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chorus-ai / Chorus_SOP

ChoRUS centralized SOP documentation site
https://chorus-ai.github.io/Chorus_SOP/
Apache License 2.0
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Chorus_SOP

ChoRUS centralized SOP documentation site

This repository is trying to organize all SOPs in an elengant manner to help each site contribute to the CHoRUS consortium. The website is built with Docusaurus and all contents are written with Markdown and MDX syntax.

Online documentation SOP site.

SOP Development

This repository is also used to track the development of SOP documentation through an associated GitHub Project.

The following SOPs are under development: SOP Title Lead Issue Link
Structured EHR data @jshoughtaling https://github.com/chorus-ai/Chorus_SOP/issues/2
Flowsheet data @jshoughtaling https://github.com/chorus-ai/Chorus_SOP/issues/3
Waveform data @briangow https://github.com/chorus-ai/Chorus_SOP/issues/4
Imaging data @edilbertoamorim https://github.com/chorus-ai/Chorus_SOP/issues/5
Data Requests @clermontg https://github.com/chorus-ai/Chorus_SOP/issues/6
Free-Text data @hol7001 https://github.com/chorus-ai/Chorus_SOP/issues/7
Data update @tcpan https://github.com/chorus-ai/Chorus_SOP/issues/9
Data quality @jshoughtaling https://github.com/chorus-ai/Chorus_SOP/issues/10
Central Processing @rkamaleswaran https://github.com/chorus-ai/Chorus_SOP/issues/11
Privacy @anotherkaizhang https://github.com/chorus-ai/Chorus_SOP/issues/12
Common data elements @ucabhkw https://github.com/chorus-ai/Chorus_SOP/issues/13
Safe Harboring Approach @anotherkaizhang https://github.com/chorus-ai/Chorus_SOP/issues/14
Clinical Validation of Mappings @p-talapova https://github.com/chorus-ai/Chorus_SOP/issues/17

How to contribute to the SOP documentation

The main way to contribute SOP documentation to this site is by opening a pull request.

Practically, this means you will need to:

  1. If you do not have a GitHub account, create one and login. If you do have one, login to your GitHub account
  2. Clone the GitHub repository to your local environment
  3. Create a new branch in the repository, prefixed with the word review (e.g. review-omop-mapping)
  4. 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)
  5. 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
  6. 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:

  1. Navigate to the relevant page of online documentation site, and click Edit this page button at the bottom.
  2. A GitHub editing page will pop up for you to edit the contents in the review branch; make your own edition and commit your changes to that branch.
  3. Submit the pull request to merge those changes into the main branch

If you would like to add topics that are not yet represented, please add your request to issues.

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