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Enabling Ontologies on your REDCap Instance

Introduction​

In a text box field in a REDCap project, a special feature can be enabled that provides auto-suggest functionality for real-time searching within biomedical ontologies, such as RxNorm, ICD-9, ICD-10, Snomed CT, LOINC, etc. The ontology serves as a validation by providing an auto-generated choice list. With this validation in place, the data is standardized.

Relevance to UDSv4​

For Form A4 in UDSv4, several medication fields are validated for the RxNorm ontology. With the RxNorm ontology enabled, the data entry person can start typing the medication name and see a list of choices with keyword matches.

Implementation on your REDCap Instance (to be performed by REDCap Administrator)

  1. The first thing you'll need to do is set up an API token for the Bioportal Ontology database. To do that, go to this page and create an account and token: bioportal.bioontology.org/accounts/new/

    Here are some notes, referenced in Control Center about this connection:

    “This service utilizes the BioPortal API web service (see documentation at bioportal.bioontology.org). For this feature to work, the REDCap web server must be able to make outbound HTTP requests to data.bioontology.org. If you do not yet have a BioPortal API token, you can obtain a token here. The service will not function without a valid API token.”

  2. Next, you will set up the connection between REDCap and the Bioportal Ontology. Click on the Modules/Services Configuration link in the System Configuration section of Control Center in REDCap:

    System Configuration navigation bar with a red box around Modules/Services Configuration.

  3. In the Settings for various modules and services section, look for Allow auto-suggest functionality for searching biomedical ontologies for fields on data entry forms and surveys?

    tip

    It may be easier to do ctrl+f and search on the term ontol to find the section on the page.

    That option defaults to disabled. Change to enabled.

  4. Enter the Bioportal token:

    Question for 'Allow auto-suggest functionality for searching biomedical ontologies for fields on data entry forms and surveys?’ with a drop-down. Next to the drop-down is the number ‘1’ and in the drop-down, the ‘Enabled’ option is checked and has a red box around it. Next to BioPortal Token is the number ‘2’ and a red box around the box into which you enter your BioPortal token.

  5. Scroll down and click the save changes button.

    Save changes button with a red button around it.

Best Practice​

You may want to consult with your institution’s IT Compliance team to ensure they approve using an API token to pull data from the BioPortal Ontology database.

Video introduction​

Coming soon

Additional Resources​

Troubleshooting & Caveats​

The Biomedical Ontologies service that fuels the ontology search feature in REDCap is provided by BioPortal using their public API web service. The BioPortal web service is operated and maintained independently of REDCap, and any changes or updates made to the BioPortal service (such as adding new ontologies or updating/deprecating existing ontologies) is performed completely by BioPortal. Neither REDCap nor Vanderbilt (who creates and maintains REDCap), have any say or jurisdiction in this process. If you have a specific question about the BioPortal API web service or about a specific feature or ontology that they maintain, you may contact them directly via email at support@bioontology.org.