
# Dataset Card for JNLPBA

## Table of Contents
- [Dataset Description](#dataset-description)
  - [Dataset Summary](#dataset-summary)
  - [Supported Tasks and Leaderboards](#supported-tasks-and-leaderboards)
  - [Languages](#languages)
- [Dataset Structure](#dataset-structure)
  - [Data Instances](#data-instances)
  - [Data Fields](#data-fields)
  - [Data Splits](#data-splits)
- [Dataset Creation](#dataset-creation)
  - [Curation Rationale](#curation-rationale)
  - [Source Data](#source-data)
  - [Annotations](#annotations)
  - [Personal and Sensitive Information](#personal-and-sensitive-information)
- [Considerations for Using the Data](#considerations-for-using-the-data)
  - [Social Impact of Dataset](#social-impact-of-dataset)
  - [Discussion of Biases](#discussion-of-biases)
  - [Other Known Limitations](#other-known-limitations)
- [Additional Information](#additional-information)
  - [Dataset Curators](#dataset-curators)
  - [Licensing Information](#licensing-information)
  - [Citation Information](#citation-information)
  - [Contributions](#contributions)

## Dataset Description

- **Homepage:** http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004
- **Repository:** [Needs More Information]
- **Paper:** https://www.aclweb.org/anthology/W04-1213.pdf
- **Leaderboard:** https://paperswithcode.com/sota/named-entity-recognition-ner-on-jnlpba?p=biobert-a-pre-trained-biomedical-language
- **Point of Contact:** [Needs More Information]

### Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus.

### Supported Tasks and Leaderboards

NER

### Languages

English

## Dataset Structure

### Data Instances

{
  'id': '1',
  'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'],
  'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0],
}

### Data Fields

- `id`: Sentence identifier.
- `tokens`: Array of tokens composing a sentence.
- `ner_tags`: Array of tags, where `0` indicates no bio-entity mentioned, `1` signals the first token of a bio-entity and `2` the subsequent bio-entity tokens.

### Data Splits

Train samples: 37094
Validation samples: 7714

## Dataset Creation

### Curation Rationale

[Needs More Information]

### Source Data

#### Initial Data Collection and Normalization

[Needs More Information]

#### Who are the source language producers?

[Needs More Information]

### Annotations

#### Annotation process

[Needs More Information]

#### Who are the annotators?

[Needs More Information]

### Personal and Sensitive Information

[Needs More Information]

## Considerations for Using the Data

### Social Impact of Dataset

[Needs More Information]

### Discussion of Biases

[Needs More Information]

### Other Known Limitations

[Needs More Information]

## Additional Information

### Dataset Curators

[Needs More Information]

### Licensing Information

[Needs More Information]

### Citation Information
@inproceedings{collier-kim-2004-introduction,
    title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}",
    author = "Collier, Nigel  and
      Kim, Jin-Dong",
    booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})",
    month = aug # " 28th and 29th",
    year = "2004",
    address = "Geneva, Switzerland",
    publisher = "COLING",
    url = "https://aclanthology.org/W04-1213",
    pages = "73--78",
}
### Contributions

Thanks to [@edugp](https://github.com/edugp) for adding this dataset.
task_categories:token-classification task_ids:named-entity-recognition annotations_creators:expert-generated language_creators:expert-generated multilinguality:monolingual size_categories:10K<n<100K source_datasets:extended|other-genia-v3.02 language:en license:unknown region:us
{"annotations_creators": ["expert-generated"], "language_creators": ["expert-generated"], "language": ["en"], "license": ["unknown"], "multilinguality": ["monolingual"], "size_categories": ["10K<n<100K"], "source_datasets": ["extended|other-genia-v3.02"], "task_categories": ["token-classification"], "task_ids": ["named-entity-recognition"], "pretty_name": "BioNLP / JNLPBA Shared Task 2004", "dataset_info": {"features": [{"name": "id", "dtype": "string"}, {"name": "tokens", "sequence": "string"}, {"name": "ner_tags", "sequence": {"class_label": {"names": {"0": "O", "1": "B-DNA", "2": "I-DNA", "3": "B-RNA", "4": "I-RNA", "5": "B-cell_line", "6": "I-cell_line", "7": "B-cell_type", "8": "I-cell_type", "9": "B-protein", "10": "I-protein"}}}}], "config_name": "jnlpba", "splits": [{"name": "train", "num_bytes": 8775707, "num_examples": 18546}, {"name": "validation", "num_bytes": 1801565, "num_examples": 3856}], "download_size": 3171072, "dataset_size": 10577272}}
TAGS
#task_categories-token-classification #task_ids-named-entity-recognition #annotations_creators-expert-generated #language_creators-expert-generated #multilinguality-monolingual #size_categories-10K<n<100K #source_datasets-extended|other-genia-v3.02 #language-English #license-unknown #region-us 


# Dataset Card for JNLPBA

## Table of Contents
- Dataset Description
  - Dataset Summary
  - Supported Tasks and Leaderboards
  - Languages
- Dataset Structure
  - Data Instances
  - Data Fields
  - Data Splits
- Dataset Creation
  - Curation Rationale
  - Source Data
  - Annotations
  - Personal and Sensitive Information
- Considerations for Using the Data
  - Social Impact of Dataset
  - Discussion of Biases
  - Other Known Limitations
- Additional Information
  - Dataset Curators
  - Licensing Information
  - Citation Information
  - Contributions

## Dataset Description

- Homepage: URL
- Repository: 
- Paper: URL
- Leaderboard: URL
- Point of Contact: 

### Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus.

### Supported Tasks and Leaderboards

NER

### Languages

English

## Dataset Structure

### Data Instances

{
  'id': '1',
  'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'],
  'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0],
}

### Data Fields

- 'id': Sentence identifier.
- 'tokens': Array of tokens composing a sentence.
- 'ner_tags': Array of tags, where '0' indicates no bio-entity mentioned, '1' signals the first token of a bio-entity and '2' the subsequent bio-entity tokens.

### Data Splits

Train samples: 37094
Validation samples: 7714

## Dataset Creation

### Curation Rationale



### Source Data

#### Initial Data Collection and Normalization



#### Who are the source language producers?



### Annotations

#### Annotation process



#### Who are the annotators?



### Personal and Sensitive Information



## Considerations for Using the Data

### Social Impact of Dataset



### Discussion of Biases



### Other Known Limitations



## Additional Information

### Dataset Curators



### Licensing Information




@inproceedings{collier-kim-2004-introduction,
    title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}",
    author = "Collier, Nigel  and
      Kim, Jin-Dong",
    booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})",
    month = aug # " 28th and 29th",
    year = "2004",
    address = "Geneva, Switzerland",
    publisher = "COLING",
    url = "URL
    pages = "73--78",
}
### Contributions

Thanks to @edugp for adding this dataset.
# Dataset Card for JNLPBA ## Table of Contents
- Dataset Description
  - Dataset Summary
  - Supported Tasks and Leaderboards
  - Languages
- Dataset Structure
  - Data Instances
  - Data Fields
  - Data Splits
- Dataset Creation
  - Curation Rationale
  - Source Data
  - Annotations
  - Personal and Sensitive Information
- Considerations for Using the Data
  - Social Impact of Dataset
  - Discussion of Biases
  - Other Known Limitations
- Additional Information
  - Dataset Curators
  - Licensing Information
  - Citation Information
  - Contributions ## Dataset Description

- Homepage: URL
- Repository: 
- Paper: URL
- Leaderboard: URL
- Point of Contact: ### Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus. ### Supported Tasks and Leaderboards

NER ### Languages

English ## Dataset Structure ### Data Instances

{
  'id': '1',
  'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'],
  'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0],
} ### Data Fields

- 'id': Sentence identifier.
- 'tokens': Array of tokens composing a sentence.
- 'ner_tags': Array of tags, where '0' indicates no bio-entity mentioned, '1' signals the first token of a bio-entity and '2' the subsequent bio-entity tokens. ### Data Splits

Train samples: 37094
Validation samples: 7714 ## Dataset Creation ### Curation Rationale ### Source Data #### Initial Data Collection and Normalization #### Who are the source language producers? ### Annotations #### Annotation process #### Who are the annotators? ### Personal and Sensitive Information ## Considerations for Using the Data ### Social Impact of Dataset ### Discussion of Biases ### Other Known Limitations ## Additional Information ### Dataset Curators ### Licensing Information




@inproceedings{collier-kim-2004-introduction,
    title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}",
    author = "Collier, Nigel  and
      Kim, Jin-Dong",
    booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})",
    month = aug # " 28th and 29th",
    year = "2004",
    address = "Geneva, Switzerland",
    publisher = "COLING",
    url = "URL
    pages = "73--78",
} ### Contributions

Thanks to @edugp for adding this dataset.
TAGS
#task_categories-token-classification #task_ids-named-entity-recognition #annotations_creators-expert-generated #language_creators-expert-generated #multilinguality-monolingual #size_categories-10K<n<100K #source_datasets-extended|other-genia-v3.02 #language-English #license-unknown #region-us 
 # Dataset Card for JNLPBA ## Table of Contents
- Dataset Description
  - Dataset Summary
  - Supported Tasks and Leaderboards
  - Languages
- Dataset Structure
  - Data Instances
  - Data Fields
  - Data Splits
- Dataset Creation
  - Curation Rationale
  - Source Data
  - Annotations
  - Personal and Sensitive Information
- Considerations for Using the Data
  - Social Impact of Dataset
  - Discussion of Biases
  - Other Known Limitations
- Additional Information
  - Dataset Curators
  - Licensing Information
  - Citation Information
  - Contributions ## Dataset Description

- Homepage: URL
- Repository: 
- Paper: URL
- Leaderboard: URL
- Point of Contact: ### Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus. ### Supported Tasks and Leaderboards

NER ### Languages

English ## Dataset Structure ### Data Instances

{
  'id': '1',
  'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'],
  'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0],
} ### Data Fields

- 'id': Sentence identifier.
- 'tokens': Array of tokens composing a sentence.
- 'ner_tags': Array of tags, where '0' indicates no bio-entity mentioned, '1' signals the first token of a bio-entity and '2' the subsequent bio-entity tokens. ### Data Splits

Train samples: 37094
Validation samples: 7714 ## Dataset Creation ### Curation Rationale ### Source Data #### Initial Data Collection and Normalization #### Who are the source language producers? ### Annotations #### Annotation process #### Who are the annotators? ### Personal and Sensitive Information ## Considerations for Using the Data ### Social Impact of Dataset ### Discussion of Biases ### Other Known Limitations ## Additional Information ### Dataset Curators ### Licensing Information




@inproceedings{collier-kim-2004-introduction,
    title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}",
    author = "Collier, Nigel  and
      Kim, Jin-Dong",
    booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})",
    month = aug # " 28th and 29th",
    year = "2004",
    address = "Geneva, Switzerland",
    publisher = "COLING",
    url = "URL
    pages = "73--78",
} ### Contributions

Thanks to @edugp for adding this dataset.
passage: TAGS
#task_categories-token-classification #task_ids-named-entity-recognition #annotations_creators-expert-generated #language_creators-expert-generated #multilinguality-monolingual #size_categories-10K<n<100K #source_datasets-extended|other-genia-v3.02 #language-English #license-unknown #region-us 
# Dataset Card for JNLPBA## Table of Contents
- Dataset Description
  - Dataset Summary
  - Supported Tasks and Leaderboards
  - Languages
- Dataset Structure
  - Data Instances
  - Data Fields
  - Data Splits
- Dataset Creation
  - Curation Rationale
  - Source Data
  - Annotations
  - Personal and Sensitive Information
- Considerations for Using the Data
  - Social Impact of Dataset
  - Discussion of Biases
  - Other Known Limitations
- Additional Information
  - Dataset Curators
  - Licensing Information
  - Citation Information
  - Contributions## Dataset Description

- Homepage: URL
- Repository: 
- Paper: URL
- Leaderboard: URL
- Point of Contact:### Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus.### Supported Tasks and Leaderboards

NER### Languages

English## Dataset Structure