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INCLUDE.md

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INCLUDE Portal Registered Tier Data

Access

To receive access to this dataset, you will need to sign up with INCLUDE and agree to the terms of use. Visit the login page, and click sign up. You will need either a Google Account or an ORCID as your authentication method. Here are instructions to create a Google Account- it can also be used for AnVIL on Terra.

INCLUDE login page with sign up highlighted

Data Resources

Portal

The INCLUDE DCC Portal UI may provide insight into the FHIR Resources.

Data Source

All data in the INCLUDE Portal is currently in a Registered Tier of access. The original data source with RNASeq-derived transcript counts are sourced from the Human Trisome Project.

FHIR Service

API Requests can be made against the FHIR Base URL: https://include-api-fhir-service.includedcc.org/

DRS Service

The file data in across INCLUDE is indexed by one of two DRS services: an INCLUDE specific service and the Kids First DRS server. The data for this project is currently in the Kids First service, which is stored underneath in AWS s3 buckets.

Authentication

Once you have registered, you can access the data using cookie-based authentication.

Within the browser

Your browser will manage the cookie to enable access transparently to you the user. You will need to login one time, then you will be able to make HTTP REST requests via the browser. Once the cookie expires or you log out, you'll need to log in again.

Supplying the cookie for programmatic requests

To access the FHIR services via programmtic requests, eg using curl, you will need to pass along a cookie. Some methods to retrieve this cookie:

  1. Visit the FHIR Service in your browser.
  2. Login, if you have not already.
  3. Using browser-specific tools, view cookies.
  • For Chrome, you can visit this settings URI: chrome://settings/cookies/detail?site=include-api-fhir-service.includedcc.org to view the specific cookies for the INCLUDE FHIR Service.
  • While at the FHIR Service URL, you can also use the Chrome developer tools -> Application -> Storage -> Cookies.
  • For Firefox, they can be found in the Storage Inspector.
  1. Find AWSELBAuthSessionCookie-0, and copy the ENTIRE value.
  2. Configure your tool to use this cookie.
  • The cookie's "key" is AWSELBAuthSessionCookie-0 and the cookie's "value" is what you recorded previously.
  • If your HTTP tool has a cookie specific option, you can add this key-value pair to the cookie list. EG:
  • For curl, you can use curl --cookie "AWSELBAuthSessionCookie-0=<your cookie here>"
  • If your HTTP tool does not have a cookie specific option, you'll need to add it to the headers, a la header = { "Cookie": "AWSELBAuthSessionCookie-0=<the value you copied>" }
  • This is demonstrated in the configuration and test bash scripts.