BigQuery is a columnar, distributed relational database management system. BigQuery accesses only the columns specified in the query, making it ideal for data analysis workflows. Read more about BigQuery in Google’s cloud documentation.
First, ensure you have been provisioned access to MIMIC III or IV on BigQuery. See the cloud page for instructions. Once you have been provisioned access to using MIMIC on BigQuery, it’s worthwhile to “pin” the dataset to see it on the BigQuery web tool.
- Go to the BigQuery console: http://console.cloud.google.com/bigquery
- If you haven’t created a BigQuery project previously you will be asked to do so. You will need to enter information to pay for the cost of queries. For more details see: https://cloud.google.com/resource-manager/docs/creating-managing-projects
- On the left sidebar, next to “Resources”, click “+ ADD DATA”, followed by “Pin a project”
- In the pop up window, type
physionet-data, and click “PIN”.
- In the sidebar on the left, you should now see the
physionet-dataproject. Click the arrow to the left of
physionet-datato expand the project.
- You should now see a number of projects (MIMIC-III:
mimic_hosp). You are now ready to query the data! Try a simple query in the main dialogue box, while logged in under your project that pays for queries: /bigquery?project=paying-project-name:
SELECT * FROM `physionet-data.mimic_core.patients` WHERE subject_id < 10000100 ORDER BY subject_id
The query should return some data, and your browser window should be similar to the below:
At this point you are ready to use MIMIC on BigQuery!
A tutorial on using BigQuery to query MIMIC-III is available here.
Note that we have a number of pre-generated “views” of the data. These are available in the
mimic_derived dataset which you are free to query. All code used to generate these views has been made openly available on the MIMIC-IV code repository.
If you are having issues, see the Troubleshooting section.
I get a pop-up about Terms of Service
You will need to agree to all GCP Terms of Service and adhere to their terms in order to use the data on BigQuery.
When I go to BigQuery, it asks me to create a project
Almost all of your interactions with GCP are associated with a project. Importantly, all billing for your usage must be allotted to a single project. In order to use BigQuery you must have an activate project associated with your account. BigQuery offers a $300 free trial for first time users.
Create a project and select it as your activate project. If you’ve done this correctly, then the top bar of the Google console page should stop saying “Select a project”, and instead have your project name. For example, in the below, I have selected the project
alistairewj, which is now the activate project:
I can only see
These datasets are fully public, so the implication is that you have not been granted access to the full versions of the databases. Please (1) double check you have entered your cloud information into your PhysioNet profile, verifying any e-mails as needed, and (2) requested access to the specific cloud project on its respective PhysioNet project page.
I want to ask a question about MIMIC or raise an issue on the MIMIC Code Repository
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