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:original language:en license:unknown region:us
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop.
In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions.
A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721.
Here we present brief descriptions of all the methods used and a statistical analysis of the results.
We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible,
and furthermore that the best result makes use of the lowest scoring submissions.

For more details, see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559986/

The original dataset can be downloaded from: https://biocreative.bioinformatics.udel.edu/resources/corpora/biocreative-ii-corpus/
This dataset has been converted to CoNLL format for NER using the following tool: https://github.com/spyysalo/standoff2conll
@article{smith2008overview,
        title={Overview of BioCreative II gene mention recognition},
        author={Smith, Larry and Tanabe, Lorraine K and nee Ando, Rie Johnson and Kuo, Cheng-Ju and Chung, I-Fang and Hsu, Chun-Nan and Lin, Yu-Shi and Klinger, Roman and Friedrich, Christoph M and Ganchev, Kuzman and others},
        journal={Genome biology},
        volume={9},
        number={S2},
        pages={S2},
        year={2008},
        publisher={Springer}
}
---
annotations_creators:
- expert-generated
language_creators:
- expert-generated
language:
- en
license:
- unknown
multilinguality:
- monolingual
size_categories:
- 10K<n<100K
source_datasets:
- original
task_categories:
- token-classification
task_ids:
- named-entity-recognition
pretty_name: Bc2GmCorpus
dataset_info:
  config_name: bc2gm_corpus
  features:
  - name: id
    dtype: string
  - name: tokens
    sequence: string
  - name: ner_tags
    sequence:
      class_label:
        names:
          '0': O
          '1': B-GENE
          '2': I-GENE
  splits:
  - name: train
    num_bytes: 6095123
    num_examples: 12500
  - name: validation
    num_bytes: 1215919
    num_examples: 2500
  - name: test
    num_bytes: 2454589
    num_examples: 5000
  download_size: 4636753
  dataset_size: 9765631
---

# Dataset Card for bc2gm_corpus

## 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:** [Github](https://github.com/spyysalo/bc2gm-corpus/)
- **Repository:** [Github](https://github.com/spyysalo/bc2gm-corpus/)
- **Paper:** [NCBI](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559986/)
- **Leaderboard:**
- **Point of Contact:**

### Dataset Summary

[More Information Needed]

### Supported Tasks and Leaderboards

[More Information Needed]

### Languages

[More Information Needed]

## Dataset Structure

### Data Instances

[More Information Needed]

### Data Fields

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

### Data Splits

[More Information Needed]

## Dataset Creation

### Curation Rationale

[More Information Needed]

### Source Data

#### Initial Data Collection and Normalization

[More Information Needed]

#### Who are the source language producers?

[More Information Needed]

### Annotations

#### Annotation process

[More Information Needed]

#### Who are the annotators?

[More Information Needed]

### Personal and Sensitive Information

[More Information Needed]

## Considerations for Using the Data

### Social Impact of Dataset

[More Information Needed]

### Discussion of Biases

[More Information Needed]

### Other Known Limitations

[More Information Needed]

## Additional Information

### Dataset Curators

[More Information Needed]

### Licensing Information

[More Information Needed]

### Citation Information

[More Information Needed]

### Contributions

Thanks to [@mahajandiwakar](https://github.com/mahajandiwakar) for adding this dataset.