---
language:
- en
tags:
- biomedical
- named-entity-recognition
- ner
- genia
- protein
- dna
- rna
- cell-type
- cell-line
task_categories:
- token-classification
pretty_name: Biomedical Named Entity Recognition (NER) Dataset
license: cc-by-4.0
size_categories:
- 10K<n<100K
---

# Biomedical Named Entity Recognition (NER) Dataset

## Overview

This dataset is a processed subset of the **GENIA corpus**, a widely used biomedical NLP dataset developed for biomedical text mining and Named Entity Recognition (NER).

The dataset contains biomedical sentences annotated with five entity categories:

- **Protein**
- **DNA**
- **RNA**
- **Cell Type**
- **Cell Line**

## Dataset Structure

Each sample contains two fields:

- **`input_text`**: The original biomedical sentence.
- **`target_text`**: A dictionary containing the identified entity mentions as keys and their corresponding entity categories as values.

### Example

```json
{
  "input_text": "In primary T lymphocytes we show that CD28 ligation leads to the rapid intracellular formation of reactive oxygen intermediates ( ROIs ) which are required for CD28 -mediated activation of the NF-kappa B / CD28 -responsive complex and IL-2 expression .",
  "target_text": {
    "primary T lymphocytes": "cell_type",
    "CD28": "protein",
    "NF-kappa B": "protein",
    "CD28 -responsive complex": "protein",
    "IL-2": "protein"
  }
}
```

## Entity Categories

### Protein

References to proteins, receptors, transcription factors, cytokines, and other protein-related entities.

Examples:

```text
IL-2
CD28
NF-kappa B
glucocorticoid receptor
```

### DNA

References to genes, promoter regions, binding sites, and other DNA-related entities.

Examples:

```text
IL-2 gene
kappa B site
CD4 promoter
```

### RNA

References to RNA molecules and transcripts.

Examples:

```text
IL-2R alpha mRNA
TNF mRNA
```

### Cell Type

References to general biological cell types.

Examples:

```text
T cells
monocytes
macrophages
eosinophils
```

### Cell Line

References to specific cultured cell lines.

Examples:

```text
U937
HeLa cells
Jurkat T cells
```

## Dataset Source and Credit

This dataset is derived from the **GENIA corpus**, which was developed for biomedical text mining and semantic annotation research.

Please cite the original GENIA publication when using this dataset:

> Kim, J.-D., Ohta, T., Tateisi, Y., & Tsujii, J. (2003). **GENIA corpus—a semantically annotated corpus for bio-textmining.** *Bioinformatics*, 19(Suppl. 1), i180–i182.

**Original dataset:** GENIA Corpus / GENIA Project

This processed dataset reorganizes the GENIA annotations into a JSON-based format containing `input_text` and `target_text` fields.