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Terminology Manager

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Pascal Brandt edited this page Aug 5, 2020 · 3 revisions

The Terminology Manager is a small application exposed as a React component that provides some functionality to prepare value sets for FHIR-native phenotyping. The main idea is to build a FHIR Bundle in the browser that contains CodeSystem and ValueSet resources. This Bundle can then be downloaded or submitted directly to a FHIR server to prepare the server for phenotyping. There are two ways to add to the Bundle, which are described below.

Note that in both cases the Terminology Manager will attempt to search for and add dependent value sets and code systems to the Bundle if a source server is selected.

Searching

If one or more FHIR servers are configured in the Connection Manager (see Architecture wiki page), then they can be searched for ValueSets. This approach is useful if the required value sets are already in a FHIR server (e.g. VSAC).

💡 Configuring VSAC

In order the search the VSAC FHIR server from the Terminology Manager, it must be configured using the CORS Proxy, since it is not correctly configured for cross-origin requests. To do so, click + Add on the FHIR tab, and use the following URL:

https://cors.phema.science:4321/http://cts.nlm.nih.gov/fhir

You will also need to configure Basic Auth using your UMLS username and password. Credentials are only stored in the browser.

Uploading

It is also possible to upload files to be added to the Bundle. Supported files are:

  • FHIR Bundles that contain ValueSet and CodeSystem resources
  • Individual ValueSet and CodeSystem resources
  • exportedConceptSets.zip files exported from the OHDSI Atlas application
  • Individual CSV files contained in the Atlas ZIP file

Saving

Once the Bundle is prepared, it can either be downloaded (to later be manually submitted to a FHIR server) or directly submitted to a target FHIR server if a relevant connection is configured.

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