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  • John Snow Labs
  • Jun 17, 2023

Pipeline to Extract the Names of Drugs & Chemicals

  • chemdner
  • chemd
  • ner
  • clinical
  • en
  • licensed

Description

This pretrained pipeline is built on the top of ner_chemd_clinical model.

Predicted Entities

Copy S3 URI

How to use

from sparknlp.pretrained import PretrainedPipeline

pipeline = PretrainedPipeline("ner_chemd_clinical_pipeline", "en", "clinical/models")

text = '''Isolation, Structure Elucidation, and Iron-Binding Properties of Lystabactins, Siderophores Isolated from a Marine Pseudoalteromonas sp. The marine bacterium Pseudoalteromonas sp. S2B, isolated from the Gulf of Mexico after the Deepwater Horizon oil spill, was found to produce lystabactins A, B, and C (1-3), three new siderophores. The structures were elucidated through mass spectrometry, amino acid analysis, and NMR. The lystabactins are composed of serine (Ser), asparagine (Asn), two formylated/hydroxylated ornithines (FOHOrn), dihydroxy benzoic acid (Dhb), and a very unusual nonproteinogenic amino acid, 4,8-diamino-3-hydroxyoctanoic acid (LySta). The iron-binding properties of the compounds were investigated through a spectrophotometric competition.'''

result = pipeline.fullAnnotate(text)

import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val pipeline = new PretrainedPipeline("ner_chemd_clinical_pipeline", "en", "clinical/models")

val text = "Isolation, Structure Elucidation, and Iron-Binding Properties of Lystabactins, Siderophores Isolated from a Marine Pseudoalteromonas sp. The marine bacterium Pseudoalteromonas sp. S2B, isolated from the Gulf of Mexico after the Deepwater Horizon oil spill, was found to produce lystabactins A, B, and C (1-3), three new siderophores. The structures were elucidated through mass spectrometry, amino acid analysis, and NMR. The lystabactins are composed of serine (Ser), asparagine (Asn), two formylated/hydroxylated ornithines (FOHOrn), dihydroxy benzoic acid (Dhb), and a very unusual nonproteinogenic amino acid, 4,8-diamino-3-hydroxyoctanoic acid (LySta). The iron-binding properties of the compounds were investigated through a spectrophotometric competition."

val result = pipeline.fullAnnotate(text)

from sparknlp.pretrained import PretrainedPipeline

pipeline = PretrainedPipeline("ner_chemd_clinical_pipeline", "en", "clinical/models")

text = '''Isolation, Structure Elucidation, and Iron-Binding Properties of Lystabactins, Siderophores Isolated from a Marine Pseudoalteromonas sp. The marine bacterium Pseudoalteromonas sp. S2B, isolated from the Gulf of Mexico after the Deepwater Horizon oil spill, was found to produce lystabactins A, B, and C (1-3), three new siderophores. The structures were elucidated through mass spectrometry, amino acid analysis, and NMR. The lystabactins are composed of serine (Ser), asparagine (Asn), two formylated/hydroxylated ornithines (FOHOrn), dihydroxy benzoic acid (Dhb), and a very unusual nonproteinogenic amino acid, 4,8-diamino-3-hydroxyoctanoic acid (LySta). The iron-binding properties of the compounds were investigated through a spectrophotometric competition.'''

result = pipeline.fullAnnotate(text)

Results

|    | ner_chunks                         |   begin |   end | ner_label    |   confidence |
|---:|:-----------------------------------|--------:|------:|:-------------|-------------:|
|  0 | Lystabactins                       |      65 |    76 | FAMILY       |     0.9841   |
|  1 | lystabactins A, B, and C           |     278 |   301 | MULTIPLE     |     0.813429 |
|  2 | amino acid                         |     392 |   401 | FAMILY       |     0.74585  |
|  3 | lystabactins                       |     426 |   437 | FAMILY       |     0.8007   |
|  4 | serine                             |     455 |   460 | TRIVIAL      |     0.9924   |
|  5 | Ser                                |     463 |   465 | FORMULA      |     0.9999   |
|  6 | asparagine                         |     469 |   478 | TRIVIAL      |     0.9795   |
|  7 | Asn                                |     481 |   483 | FORMULA      |     0.9999   |
|  8 | formylated/hydroxylated ornithines |     491 |   524 | FAMILY       |     0.50085  |
|  9 | FOHOrn                             |     527 |   532 | FORMULA      |     0.509    |
| 10 | dihydroxy benzoic acid             |     536 |   557 | SYSTEMATIC   |     0.6346   |
| 11 | amino acid                         |     602 |   611 | FAMILY       |     0.4204   |
| 12 | 4,8-diamino-3-hydroxyoctanoic acid |     614 |   647 | SYSTEMATIC   |     0.9124   |
| 13 | LySta                              |     650 |   654 | ABBREVIATION |     0.9193   |

Model Information

Model Name: ner_chemd_clinical_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
  • NerConverterInternalModel