|
--- |
|
license: cc-by-nc-sa-4.0 |
|
language: |
|
- en |
|
tags: |
|
- patient summary |
|
- medical |
|
- biology |
|
size_categories: |
|
- 100K<n<1M |
|
--- |
|
|
|
# Dataset Card for PMC-Patients |
|
|
|
## 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](https://huggingface.co/datasets/zhengyun21/PMC-Patients-ReCDS)** |
|
|
|
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_full.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. |
|
- `similar_patients`: list of string. `patient_uid` of the similar patients. |
|
- `relevant_articles`: list of string. `PMID` of the relevant articles. |
|
|
|
## 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} |
|
} |
|
``` |
