| --- |
| 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](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.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](https://github.com/zhao-zy15/PMC-Patients). |
| |
| ### 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} |
| } |
| ``` |
