<commit_before><commit_msg>Add model 2022-03-21-ner_cellular_pipeline_en_3_0<commit_after>---
layout: model
title: Pipeline to Detect Cellular/Molecular Biology Entities
author: <NAME>
name: ner_cellular_pipeline
date: 2022-03-21
tags: [licensed, ner, clinical, en]
task: Named Entity Recognition
language: en
edition: Spark NLP for Healthcare 3.4.1
spark_version: 3.0
supported: true
article_header:
  type: cover
use_language_switcher: "Python-Scala-Java"
---

## Description

This pretrained pipeline is built on the top of [ner_cellular](https://nlp.johnsnowlabs.com/2021/03/31/ner_cellular_en.html) model.

{:.btn-box}
<button class="button button-orange" disabled>Live Demo</button>
<button class="button button-orange" disabled>Open in Colab</button>
[Download](https://s3.amazonaws.com/auxdata.johnsnowlabs.com/clinical/models/ner_cellular_pipeline_en_3.4.1_3.0_1647870149220.zip){:.button.button-orange.button-orange-trans.arr.button-icon}

## How to use



<div class="tabs-box" markdown="1">
{% include programmingLanguageSelectScalaPythonNLU.html %}
```python
pipeline = PretrainedPipeline("ner_cellular_pipeline", "en", "clinical/models")


pipeline.annotate("Detection of various other intracellular signaling proteins is also described. Genetic characterization of transactivation of the human T-cell leukemia virus type 1 promoter: Binding of Tax to Tax-responsive element 1 is mediated by the cyclic AMP-responsive members of the CREB/ATF family of transcription factors. To achieve a better understanding of the mechanism of transactivation by Tax of human T-cell leukemia virus type 1 Tax-responsive element 1 (TRE-1), we developed a genetic approach with Saccharomyces cerevisiae. We constructed a yeast reporter strain containing the lacZ gene under the control of the CYC1 promoter associated with three copies of TRE-1. Expression of either the cyclic AMP response element-binding protein (CREB) or CREB fused to the GAL4 activation domain (GAD) in this strain did not modify the expression of the reporter gene. Tax alone was also inactive.")
```
```scala
val pipeline = new PretrainedPipeline("ner_cellular_pipeline", "en", "clinical/models")


pipeline.annotate("Detection of various other intracellular signaling proteins is also described. Genetic characterization of transactivation of the human T-cell leukemia virus type 1 promoter: Binding of Tax to Tax-responsive element 1 is mediated by the cyclic AMP-responsive members of the CREB/ATF family of transcription factors. To achieve a better understanding of the mechanism of transactivation by Tax of human T-cell leukemia virus type 1 Tax-responsive element 1 (TRE-1), we developed a genetic approach with Saccharomyces cerevisiae. We constructed a yeast reporter strain containing the lacZ gene under the control of the CYC1 promoter associated with three copies of TRE-1. Expression of either the cyclic AMP response element-binding protein (CREB) or CREB fused to the GAL4 activation domain (GAD) in this strain did not modify the expression of the reporter gene. Tax alone was also inactive.")
```
</div>

## Results

```bash
|chunk                                                      |ner      |
+-----------------------------------------------------------+---------+
|intracellular signaling proteins                           |protein  |
|human T-cell leukemia virus type 1 promoter                |DNA      |
|Tax                                                        |protein  |
|Tax-responsive element 1                                   |DNA      |
|cyclic AMP-responsive members                              |protein  |
|CREB/ATF family                                            |protein  |
|transcription factors                                      |protein  |
|Tax                                                        |protein  |
|human T-cell leukemia virus type 1 Tax-responsive element 1|DNA      |
|TRE-1),                                                    |DNA      |
|lacZ gene                                                  |DNA      |
|CYC1 promoter                                              |DNA      |
|TRE-1                                                      |DNA      |
|cyclic AMP response element-binding protein                |protein  |
|CREB                                                       |protein  |
|CREB                                                       |protein  |
|GAL4 activation domain                                     |protein  |
|GAD                                                        |protein  |
|reporter gene                                              |DNA      |
|Tax                                                        |protein  |
+-----------------------------------------------------------+---------+
```

{:.model-param}
## Model Information

{:.table-model}
|---|---|
|Model Name:|ner_cellular_pipeline|
|Type:|pipeline|
|Compatibility:|Spark NLP for Healthcare 3.4.1+|
|License:|Licensed|
|Edition:|Official|
|Language:|en|
|Size:|1.7 GB|

## Included Models

- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter
{'fraction_non_alphanumeric': 0.0996116504854369, 'fraction_numerical': 0.015533980582524271, 'mean_word_length': 2.0443262411347516, 'pattern_counts': {'":': 0, '<': 10, '<?xml version=': 0, '>': 10, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 30, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5396114', 'n_tokens_mistral': 1387, 'n_tokens_neox': 1188, 'n_words': 457}