| 5 | chromosome 1q21-23 | 188 | 205 | Cellular_component | 0.80115 |
| 6 | pancreas | 697 | 704 | Organ | 0.9994 |
| 7 | tissues | 740 | 746 | Tissue | 0.975 |
| 8 | fat andskeletal muscle | 749 | 770 | Tissue | 0.955433 |
| 9 | KCNJ9 | 801 | 805 | Gene_or_gene_product | 0.9172 |
| 10 | Type II | 940 | 946 | Gene_or_gene_product | 0.98845 |
Model Information
| Model Name: | ner_bionlp_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 4.4.4+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter