N3C Training

While getting involved in N3C is easy, there’s a lot to know. Where do the data come from? What kind of data are available, and what do the tools to work with it look like?

We offer two orientation sessions on a monthly basis: Session A covering N3C data and organization, and Session B providing a tour of the N3C Enclave and analysis tools. Future live runs can be found on the N3C calendar, and see below for recordings of previous sessions and other helpful resources.

Orientation Session A, 4/13/21
Reviews N3C’s data partnership model, OMOP data format, access requirements and regulations, and community resources.

Orientation Session B, 4/4/21
Reviews the N3C Data Enclave, tools and techniques for analysis including R, Python, and SQL, medical concept sets, and N3C shared resources.

Projects and Data Use Requests (DUR)
Reviews the Data Use Request process for gaining access to secure N3C data in the Enclave.


Enclave Training Portal

Within the Enclave itself you can find the N3C Training Portal (Enclave access required), with training modules covering topics ranging from the OMOP data model to Apache Spark and Enclave-specific tooling such as the N3C Knowledge Store and Concept Set Browser.

N3C Training Portal List

N3C Training Portal Paths


Community Learning

In addition to community-contributed modules in the training portal, N3C supports interdisciplinary research by connecting and sharing expertise in several ways.

Enclave Users Group

The Enclave Users Group (EUG) is a community-focused forum where members can share practical information on techniques, tips, and methods in the N3C Data Enclave. Each session one or more presenters share a topic, emphasizing live Q&A, discussions, and meeting new people. See the FAQ for details and upcoming topics. Previous meeting recordings and materials are available in the Training Portal.

N3C EUG 5/7/2021
Identifying COVID Positive Patients

With Shawn O’Neil (CU Anschutz) and Saad Ljazouli (Palantir)

N3C EUG 6/11/2021
Cohort Matching with R MatchIt Package
With Sarah Ratcliffe (University of Virginia)

Other EUG Topics:

  • Machine Learning in N3C
  • Understanding Patient Mortality Data
  • Macrovisits: Reconstructing hospital stays from individual OMOP visits
  • Cohort Paper Logic and Templates
  • Guide to Building Person Level Table for Analysis

Shared Resources

The Enclave-hosted Knowledge Store, Concept Set Browser, Data Catalog, and Community Notes application contain hundreds of reusable analysis components and associated documentation, including code templates and derived datasets useful for common analysis steps, externally-sourced public datasets (such as US Census or USDA datasets), and concept sets providing curated sets of medical vocabulary codes for use in cohort definitions.

N3C Knowledge Store

N3C Knowledge Store
Access and secure sharing platform for analysis templates and derived or ingested publicly available datasets.

N3C Concept Set Browser

N3C Concept Set Browser
Browse curated medical code sets, including peer-review validation information.

N3C Data Catalog

Data Catalog
Browse the most commonly accessed data tables as well as notional data for learning.

Community Notes

Community Notes
The N3C Community Notes application provides a place for users to asynchronously share documentation, tips, and links to other resources with the N3C community.

Additional N3C and Partner Resources

N3C General Office Hours

Researchers and those who support them are welcome to stop by our general office hours Tuesdays and Thursdays at 10a PST/1p EST. Whether your question is about a DUR or accessing the enclave, navigating or understanding the data, or even if you’re looking for tips on improving the performance of your code and analyses, stop by for a friendly discussion with N3C experts and other office hour attendees. If we don’t know how to answer your question we’ll point you to the appropriate support resource.

Office Hours Zoom Information

Phenotype & Data Acquisition Office Hours

These office hours are specifically for our N3C data partners, to help with pulling, preparing, and securely uploading data for ingestion and harmonization. Other relevant questions from data partner personnel are welcome as well. These office hours run every other week on Thursdays at 9a PST/12p EST, and the zoom link is accessible from the N3C Calendar.

N3C Calendar

Enclave-Internal Support Desk

Has your analysis pipeline recently stopped working, and you’re not sure why? Have you encountered an issue with a tool or resource inside the enclave? Did you notice something strange in the data itself to report or get more information on? The enclave-internal support ticket system is the best venue for these types of questions, especially if they involve patient information. Submit a ticket from within the enclave via the “Help & Support” menu under “Report an issue”, or jump directly to the issues application below.

Enclave-Internal Support Desk

Enclave-External Support Desk (JIRA)

While the enclave-internal support system is great for issues regarding data quality and support for data analysis, not all issues are best handled inside the enclave (especially if the issue is you can’t log into the enclave!) N3C hosts a JIRA-based support desk for all non-analysis, non-data questions, including questions about DUR status and approvals, DUAs, accessing N3C Slack or Google resources, and more.

Enclave-External (JIRA) Support Desk Information

Observational Health Data Sciences and Informatics (OHDSI)

OHDSI, creators of the OMOP Common Data Model, and the European Health Data & Evidence Network (EHDEN) have partnered to provide on-demand training resources to help researchers learn more about their tools and standards. N3C recommends completing the OMOP CDM and Standardised Vocabularies course before working in the N3C data enclave.

The Book of OHDSI EHDEN Academy

NCATS Life Course Research Visual Toolkit

The Life Course Visual Toolkit serves to increase knowledge about innovative life course research methods by providing content that is widely available and accessible to researchers across multiple disciplines. The toolkit includes six full-length Webinars designed to advance the process recommendations outlined in , Charting the Life Course: Emerging Opportunities to Advance Scientific Approaches Using Life Course Research. These webinars have also been parsed into shorter 5 – 10 minute videos to accommodate the asynchronous learner.

Toolkit Video Series

NIH Information Security and Information Management Training

NIH provides security training that users must complete before accessing the Enclave. The “2020 Information Security” course consists of 5 required modules: Information Security, Counterintelligence & Insider Threat, Privacy, Records Management, and Emergency Preparedness. (Allow 60-90 minutes to complete all 5 modules.)

Training Course Portal

The Palantir Foundry

Palantir offers several training options to registered users within their platform. Users can walk through self-guided training using Palantir Academy, accessible through the "Help & Support" tab. Additional recommendations and tutorials can also be found within the portal under "Documentation". More information can be found after registering and logging in to the portal.

Palantir Blog