N3C Assist tool now available for N3C Researchers

N3C Assist is a new enclave tool designed to make it easier to get quick information about N3C Governance and Resources. This Large Language Model (LLM) is currently trained on information from enclave resources like the Knowledge Store, Training Modules, and off-platform resources like the Guide to N3C and public N3C FAQs. N3C Assist makes it easy to find the links you need, ask the questions you have, and identify resources you weren’t aware of. In addition to N3C Assist, N3C is working with the community to explore ways to integrate LLMs into research.

Try N3C Assist here!

TermHub (Beta) tool now available for N3C Researchers



TermHub version 0.3.2 (Beta) is an N3C enclave tool for comparing, analyzing, updating, and creating concept sets. It integrates vocabulary hierarchy, multiple concept set comparison, usage counts, and concept set editing in a novel, information-rich user interface.

What can you do with TermHub?

• Choose between similar concept sets to compare for clinical conditions or events
• View the vocabulary hierarchy of a concept set
• Find N3C recommended concept sets
• Author or modify a concept set
• Analyze and explore one or more concept sets
• Engage with clinical experts who do not have access to the enclave

Click Here to Visit TermHub

For a demo on TermHub, check out this video: https://youtu.be/BWDJ0DCPWYc

Medication Concept Set Release

The N3C Data Liaisons and Logic Liaisons have recently designated an additional 50+ commonly used medication concept sets as “N3C Recommended”. They are concept sets often used in research that support the analytics pipeline and have been selected and vetted by subject matter experts. Concept sets are diagnostic or other codes that, for the sake of a research question, are synonymous. So, “Diabetes mellitus” and “Type 2 Diabetes mellitus” are different codes, and different patients have data under these codes, but for a study of diabetes, an analyst would want to pool these data together. The N3C Recommended concept sets were created as an aid for researchers who want to either use or build phenotypes from these existing concept sets to analyze real-world data.

To view the N3C Recommended concept sets, log into the N3C Enclave, navigate to the Concept Set Browser, and check the filter box “N3C Recommended”. The latest version of the listed concept sets should always be used, as earlier versions represent iterations and have not passed the final review. Make sure you review the concept set limitations, intention, and provenance metadata to understand how these concepts were selected and any limitations they may have. 

Concept Set Vocabulary Changes

The purpose of Vocabulary Change Management is to provide concept set authors (and their analyst-subscribers) to see what changes have been made and to address them: Either by ignoring them or by making modifications to the relevant concept sets. Authors received an additional email notification giving them the opportunity to see and address those changes. 

Helpful Links:

Vocabulary Change Exploration Page

How to Browse for Vocabulary Changes

Click Here to Read the Full Announcement

JupyterLab

JupyterLab is now available in the N3C Enclave. Click New > Code Workspaces from your research project workspace to get started. Click here to view more instructions.

More information regarding training sessions will be communicated soon. Please visit office hours or submit a Support Desk Ticket (option 2) if you have any questions or feedback!

Protocol Pad: RWE and RWE Protocol Browser

We are pleased to introduce new tools for documenting real-world evidence (RWE) study methodology - Protocol Pad: RWE and RWE Protocol Browser - to the N3C Enclave. 

Protocol Pad: RWE application allows a researcher to work together with their collaborators to develop protocols for their observational studies. Protocols are visible only to the collaborators within the research project that the protocol pertains to.

The Protocol Overview tool lists objectives, methodology checklist items, linked metadata, variables, and step-by-step instructions on how to reproduce the protocol. This document can be submitted for download request and attached to N3C Publication Intent submissions, and provided as Supplementary Methods text for journal submissions. Finished, public protocols can also be displayed in RWE Protocol Browser, for the N3C Committee to gain extra insight into the N3C components required to reproduce a study and discussion points on protocol steps to bear in mind when performing similar or incremental studies.

The QuickStart guide can be found here, and a video of the workflow to produce protocols is here. Protocol Pad: RWE is easily accessible from the N3C Enclave Homepage.

CMS Medicare Data available in non-OMOP Format

CMS Medicare data in its original Claims format (i.e. not converted to OMOP) linked to N3C EHR data via privacy preserving record linkage (PPRL) is now available in the Data Catalog. To access these Datasets from your Workspace, you can file a Data Use Request and request the ‘CMS’ PPRL External Dataset option.

CMS Medicaid Data available in the OMOP Format

N3C continues to expand the availability of claims data. Medicaid data in OMOP format is now available in the Data Enclave. This data along with the Medicare data added last fall, provides researchers the ability to complete a patient’s medical history. With 16 data partners currently submitting CMS data, the N3C Enclave houses 173k Medicare patients and 38K Medicaid patients in total.

Investigators registered with N3C and whose institutions have signed the NCATS Data Use Agreement will be eligible to submit Data Use Request in the Enclave to access the CMS data (Medicare and Medicaid).

Publication Intent Forms accessible within the Enclave

The N3C Publication Intent Form (formerly known as the Manuscript Concept Form) is designed to inform the N3C Publication Committee, the N3C Leadership, and NCATS of all N3C publications and presentations. All works using N3C community resources must be reviewed by the Publication Committee including manuscripts, posters, conference abstracts, and presentations.

If you have research that is ready for publication, please use the new Publication Intent Form within the Enclave to submit your work.

For a quick tutorial on the form and overall process, check out this video: https://youtu.be/TaC4nmfpGX0

Click Here to Access the Form

Patient De-Duplication Functionality

N3C is announcing the ongoing development of new functionality that has never been done before on a national scale! Patient deduplication and data enrichment in the N3C enclave uses PPRL (Privacy Preserving Record Linkage) to securely allow for duplicate patient data from across the U.S. to be combined without the use of personally identifiable information.

Read the full Announcement Here