Datasets:

zinzinmit
/

MedNLPCombined

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 ---
 license: apache-2.0
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 ---
 license: apache-2.0
+tags:
+- medical
+- nlp
+- ner
+- relation-extraction
+- chemistry
+- biology
+pretty_name: MedNLPCombined
 ---
+# MedNLPCombined
+## Dataset Description
+**MedNLPCombined** is a collected repository of medical Natural Language Processing (NLP) datasets, primarily focused on **Chemical-Disease Relations (CDR)** and **Toxicogenomics**. This repository is designed to facilitate research in Named Entity Recognition (NER) and Relation Extraction (RE) within the biomedical domain.
+The repository currently includes two major components:
+1. **BioCreative V CDR (BC5CDR) Task Corpus**
+2. **Comparative Toxicogenomics Database (CTD) Derived Data**
+## Repository Structure
+The dataset is organized into the following directories:
+### 1. `bc5cdr/`
+Contains the **BioCreative V CDR** corpus resources.
+- **`data/`**: The core dataset files.
+  - `benchmark/`: Evaluation/test sets.
+  - `training/`: Training and development sets.
+- **`related_documents/`**: Documentation and guidelines for the BC5CDR task.
+  - `BC5CDR.corpus.pdf`
+  - `BC5CDR.overview.pdf`
+  - `bc5_CDR_data_guidelines.pdf`
+### 2. `CTD/`
+Contains data derived from the **Comparative Toxicogenomics Database**.
+- **`CTD.zip`**: A compressed archive likely containing processed abstracts, relationships, and entity annotations derived from CTD.
+  - *Note: You may need to unzip this file to access the raw `.tsv` or `.txt` files.*
+## Dataset Details
+### BioCreative V CDR (BC5CDR)
+The BC5CDR corpus consists of **1,500 PubMed articles** with annotated chemical and disease entities, as well as their chemical-induced disease (CID) relations. It was created for the BioCreative V challenge.
+- **Entities**: Chemicals, Diseases
+- **Relations**: Chemical-Induced Disease (CID)
+### Comparative Toxicogenomics Database (CTD)
+The CTD data provides manually curated information about chemical-gene/protein interactions, chemical-disease and gene-disease relationships. This component of the repository is likely a snapshot or a derived subset focusing on specific interaction types (e.g., chemical-disease-gene networks).
+## Usage
+To use this dataset in your Python project:
+```python
+from datasets import load_dataset
+# Example loading (if configured with a loading script, otherwise access files directly)
+# dataset = load_dataset("username/MedNLPCombined")
+```
+For local usage, clone the repository and unzip the CTD archive:
+```bash
+git clone https://huggingface.co/username/MedNLPCombined
+cd MedNLPCombined/CTD
+unzip CTD.zip
+```
+## Citation
+If you use these datasets, please cite the original authors:
+**BC5CDR:**
+```bibtex
+@article{li2016biocreative,
+  title={BioCreative V CDR task corpus: a resource for chemical disease relation extraction},
+  author={Li, Jiao and Sun, Yueping and Johnson, Robin J and Sciaky, Daniela and Wei, Chih-Hsuan and Leaman, Robert and Davis, Allan Peter and Mattingly, Carolyn J and Lu, Zhiyong},
+  journal={Database},
+  volume={2016},
+  year={2016},
+  publisher={Oxford Academic}
+}
+```
+**CTD:**
+Please refer to the [CTD citation policy](http://ctdbase.org/about/publications/).
+## License
+This repository is licensed under **Apache 2.0**. Please also adhere to the specific license agreements of the original datasets (BC5CDR and CTD) if applicable.

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