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README.md
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- split: test
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path: data/test-*
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- split: test
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path: data/test-*
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---
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# Dataset Card for BioRel
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## Dataset Description
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- **Repository:** https://drive.google.com/drive/folders/1vw2zIxdSoqT2QALDbRVG6loLsgi2doBG
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- **Paper:** [BioRel: towards large-scale biomedical relation extraction](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03889-5)
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#### Dataset Summary
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<!-- Provide a quick summary of the dataset. -->
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**BioRel Dataset Summary:**
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BioRel is a comprehensive dataset designed for biomedical relation extraction, leveraging the vast amount of electronic biomedical literature available.
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Developed using the Unified Medical Language System (UMLS) as a knowledge base and Medline articles as a corpus, BioRel utilizes Metamap for entity identification and linking, and employs distant supervision for relation labeling.
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The training set comprises 534,406 sentences, the validation set includes 218,669 sentences, and the testing set contains 114,515 sentences.
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This dataset supports both deep learning and statistical machine learning methods, providing a robust resource for training and evaluating biomedical relation extraction models.
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The original dataset is available here: https://drive.google.com/drive/folders/1vw2zIxdSoqT2QALDbRVG6loLsgi2doBG
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We converted the dataset to the OpenNRE format using the following script: https://github.com/GDAMining/gda-extraction/blob/main/convert2opennre/convert_biorel2opennre.py
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### Languages
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The language in the dataset is English.
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## Dataset Structure
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<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
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### Dataset Instances
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An example of 'train' looks as follows:
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```json
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{
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"text": "algal polysaccharide obtained from carrageenin protects 80 to 100 percent of chicken embryos against fatal infections with the lee strain of influenza virus .",
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"relation": "NA",
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"h": {
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"id": "C0032594",
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"name": "polysaccharide",
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"pos": [6, 20]
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},
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"t": {
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"id": "C0007289",
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"name": "carrageenin",
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"pos": [35, 46]
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}
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}
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```
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### Data Fields
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- `text`: the text of this example, a `string` feature.
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- `h`: head entity
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- `id`: identifier of the head entity, a `string` feature.
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- `pos`: character offsets of the head entity, a list of `int32` features.
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- `name`: head entity text, a `string` feature.
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- `t`: tail entity
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- `id`: identifier of the tail entity, a `string` feature.
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- `pos`: character offsets of the tail entity, a list of `int32` features.
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- `name`: tail entity text, a `string` feature.
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- `relation`: a class label.
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## Citation
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<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
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**BibTeX:**
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```
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@article{xing2020biorel,
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title={BioRel: towards large-scale biomedical relation extraction},
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author={Xing, Rui and Luo, Jie and Song, Tengwei},
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journal={BMC bioinformatics},
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volume={21},
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pages={1--13},
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year={2020},
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publisher={Springer}
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}
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```
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**APA:**
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- Xing, R., Luo, J., & Song, T. (2020). BioRel: towards large-scale biomedical relation extraction. BMC bioinformatics, 21, 1-13.
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## Dataset Card Authors
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[@phucdev](https://github.com/phucdev)
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