This repository provides documentation on the processes for contributing data to the CHoRUS consortium. Content is written in Markdown, which is then converted to HTML with Docusaurus.
Online documentation SOP site.
View the Interactive CHoRUS Workflow Flowchart to navigate the complete data processing pipeline with clickable links to relevant SOPs.
This repository is also used to track the development of SOP documentation through an associated GitHub Project.
The following SOPs are under development on GitHub:
| SOP Title | Lead | Issue Link | Status |
|---|---|---|---|
| Structured EHR data | @jshoughtaling | chorus-ai#2 | ✅ COMPLETE |
| Flowsheet data | @jshoughtaling | chorus-ai#3 | ✅ COMPLETE |
| Waveform data | @briangow | chorus-ai#4 | ✅ COMPLETE |
| Imaging data | @edilbertoamorim | chorus-ai#5 | ✅ COMPLETE |
| Free-Text data | @hol7001 | chorus-ai#7 | ✅ COMPLETE |
| Data update | @tcpan | chorus-ai#9 | ✅ COMPLETE |
| Data quality | @jshoughtaling | chorus-ai#10 | ✅ COMPLETE |
| Central Processing | @rkamaleswaran | chorus-ai#11 | ✅ COMPLETE |
| Privacy | @anotherkaizhang | chorus-ai#12 | ✅ COMPLETE |
| Safe Harboring Approach | @anotherkaizhang | chorus-ai#14 | ✅ COMPLETE |
| Clinical Validation of Mappings | @p-talapova | chorus-ai#17 | ✅ COMPLETE |
| Multimodal Data Linkage | @jshoughtaling | chorus-ai#28 | ✅ COMPLETE |
| Cataloging Unmapped Terms | @p-talapova | chorus-ai#33 | ✅ COMPLETE |
| Concept set creation | @p-talapova | chorus-ai#64 | ✅ COMPLETE |
| Microbiology Methods | @jshoughtaling | chorus-ai#74 | ✅ COMPLETE |
| Waveform Extension | @jshoughtaling | chorus-ai#75 | ✅ COMPLETE |
| Exposure Data | @jshoughtaling | chorus-ai#73 | ✅ COMPLETE |
| 2nd Data Request/re-upload | @clermontg | ✅ COMPLETE | |
| Date Shifting SOP | @clermontg | ✅ COMPLETE | |
| Tier-1 Data Elements | @clermontg | ✅ COMPLETE |
The main way to contribute SOP documentation to this site is by opening a pull request.
Practically, this means you will need to:
- If you do not have a GitHub account, create one and login. If you do have one, login to your GitHub account
- Clone the GitHub repository to your local environment
- If you're not familiar with GitHub, the easiest route is to install GitHub Desktop, login, and clone the repository via url with: https://github.com/chorus-ai/Chorus_SOP.git
- If you are familiar with GitHub, you can clone the repo via the GitHub CLI through
git clone https://github.com/chorus-ai/Chorus_SOP.git
- Create a new branch in the repository, prefixed with the word
review(e.g.review-omop-mapping) - On that branch, add your SOP - using the provided template - into the relevant SOP category subdirectory in the docs directory (see the OMOP Mapping PR as an example)
- Push your new branch from your local directory to origin, and open a Pull Request where you describe any relevant details or context to be reviewed
- Once reviewed and approved by other CHoRUS members, you can merge your branch into the main branch, where it will then be automatically built into the webpage
Alternatively, if you notice minor changes that you'd like to suggest to existing SOPs, you can browse the built site (rather than the GitHub repository) and perform the following steps:
- Navigate to the relevant page of online documentation site, and click
Edit this pagebutton at the bottom. - A GitHub editing page will pop up for you to edit the contents in the
reviewbranch; make your own edition and commit your changes to that branch. - Submit the pull request to merge those changes into the main branch
The following SOPs are still under development outside of GitHub:
| SOP Title | Lead | Status | Provisional Created | Publish Due Date | Notes |
|---|---|---|---|---|---|
| Azure Roles | Pending (Sara helping create) | In Progress | 🔴 Unknown | 1 October 2025 | |
| Common data elements | Eric (need GitHub handle) | In Progress | Yes | 1 October 2025 | |
| Annotations/Chart Review | Joo (need GitHub handle) | In Progress | 🔴 Unknown | 1 October 2025 | |
| Data provenance & institution specific data generation | Standards Team | To do | No | TBD | |
| Amendment to Linkage SOP | Standards Team | In Progress | Yes | TBD |
To add or update the guidelines, you will need to edit the relevant markdown files. The easiest way to do this is to find the relevant file on GitHub, click "edit", and then follow the steps to create a "pull request". You can navigate to the relevant markdown file on GitHub from the website by clicking the Edit this page button at the bottom. Alternatively, if you are familiar with git, you can submit a pull request in the usual way.
Once a pull request is opened it will be reviewed by CHoRUS colleagues. After the pull is request is approved, you may merge it into the repository by clicking "Merge". Merging a pull request will trigger a rebuild of the website.
If you would like to add topics that are not yet represented, please add your request to issues.