Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add benchmark dataset to derived data repository #34

Open
alistairewj opened this issue Jan 16, 2018 · 5 comments
Open

Add benchmark dataset to derived data repository #34

alistairewj opened this issue Jan 16, 2018 · 5 comments
Assignees

Comments

@alistairewj
Copy link
Collaborator

We just launched a repo to host derived data from MIMIC.

A static snapshot of the code is hosted here: https://physionet.org/physiotools/mimic-code/
A static snapshot of the data is hosted on PhysioNetWorks - everyone who has access to MIMIC will have access to the data: https://physionet.org/works/MIMICIIIDerivedDataRepository/

Would be good to make a GitHub release of the code, and upload that zip + the generated data to the PNW repository. Should make it easier for people to use the benchmarks. Also worth it to track this repo with Zenodo so that the releases are automatically assigned a DOI.

@turambar
Copy link
Collaborator

@alistairewj sweet. We're working on our "1.0" release to coincide with a journal submission, so we should be ready to contribute within a few weeks at the latest.

@turambar turambar self-assigned this Jan 16, 2018
@turambar
Copy link
Collaborator

^^^^^ @Hrant-Khachatrian @Harhro94

@turambar
Copy link
Collaborator

We should do this upload! :)

@partizanos
Copy link
Contributor

Related issue: #127

@tompollard
Copy link
Collaborator

tompollard commented May 14, 2022

Since @alistairewj posted the message above, we have entirely rebuilt PhysioNet. It's now fairly straightforward to publish derived datasets with the same permissions as the parent dataset. We'd love to share the benchmark dataset alongside MIMIC.

Instructions for submitting the dataset to PhysioNet are at: https://physionet.org/about/publish/#submission_overview. Essentially the process is:

  1. Go to https://physionet.org/projects/ and click "Create new project"
  2. Follow the instructions to populate the data description, add collaborators, etc.
  3. On the "Access" tab, select the "Credentialed" access policy
  4. On the "Discovery" tab, select "MIMIC" as the parent project.
  5. Click "submit" to submit the dataset to our team for review.

Thanks, and let us know if you need help. It may be tricky to upload a large dataset using the web form. We're working on a new tool for uploads, but for now you can ping us and we can upload on your behalf.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

4 participants