pubmed_filtered

# PubMed

## Description
[PubMed Central](https://pmc.ncbi.nlm.nih.gov/) is an open-access archive of biomedical and life sciences research papers maintained by the U.S. National Institutes of Health’s National Library of Medicine.
We collected papers from PubMed whose metadata indicated that the publishing journal had designated a CC BY, CC BY-SA, or CC0 license.
PubMed stores the text content of each article as a single nXML file, which we convert to markdown using [pandoc](https://pandoc.org/).
Per-document license information is available in the `license` entry of the `metadata` field of each example.
Code for collecting, processing, and preparing this dataset is available in the [common-pile GitHub repo](https://github.com/r-three/common-pile).

## Dataset Statistics
| Documents | UTF-8 GB |
|-------------|-----------|
| 3,829,689 | 147.1 |

## License Issues
While we aim to produce datasets with completely accurate licensing information, license laundering and inaccurate metadata can cause us to erroneously assign the incorrect license to some documents (for further discussion of this limitation, please see [our paper](https://huggingface.co/papers/2506.05209)).
If you believe you have found an instance of incorrect licensing in this dataset, please [start a discussion](https://github.com/r-three/common-pile/discussions/new) on this repository.

## Other Versions
This is the "filtered" version of the PubMed dataset.
If you are looking for the raw version, you can find it [here](https://huggingface.co/datasets/common-pile/pubmed_raw).

## Citation
If you use this dataset, please cite:
```bibtex
@article{kandpal2025common,
title={{The Common Pile v0.1: An 8TB Dataset of Public Domain and Openly Licensed Text}},
author={Nikhil Kandpal and Brian Lester and Colin Raffel and Sebastian Majstorovic and Stella Biderman and Baber Abbasi and Luca Soldaini and Enrico Shippole and A. Feder Cooper and Aviya Skowron and Shayne Longpre and Lintang Sutawika and Alon Albalak and Zhenlin Xu and Guilherme Penedo and Loubna Ben and Elie Bakouch and John David and Honglu Fan and Dashiell Stander and Guangyu Song and Aaron Gokaslan and John Kirchenbauer and Tom Goldstein and Brian R and Bhavya Kailkhura and Tyler Murray},
journal={arXiv preprint},
year={2025}
}
```

# PubMed

## 数据集描述
[PubMed中心（PubMed Central）](https://pmc.ncbi.nlm.nih.gov/) 是由美国国立卫生研究院下属的美国国家医学图书馆维护的开放获取生物医学与生命科学研究论文存档库。
我们从PubMed中采集了元数据显示出版期刊已指定CC BY、CC BY-SA或CC0许可的论文。PubMed将每篇文章的文本内容存储为单个nXML文件，我们使用[pandoc](https://pandoc.org/)将其转换为markdown格式。
每个样本的元数据（metadata）字段中的`license`条目包含了单篇文档的许可信息。
本数据集的采集、处理与制备代码可在[common-pile GitHub仓库](https://github.com/r-three/common-pile)获取。

## 数据集统计信息
| 文档数量 | UTF-8 存储量（GB） |
|---------|-------------------|
| 3,829,689 | 147.1 |

## 许可相关问题
尽管我们致力于生成许可信息完全准确的数据集，但许可洗白与元数据不准确可能导致我们为部分文档错误分配了错误的许可（关于此局限性的进一步讨论，请参阅[我们的论文](https://huggingface.co/papers/2506.05209)）。
如果您认为本数据集存在许可信息错误的情况，请在本仓库发起讨论：[发起讨论](https://github.com/r-three/common-pile/discussions/new)。

## 其他版本
本数据集为PubMed数据集的「过滤版」。若您需要原始版本，可在此处获取：[原始版本数据集](https://huggingface.co/datasets/common-pile/pubmed_raw)。

## 引用格式
若您使用本数据集，请引用如下文献：
bibtex
@article{kandpal2025common,
title={{The Common Pile v0.1: An 8TB Dataset of Public Domain and Openly Licensed Text}},
author={Nikhil Kandpal and Brian Lester and Colin Raffel and Sebastian Majstorovic and Stella Biderman and Baber Abbasi and Luca Soldaini and Enrico Shippole and A. Feder Cooper and Aviya Skowron and Shayne Longpre and Lintang Sutawika and Alon Albalak and Zhenlin Xu and Guilherme Penedo and Loubna Ben and Elie Bakouch and John David and Honglu Fan and Dashiell Stander and Guangyu Song and Aaron Gokaslan and John Kirchenbauer and Tom Goldstein and Brian R and Bhavya Kailkhura and Tyler Murray},
journal={arXiv preprint},
year={2025}
}