For this event, we have generated a Google Healthcare API FHIR Datastore from Open Access GTEx data. The Resources present focus around the individuals, their samples, the assays, and the resulting Gene TPM files. FHIR services are not generally available for the AnVIL at this time, and this datastore will only be up for a limited time.
There are two primary data resources:
- Google Healthcare API FHIR datastore
- Google Cloud Storage containing the assay results Authentication is linked to your Terra-linked Google account, with details to gain access below.
All data is Open Access, sourced from the GTEx Portal. We are using the GTEx Analysis V8 set.
API Requests can be made against the FHIR Base URL: https://healthcare.googleapis.com/v1/projects/ncpi-fhir-cat-2022/locations/us-central1/datasets/GTEx_Open_Access/fhirStores/gtex_v8/fhir/
The web cloud console interface, which allows some viewing of resources, can be found here: https://console.cloud.google.com/healthcare/fhirviewer/us-central1/GTEx_Open_Access/fhirStores/gtex_v8/browse?authuser=0&project=ncpi-fhir-cat-2022
Note that some project configured commands, eg gcloud healthcare fhir-stores list, won't work unless you specify another project as the Terra workspace project does not have the healthcare API enabled. You can use the ncpi-fhir-cat-2022 project, eg with the --project flag, to perform queries in these cases.
Participants in this Code-a-thon will have access provided to this workspace. The workspace bucket contains the Gene TPM data.
The cloud storage uri is: gs://fc-a2df0708-c407-468e-a93f-00a42640ee56
The web cloud console interface, which allows some browsing, can be found here: https://console.cloud.google.com/storage/browser/fc-a2df0708-c407-468e-a93f-00a42640ee56;tab=objects?authuser=0&prefix=&forceOnObjectsSortingFiltering=false
To receive access to this dataset, please reach out to Robert Carroll leading up to or during the event. Access is controlled via the NCPI-FHIR-CAT-2022 group managed within Terra. This will enable access to both the bucket and the FHIR Service. If you have not used Terra before, you will need to login with an existing Google Account. If you do not have one, you will need to create one.
Once you have received permissions, you can access the data in either of the following ways.
Terra creates pet service accounts for each user that are given permissions to the resources shared with you in Terra or shared with Terra groups or Terra identity proxies. See here for more details.
When using the provided workspace images in Terra, one is able to easily generate a Bearer token for use in API calls:
gcloud auth print-access-token
Note that you can also use gcloud auth list and then specify the service account instead of relying on the default behavior.
You can use a standard OAuth flow to generate a Bearer token that can be sent with your requests.
Per this page, the scope https://www.googleapis.com/auth/cloud-platform is required. Note that this is a broad scope and care should be taken. These tokens will allow access to any Google Cloud resources you have access to, as compared to the service account approach with is limited to what you can access managed by Terra.
Some References: