Cloud

Access MIMIC-IV on the Cloud

We are primarily sharing MIMIC-IV via BigQuery. We highly recommend using BigQuery as updates to MIMIC-IV will be uploaded to BigQuery as they occur. If absolutely necessary, it is possible to download the data from a Google cloud bucket; instructions are provided at the end of the document.

Cloud access

MIMIC is available for use via two cloud platforms: Google Cloud Platform (GCP) and Amazon Web Services (AWS). Access to these services is directly controlled via your PhysioNet account.

In order to use MIMIC on the cloud, you must:

  1. Be an approved user on PhysioNet. Read this page for instructions on gaining access to MIMIC-IV.
  2. Add cloud credentials to your PhysioNet profile
  3. Request access on the MIMIC-IV PhysioNet project page

We will assume you are a credentialed user on PhysioNet and have signed the MIMIC data use agreement.

Adding cloud credentials

Go to your PhysioNet profile page.

Profile page on PhysioNet

Click “Emails”:

Navigate to the e-mails page

For GCP access, ensure that one of your e-mails is a Google account. This can either be a gmail account (as in the picture), or a G Suite account if your organization is a member of G Suite. You can add an e-mail at the bottom of the page:

Navigate to the Cloud page

You will need to verify your e-mail address before continuing (note: e-mail addresses are only used for GCP access, and not for AWS access).

Once you have a verified e-mail address ready, navigate to the “Cloud” page on PhysioNet.

Navigate to the Cloud page

You should see two options on this page: one for GCP, and one for AWS.

Profile cloud credentials

For GCP, click the drop down menu and set your GCP e-mail to the Google account you provided in the earlier step.

For AWS, add your AWS canonical ID. This is not your e-mail. It is a numeric identifier that can be found in your AWS cloud profile. Click here to go to your AWS profile page. Then look for your “Account Id”:

AWS ID

Accessing MIMIC-IV on the cloud

Now that your cloud credentials are available in PhysioNet, you can request access to databases within those cloud systems. Cloud access to PhysioNet projects such as MIMIC-IV and MIMIC-III are managed independently. You must request access to the cloud systems via their project pages (access is provisioned instantly for credentialed users who have signed the DUA).

For MIMIC-IV, go to the MIMIC-IV PhysioNet project page.

Once there, scroll to the bottom to the “Files” section. If the page shows a restricted-access warning, you need to get access to MIMIC-IV. Otherwise, you should see the following:

Methods for accessing MIMIC-IV

The following describes the access options listed above in the order they are listed:

  1. Downloading the data as one large zip file
  • This downloads the data directly from the PhysioNet servers.
  1. Cloud: Adds your GCP e-mail to the access list for GCP BigQuery.
  • This option adds the GCP e-mail in your PhysioNet account to a BigQuery access list; it’s required in order to use the data in BigQuery.
  1. Cloud: Adds your GCP e-mail to the access list for downloading the data from a GCP Storage Bucket.
  • This option adds the GCP e-mail in your PhysioNet account to a GCP access list; it’s required in order to download the data from a storage bucket on GCP.
  1. TBD. AWS is not yet available for MIMIC-IV.
  2. TBD. AWS is not yet available for MIMIC-IV.
  3. Provides a command for downloading the data from PhysioNet as individual CSV files using wget (when compared to the image above, your command will have a distinct username).
  • This downloads the data directly from PhysioNet servers, but in their raw (usually uncompressed) form.

Options #1, #3, #4, and #6 all provide the ability to download the data locally. For users interested in using BigQuery, you can read the getting started with using MIMIC-IV on BigQuery page and subsequently read the querying tutorial on BigQuery.

Once you have access to MIMIC-IV, we highly recommend you read the database introduction.


Last modified August 17, 2020: fix links (2aa57eb)