Datasets:

dtan
/

PrionNER

pretty_name: PrionNER
license: other
license_name: prionner-mixed-data-license
language:
  - en
task_categories:
  - token-classification
task_ids:
  - named-entity-recognition
tags:
  - biomedical
  - pubmed
  - prion-disease
  - named-entity-recognition
  - brat
  - json
configs:
  - config_name: fine
    default: true
    data_files:
      - split: train
        path: data/fine/json/train/*.json
      - split: test
        path: data/fine/json/test/*.json
  - config_name: coarse
    data_files:
      - split: train
        path: data/coarse/json/train/*.json
      - split: test
        path: data/coarse/json/test/*.json

PrionNER

This repository accompanies the paper "PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature" and provides a data-only Hugging Face release of PrionNER.

PrionNER is a named entity recognition dataset for prion disease biomedical literature. This release contains canonical train/test splits, fine-grained and coarse-grained annotations, and multiple synchronized data views derived from the same document set.

Dataset Summary

Total documents: 317
Train documents: 247
Test documents: 70
Fine-grained schema: 31 defined labels, 30 observed in the released data
Coarse-grained schema: 15 labels
Fine/coarse entity count: 4,655 train and 1,650 test
Discontinuous entities: 97 train and 34 test

The fine-grained schema defines VPSPr, but that label does not appear in the current released splits.

Configurations

This dataset card defines two main configurations for loading with datasets:

fine: fine-grained JSON documents with train and test splits
coarse: coarse-grained JSON documents with train and test splits

Example:

from datasets import load_dataset

fine = load_dataset("daotuanan/PrionNER", "fine")
coarse = load_dataset("daotuanan/PrionNER", "coarse")

The repository also includes auxiliary release files:

data/raw/: original BRAT source pairs
data/raw_text/: text-only files
data/fine/brat/ and data/coarse/brat/: BRAT exports
data/fine/conll/ and data/coarse/conll/: CoNLL exports
metadata/: schema files, BRAT config, and summary metadata

Data Format

Each JSON document includes:

doc_id: document identifier
text: full document text
entities: list of entity annotations

Each entity includes:

id: original BRAT entity ID
label: entity type
start, end: document-level character offsets
text: entity surface form
spans: one or more span objects
is_discontinuous: present when the entity spans multiple non-contiguous segments

Licensing and Rights

This Hugging Face repository uses license: other because it contains mixed-rights data.

The PrionNER annotation layer and project-authored metadata are intended to be released under CC BY 4.0, to the extent the repository maintainers hold the necessary rights in those materials.
The underlying article titles, abstracts, and other source text are included publicly in this repository, but they are not blanket-relicensed by the project.
Please review LICENSE, DATA_LICENSE.md, and THIRD_PARTY_RIGHTS.md before redistributing the source text.

Provenance

Some released text may be derived from PubMed or MEDLINE records. Where PubMed- or MEDLINE-derived material is used, please acknowledge the U.S. National Library of Medicine as the source of the bibliographic data and do not imply endorsement by NLM or the U.S. Government.

Citation

If you use PrionNER, please cite the repository and the associated paper:

"PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature"

@misc{dao2026prionnernamedentityrecognition,
      title={PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature},
      author={An Dao and Nhan Ly and Thao Tran and Yuji Matsumoto and Akiko Aizawa},
      year={2026},
      eprint={2605.28375},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2605.28375},
}