N3C Linkage Honest Broker - Regenstrief Institute

N3C PPRL Dashboard
Data Flow
Onboarding
Tokenization
Manifest
Data Package
Submit Data
Support
Resources & Documents
FAQs & Troubleshooting

Public N3C PPRL Dashboard

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About Privacy Preserving Record Linkage

Thank you for joining National Clinical Cohort Collaborative (N3C) hashing community performing Privacy Preserving Record Linkage (PPRL). PPRL is a secure, HIPAA-deidentified method of connecting records across different data sources that refer to the same individual, using pseudonymization processes to maintain privacy.

Regenstrief is the contracted Linkage Honest Broker (LHB) for N3C. The LHB is a neutral, vendor-agnostic entity external to the data enclave. It serves as a Governance Firewall, acting as an independent custodian to maintain strict separation between identity tokens and clinical data. Personal Identifiable Information (PII) never leaves the provider. The LHB does not receive, store, or process clinical information or PHI/PII. It only utilizes encrypted tokens and metadata consistent with established enclave policies.

The Data Enclave is a secure platform through which the harmonized clinical data provided by our contributing members is stored. The data itself can only be accessed through a secure cloud portal hosted by NCATS and cannot be downloaded or removed.

In addition to sending data to the N3C Data Enclave, sites will prepare an additional set of files that will be submitted directly to the LHB service at Regenstrief Institute. These additional files include hashed identifiers (tokens), which correspond to a unique patient ID, as well as a Manifest file that includes metadata describing site-specific information.

There are three main reasons why privacy preserving record linkage is key to this effort:

De-identified Duplication: PPRL enables the deduplication of patients across institutions, accounting for care fragmentation without compromising privacy.
Multi-Model Data Linkage: PPRL facilitates the de-identified linking to multi-model data, such as image data from various health system PACS systems.
Cohort Discovery: PPRL allows for the discovery of de-identified cohort overlaps with other research studies, such as understanding the extent of overlap between the N3c and other data cohorts such as mortality.

Support / Questions

Submit a Service Desk Ticket at

https://n3c-help.atlassian.net/servicedesk/customer/portal/2

Select N3C Record Linkage

Choose appropriate area for PPRL Category

Participating Entities

Supported by:

The three main parties involved in the data flow:

Data Contributing Sites: healthcare sites participating in N3C by providing a limited data set to the N3C Data Enclave, and a de-identified encrypted token file using Datavant software to the Linkage Honest Broker. For information on preparing your phenotype for the N3C Data Enclave, please visit this link.

N3C Data Enclave: the Data Enclave is a secure platform data contributing sites submit their clinical payload based on the approved phenotype. The Data Enclave’s technology partner is Palantir.

Linkage Honest Broker at Regenstrief Institute: the LHB service performs privacy preserving record linkage on de-identified token file received from the data contributing sites. Files sent to the LHB are not intended to be shared with the Data Enclave. For questions on how to prepare this file, please refer to the site engagement packet sent upon enrollment.

N3C Overview

N3C is a national resource of real-world data that researchers are using to speed medical research.

With stewardship from NCATS, more than 90 institutions worked together to build N3C, which systematically collects electronic health record (EHR) data from different institutions and harmonizes them into a central enclave. The enclave offers spaces for collaborative research. In addition, EHR data within the enclave can connect to other data sets, which creates a more complete picture of patients’ health journeys.

NCATS is leveraging the original N3C infrastructure in new ways to expand into more disease domains and cover real-world data training needs for researchers.

We know that the data in the enclave represents people. As the steward, we take seriously the responsibility of keeping those data safe. Our comprehensive approach addresses the security of the N3C Enclave and protects patient privacy.

For more information visit: https://n3c.ncats.nih.gov/clinical-cohort

High Level Overview of Data Flow

LHB Onboarding Process

NOTE: The Linkage Honest Broker Agreement (LHBA) must be signed prior to onboarding with the LHB.

Onboarding with the LHB can be completed in 3 easy steps:
1) Site Registration – Provision Firewall
2) Individual Registration – Create SFTP Account
3) Setup and Connect to LHB SFTP

Complete the Site Registration Form. In the form, list the site personnel who require access to the LHB SFTP
- Formal site name (full name of your institution)
- Site Abbreviation
- Principal Investigator’s Name
- Public Static IP or CIDR block
- List of names (first and last) and email addresses for users who should have access to the LHB SFTP
- Primary Technical Contact Name and email address for your site
After the firewall has been set up and your IP address whitelisted, an e-mail noting completion will be sent.
Concurrently, once the Site Registration Form is submitted, the users who require an LHB SFTP account will receive an e-mail from RILHB@regenstrief.org with a link to the Individual User Access Form.
To complete the Individual User Access Form, you will need your public SSH key. Instructions to complete this are in the e-mail with the form link. You may also download the instructions in the SSH section below.
Once your account has been set up, an e-mail will be sent with your username and instructions on connecting to the LHB SFTP.

Tokenization

Tokenization is a process that replaces PII with encrypted hashes called tokens. Datavant tokens are unique, irreversible, and site-specific, so that N3C project tokens for a given patient can only ever be used to link within the N3C project. These tokens are created in two steps:

Irreversible hashing: An irreversible cryptographic hash function is applied, ensuring that the patient’s PII used as input cannot be recovered from the output value

Site-specific encryption: The hash value from step 1 is encrypted with another layer of site- and project-specific encryption, protecting every Datavant partner from potential security breaches and making tokens linkable to only other tokens permitted within their project

You will be using the Datavant software to create N3C tokens in your own environment from patient PII, encrypt them for transit, and then submit them to the Linkage Honest Broker. You will receive information and resources on Datavant tokenization upon onboarding, as well as a technical support contact for the duration of your participation.

For more general Datavant software or portal questions, you may contact support@datavant.com.

Manifest

Manifest file contains metadata about submission and should be created for each submission to LHB.
You can script the creation of the files for one project; most fields will be the same across submissions for one project.

LHB Data Package

The data package submitted to the Linkage Honest Broker (LHB) consists of 2 files zipped together:

File 1 – Transit tokens
File 2- Manifest

Data Package:

There are 2 files (Tokens/Manifest) that are zipped into a folder and submitted to the Linkage Honest Broker.

The naming convention includes your site abbreviation (provided during onboarding), project name (N3C) and the date. The date format is YYYYMMDD. Important: File names must be in all capital letters. Otherwise, it will fail the ingestion process.

N3C

Zip File (contains tokens and manifest)

SiteAbbreviation_Date.zip
Example: ABC_N3C_20260901.zip

Token ﬁle:
Abbreviation_N3C_Date_Tokens.csv
Example: ABC_N3C_20260901_Tokens.csv

Manifest ﬁle: Site
Abbreviation_N3C_Date_Manifest.csv
Example: ABC_N3C_20260901_Manifest.csv

Transfer Data Package to the LHB SFTP

Transfer the .zip file to the remote site from your local site
Ensure all files are named according to the file naming conventions.
Refer to the Resources and Documents section or Site Engagement Packet, Part 2 for more detailed instructions

Support

If you have questions and/or issues regarding the Linkage Honest Broker please submit a service desk ticket at https://n3c-help.atlassian.net/servicedesk/customer/portal/2.

Select N3C Record Linkage.
Choose Linkage Honest Broker Questions as the PPRL Question Category.

If you have any questions regarding Datavant software please submit a service desk ticket at https://n3c-help.atlassian.net/servicedesk/customer/portal/2.

Select N3C Record Linkage.
Choose Datavant Software Questions as the PPRL Question Category.

Resources and Documents

Private and Public SSH Key Generation

Download step-by-step instructions

SFTP Setup Instructions

Download step-by-step instructions

FAQs & Troubleshooting

Do I have to use FileZilla as SFTP client?

No. The Linkage Honest Broker supports any SFTP setup.

What port do I use when connecting to LHB SFTP?

Port 2222

What is the host?

lhbsftp.regenstrief.org

Do I need a password?

No. You will use the private SSH key created when submitting for your SFTP account creation.

What is the logon type?

Key File

What is my username?

E-mail address used when submitting the Individual User Access Form (usually your institution email address)

I am having trouble connecting to the LHB SFTP. What do I do?

Confirm IP address / Range – In firewall
– https://whatismyipaddress.com/ (to get ipv4 and ipv6)
Confirm using open SSH format
Verify private key format is .pem vs. .ppk
– .pem is typically used by Linux/MAC
– .ppk is used by FileZilla client – Windows
Confirm username
– Username is the e-mail address registered with the Linkage Honest Broker

My file contains all error tokens.

Confirm column headers in correct order.
Verify submitting the correct file to the LHB.

If unable to resolve:

Please contact the Linkage Honest Broker by submitting a service desk ticket.

PPRL Linkage Honest Broker

Public N3C PPRL Dashboard

About Privacy Preserving Record Linkage

Support / Questions

Participating Entities

Sponsored by:

Supported by:

The three main parties involved in the data flow:

N3C Overview

High Level Overview of Data Flow

LHB Onboarding Process

Tokenization

Manifest

LHB Data Package

N3C

Transfer Data Package to the LHB SFTP

Support

Resources and Documents

Private and Public SSH Key Generation

SFTP Setup Instructions

FAQs & Troubleshooting

Do I have to use FileZilla as SFTP client?

What port do I use when connecting to LHB SFTP?

What is the host?

Do I need a password?

What is the logon type?

What is my username?

I am having trouble connecting to the LHB SFTP. What do I do?

My file contains all error tokens.

If unable to resolve:

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PPRL Linkage Honest Broker

Public N3C PPRL Dashboard

About Privacy Preserving Record Linkage

Support / Questions

Participating Entities

Sponsored by:

Supported by:

The three main parties involved in the data flow:

N3C Overview

High Level Overview of Data Flow

LHB Onboarding Process

Tokenization

Manifest

LHB Data Package

N3C

Transfer Data Package to the LHB SFTP

Support

Resources and Documents

Private and Public SSH Key Generation

SFTP Setup Instructions

FAQs & Troubleshooting

Do I have to use FileZilla as SFTP client?

What port do I use when connecting to LHB SFTP?

What is the host?

Do I need a password?

What is the logon type?

What is my username?

I am having trouble connecting to the LHB SFTP. What do I do?

My file contains all error tokens.

If unable to resolve: