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---
license: cc-by-nc-sa-4.0
language:
- en
tags:
- information retrieval
- patient similarity
- clinical decision support
size_categories:
- 100K<n<1M
---
# Dataset Card for PMC-Patients
## Dataset Description
- **Homepage:**
- **Repository:**
- **Paper:**
- **Leaderboard:**
- **Point of Contact:**
### 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
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](https://arxiv.org/pdf/2202.13876.pdf) and [leaderboard](https://pmc-patients.github.io/).
### Languages
English (en).
## Dataset Structure
### PMC-Paitents.json
This file contains all information about patients summaries in PMC-Patients, which is a list of dict with keys:
- `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.
### PAR & PPR Datasets
We present data of the two retrieval tasks in exactly the same format as [BEIR](https://github.com/beir-cellar/beir/wiki/Load-your-custom-dataset). we refer the readers to their wiki page for the data format.
The PAR and PPR tasks share queries and query splits. The `_id` field for queries and PPR corpus is `patient_uid` in PMC-Patients, and the `_id` for PAR corpus is the PMID of the article.
### Data Instances
[More Information Needed]
### Data Fields
[More Information Needed]
### Data Splits
[More Information Needed]
## Dataset Creation
If you are interested in the collection of PMC-Patients and reproducing our baselines, please refer to [this reporsitory](https://github.com/zhao-zy15/PMC-Patients).
### Citation Information
If you find PMC-Patients helpful in your research, please cite our work by:
```
@misc{zhao2023pmcpatients,
title={PMC-Patients: A Large-scale Dataset of Patient Summaries and Relations for Benchmarking Retrieval-based Clinical Decision Support Systems},
author={Zhengyun Zhao and Qiao Jin and Fangyuan Chen and Tuorui Peng and Sheng Yu},
year={2023},
eprint={2202.13876},
archivePrefix={arXiv},
primaryClass={cs.CL}
}
```
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