File size: 2,504 Bytes
26fe5eb 12d92c9 94df3ea 12d92c9 111f2d4 94df3ea d8de3e5 94df3ea 33ca16d 94df3ea ffce62a 94df3ea 33ca16d 94df3ea 26fe5eb |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 |
---
license: cc0-1.0
language:
- en
tags:
- pubmed
pretty_name: PubMedAbstractSubset
---
# PubMed Abstracts Subset
This dataset contains a probabilistic sample of publicly available PubMed metadata sourced from the [National Library of Medicine (NLM)](https://pubmed.ncbi.nlm.nih.gov/).
If you're looking for the precomputed embedding vectors (MedCPT) used in our work [*Efficient and Reproducible Biomedical Question Answering using Retrieval Augmented Generation*](https://arxiv.org/abs/2505.07917), they are available in a separate dataset: [slinusc/PubMedAbstractsSubsetEmbedded](https://huggingface.co/datasets/slinusc/PubMedAbstractsSubsetEmbedded).
---
## 📄 Description
Each entry in the dataset includes:
- `title`: Title of the publication
- `abstract`: Abstract text
- `PMID`: PubMed identifier
The dataset is split into 24 `.jsonl` files, each containing approximately 100,000 entries, for a total of ~2.39 million samples.
---
## 🔍 How to Access
### ▶️ Option 1: Load using Hugging Face `datasets` (streaming)
```python
from datasets import load_dataset
dataset = load_dataset("slinusc/PubMedAbstractsSubset", streaming=True)
for doc in dataset:
print(doc["title"], doc["abstract"])
break
```
> Streaming is recommended for large-scale processing and avoids loading the entire dataset into memory.
---
### 💾 Option 2: Clone using Git and Git LFS
```bash
git lfs install
git clone https://huggingface.co/datasets/slinusc/PubMedAbstractsSubset
cd PubMedAbstractsSubset
```
> After cloning, run `git lfs pull` if needed to retrieve the full data files.
---
## 📦 Format
Each file is in `.jsonl` (JSON Lines) format, where each line is a valid JSON object:
```json
{
"title": "...",
"abstract": "...",
"PMID": 36464820
}
```
---
## 📚 Source and Licensing
This dataset is derived from public domain PubMed metadata (titles and abstracts), redistributed in accordance with [NLM data usage policies](https://www.nlm.nih.gov/databases/download/data_distrib_main.html).
- Used in:
**Stuhlmann et al. (2025)**, *Efficient and Reproducible Biomedical QA using RAG*, [arXiv:2505.07917](https://arxiv.org/abs/2505.07917)
https://github.com/slinusc/medical_RAG_system
---
## 🏷️ Version
- `v1.0` – Initial release (2.39M entries, 24 JSONL files)
---
## 📬 Contact
Maintained by [@slinusc](https://huggingface.co/slinusc).
For questions or issues, please open a discussion or pull request on the Hugging Face dataset page. |