Concept Set Tools

Owned by Maryam Abdallah
Nov 21, 2024
4 min read

A concept set is a list of standardized medical terminologies or OMOP medical codes representing clinical concepts (e.g. treatments, disease states, or lab tests), used to define variables and patient cohorts for research, ensuring consistency and clarity across studies.

Enclave Applications:

Users are encouraged to focus on N3C products like the N3C concept set library and the concept set editor.

Phenotype Explorer:

Allows researchers to become familiar with the N3C phenotype by browsing common comorbidities among All N3C Patients as well as the Confirmed and Possible COVID-19 sub-cohorts.

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Concept Set Browser:

A repository where all created concept sets are stored, allowing researchers to browse, explore, and modify them. Researchers can view details like metadata, concept lists, and version history. The overlap feature helps compare sets for alignment with research needs. Users can adopt existing sets for analysis or create new versions as needed.

Concept Set Browser:

A repository where all created concept sets are stored, allowing researchers to browse, explore, and modify them. Researchers can view details like metadata, concept lists, and version history. The overlap feature helps compare sets for alignment with research needs. Users can adopt existing sets for analysis or create new versions as needed.

Browse:

  • N3C Recommended Concept Sets: Approved for broad reuse. Find them by selecting the "N3C Recommended Concept Set" filter in the browser.

  • Provisionally Approved Concept Sets: Community concept sets with documented reviews. Filter for "Provisionally Approved" in the browser.

  • Bundles: Topically related concept sets with distinct uses, requested by Domain Teams and assembled by data liaisons.

  • More Information: Foundry Concept Set Browse Documentation

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→ Concept Set Editor and Builder

Allows researchers to create, modify, and manage concept sets tailored to their project specific needs.

  • Metadata and Saving: Creators must Articulate the purpose, limitations, and provenance of the concept set. Save regularly and use version control for significant updates.

  • Submit the concept set or revised concept set for approval. Once approved, the concept set or its revision will be published to the master concept set dataset 30 minutes after submission.

More information:

→ Using Concept Sets:

  • You can use Concept sets in Contour and the Code Workbook.

  • Reference the concept set and its specific version using its codeset ID in the concept_set_members table during data analysis to ensure consistency and avoid invalidated modifications.

  • If the team modifies the concept set during the analysis, update the referenced codeset ID in the code accordingly.

More Information:

 

 

Non-enclave Tools:

Athena

Search across standardized and non-standardized vocabularies to accumulate a list of IDs for a concept of interest.

  • Filter across domains (e.g. conditions, drugs, procedures).

  • Download excel tables of your desired IDs to create queries of your desired concepts.

 

 

ATLAS

Search and browse medical concepts using standardized terminologies to build comprehensive concept sets, navigate hierarchies, and map non-standard concepts to standard OMOP concepts.

Although ATLAS, a tool used by the OHDSI community, cannot be implemented in the Enclave due to technical reasons, you can still export your ATLAS Concept Sets in JSON format to the N3C Enclave.

More information:

1. Accessing ATLAS

  • Public Access: Visit the publicly available ATLAS instance on the OHDSI website.

  • Local Deployment: Access your institution's ATLAS instance.

2. Creating a Concept Set in ATLAS

  • Login: Ensure you are logged into ATLAS.

  • Navigate to Concept Sets: Click on "Concept Sets" in the main menu.

  • Create New Concept Set: Click “New Concept Set,” search for concepts by name or code, add them, and save with a meaningful name and description.

3. Refining and Exporting Your Concept Set

  • Review and Exclude: Explore hierarchies, exclude irrelevant concepts, and validate using the Concept Set Overlap feature.

  • Export to JSON: Finalize and export your concept set in JSON format by selecting "Export" on your concept set page.

4. Importing Concept Set to N3C Enclave

  • Access N3C Enclave: Log into the N3C Data Enclave.

  • Import JSON: Click “Import Concept Set” in the Concept Set Library and upload the JSON file from ATLAS.

More Information: