metadata

license: cc-by-nc-sa-4.0
language:
  - en
tags:
  - patient summary
  - medical
  - biology
size_categories:
  - 100K<n<1M

Dataset Card for PMC-Patients

News

We released PMC-Patients-V2 (in JSON format with the same keys), which is based on 2024 PMC baseline and contains 250,294 patients. The data collection pipeline remains the same except for using more PMC articles.

Dataset Description

Homepage: https://github.com/pmc-patients/pmc-patients
Repository: https://github.com/pmc-patients/pmc-patients
Paper: https://arxiv.org/pdf/2202.13876.pdf
Leaderboard: https://pmc-patients.github.io/
Point of Contact: zhengyun21@mails.tsinghua.edu.cn

Dataset Summary

PMC-Patients is a first-of-its-kind dataset consisting of 167k patient summaries extracted from case reports in PubMed Central (PMC), 3.1M patient-article relevance and 293k patient-patient similarity annotations defined by PubMed citation graph.

Supported Tasks and Leaderboards

This is purely the patient summary dataset with relational annotations. For ReCDS benchmark, refer to this dataset

Based on PMC-Patients, we define two tasks to benchmark Retrieval-based Clinical Decision Support (ReCDS) systems: Patient-to-Article Retrieval (PAR) and Patient-to-Patient Retrieval (PPR). For details, please refer to our paper and leaderboard.

Languages

English (en).

Dataset Structure

PMC-Paitents.csv

This file contains all information about patients summaries in PMC-Patients, with the following columns:

patient_id: string. A continuous id of patients, starting from 0.
patient_uid: string. Unique ID for each patient, with format PMID-x, where PMID is the PubMed Identifier of the source article of the patient and x denotes index of the patient in source article.
PMID: string. PMID for source article.
file_path: string. File path of xml file of source article.
title: string. Source article title.
patient: string. Patient summary.
age: list of tuples. Each entry is in format (value, unit) where value is a float number and unit is in 'year', 'month', 'week', 'day' and 'hour' indicating age unit. For example, [[1.0, 'year'], [2.0, 'month']] indicating the patient is a one-year- and two-month-old infant.
gender: 'M' or 'F'. Male or Female.
relevant_articles: dict. The key is PMID of the relevant articles and the corresponding value is its relevance score (2 or 1 as defined in the ``Methods'' section).
similar_patients: dict. The key is patient_uid of the similar patients and the corresponding value is its similarity score (2 or 1 as defined in the ``Methods'' section).

Dataset Creation

If you are interested in the collection of PMC-Patients and reproducing our baselines, please refer to this reporsitory.

Citation Information

If you find PMC-Patients helpful in your research, please cite our work by:

@article{zhao2023large,
  title={A large-scale dataset of patient summaries for retrieval-based clinical decision support systems},
  author={Zhao, Zhengyun and Jin, Qiao and Chen, Fangyuan and Peng, Tuorui and Yu, Sheng},
  journal={Scientific Data},
  volume={10},
  number={1},
  pages={909},
  year={2023},
  publisher={Nature Publishing Group UK London}
}