SNOMED CT Entity Linking Challenge

Link spans of text in clinical notes to concepts in the SNOMED CT clinical terminology. #health

$25,000 in prizes
mar 2024
553 joined

Data access instructions

Real-world patient data is highly sensitive and difficult to share safely. The data for this competition has identifying factors removed, but still details the care of vulnerable and still-living people.

To access the competition data, each participant will need to register with PhysioNet under MIT’s agreement and complete an online training course. Then you will have access to the world’s largest publicly available repository of patient data!

Detailed steps to register for data access are below:

  1. Create an account on the PhysioNet platform by visiting
  2. The online training course is provided by the CITI Program. Go to and create an account there there using the following steps:
    • Click on “Register” in the upper right hand corner
    • On the registration page, click the “Select your organization affiliation” button on the left. When asked to enter your affiliation during this process, type/select “Massachusetts Institute of Technology Affiliates” as your organization affiliation.
    • Agree to the terms of service, the privacy policy, and affirm that you are an affiliate by checking the appropriate checkboxes
    • Enter your information (name, email) in step 2, select your username/password in step 3, and answer questions in step 4
    • On the subsequent “Your CE Credit Status” page, you may respond “NO” to the CE Credit Status prompt
    • On the subsequent “Affiliate with an Institution” page, fill out all required information. You do not need to use an institutional email address
    • Enter “SNOMED Entity Linking Challenge” as your “Department”
    • Enter “Statistician” as your “Role”
    • On the “Select Curriculum” page, answer “Basic IRB Data or Specimens Only Research” to question 1 and fill out any other required fields.
  3. You should now see the “Data or Specimens Only Research” course in your active courses. Complete this course, which contains 9 segments. You need to achieve an overall score of 90% or higher.
  4. Once you have completed the course, click “View/Print” and save a copy of the Completion Report (not the certificate).
  5. Go to and upload the report, then click “Submit Training”.
  6. Go to to submit a credential application
    • For “Researcher Category”, select the “Independent Researcher”
    • For the “Reference”, fill out the following fields
      • Reference Category: Other
      • Reference name: SNOMED CT Entity Linking Challenge
      • Reference email:
      • Reference organization: SNOMED
      • Reference job title or position: Challenge
      • Research topic: I will be using the MIMIC-IV-Note dataset to participate in the SNOMED CT Entity Linking Challenge hosted on the DrivenData platform.
  7. At this point the PhysioNet team will process your credentialing and training applications. The process is normally complete within 24-48 hours.
  8. Once you have received email notifications that each of your “credentialing” and “training” applications have been accepted, there is a final step: complete the Data Usage Agreement (DUA). To do this, log into your PhysioNet account and navigate to the PhysioNet challenge page.
  9. Scroll to the very bottom of the page and you will see a red box reading: “sign the data use agreement for the project”. Click that to agree.

At this point, you should be able to download the training notes and annotations files for this competition. If you encounter any issues, please post to the forum or send an email to