The NCATS N3C resources webpage provides high-level regulatory and governance Frequently Asked Questions (FAQs), the Data Transfer Agreement (DTA), and other important information to get started with N3C. Below are frequently asked questions specifically related to the access and flow of data in the N3C Data Enclave.
N3C Data Enclave
To register with N3C, go to the N3C Login/Registration Page and select the button that says “Click here to Register with N3C”. You must use an institutional email address linked to an individual (not a shared account) to register with N3C. If you are affiliated with an institution that is not part of the InCommon authentication framework, or are a citizen scientist and do not have an institutional email address, click on the “Login.gov” button and follow the instructions.
Registering with N3C is the first step to establish an N3C Data Enclave account and necessary to link users to a Data Use Agreement. In addition, it allows you to become a member of the N3C community and gain access to the team document drive, Google groups, Slack channels, calendar meeting invitations, and the workstreams. (It is not mandatory to join a workstream to be a member of the N3C community.) Other incentives to becoming an N3C community member include collaborations, community input, joint publications, and governance. Requests for N3C membership and joining of Google groups are reviewed and granted rapidly during the week, but can take longer on weekends (up to 48 hours).
Anyone can apply to be the Lead Investigator on an N3C project. However, the person listed on the account as the Lead Investigator must agree to uphold the following responsibilities:
- Serve as the N3C contact person for questions, concerns, and requests to join the project.
- Serve as the individual responsible for assuring completion of the project. Projects are renewed annually, per the Data Use Request (DUR).
- Identify and/or approve requests for collaborators to join the approved project-specific DUR. Collaborators from other institutions must still submit a DUR and follow their own institutions’ policies for human subjects research, as applicable.
Before creating your account, you will need to have the following available:
- The N3C Data Enclave is hosted by NIH, so all users are required to have annual NIH Information Security and Information Management Training and should be prepared to provide a certificate of completion upon request. This training is freely available to the public and a certificate of completion can be printed provided that the course is taken in one setting. Researchers must complete training before they can submit a Data Use Request.
- Only the 2020 Information Security course at the top of the list is required to be completed consisting of these segments: Information Security, Counterintelligence & Insider Threat, Privacy, Records Management, Emergency Preparedness. (Allow 60-90 minutes to complete.)
- Upon completion, you can click on “Print Certificate”, add your name, and save to PDF or print to make it available upon request.
- You will be asked for the training completion date, and may be asked by NCATS to provide evidence of completion (i.e., a screenshot or copy of the Certificate of Completion).
- If you are requesting access to the de-identified dataset or the limited dataset, you must also have completed Human Subjects Research (HSR) protection training per your home institutional requirements. (CITI Program and NIH courses are most common.) You will be required to enter your HSR training completion date. (HSR training is not needed to access the synthetic dataset.)
The goal is to update data from contributing sites on average intervals of two times per week. This includes new patient records as well as updates to existing ones. When data are refreshed, information about the data will be provided via Fact Sheets and User Notes.
- Fact Sheets provide a description of the data, such as number of sites available, persons, and COVID cases, and will be available on both the N3C and NCATS websites.
- Release Notes describe any known issues about the data and missing data, interpretation of qualitative results, and implemented crosswalks. Release Notes will only be available to users who are logged into the N3C Data Enclave.
Yes; however, this will be done on a case-by-case basis to ensure that data are secure and all legal and regulatory requirements have been met. Governance processes for data uploads are in development. For more information, contact the N3C Data Enclave technical support team at NCATSN3CSupport@mail.nih.gov.
The N3C Enclave is capable of integrating external tools, such as the OHDSI ATLAS platform. However, the tools must conform to the security requirements as specified by the Data Transfer Agreement and Data Use Agreement, and they may require special configuration and auditing. Extra controls are required to install packages and tools, since the enclave is a FedRamp certified environment. For further questions on software and tools in the enclave, contact the N3C Data Enclave technical support team at NCATSN3CSupport@mail.nih.gov.
Data analysis within the N3C Data Enclave is supported by R and Python, the most widely used open source platforms for statistical analysis and data science. It is also supported by Slate, the Palantir Foundry programming language.
- Commonly used R and Python analysis packages, such as SciPy and scikit-learn, have been pre-installed to use in your pipelines. If additional R or Python packages are needed, contact the N3C Data Enclave technical support team at NCATSN3CSupport@mail.nih.gov.
- Data and code provenance is fully tracked throughout the course of the project by use of the platform’s native functions, which facilitate tracing of all data and code development. Training materials for the platform’s native tooling and for use of R and Python code and SQL within the environment are readily available inside the N3C Data Enclave.
- Other data analysis tools are currently being evaluated for use in N3C, including the OHDSI tool stack, Leaf, and the NIH Biomedical Translator Knowledge Graph Engine.
Learn more about supported tools and resources and suggest new ones at the Tools and Resources subgroup meetings, which usually is held on Fridays 1:00pm PT/4:00pm ET.
There are recommended training materials and resources available within the N3C Data Enclave. There is an N3C Quickstart Tour and an Intro to Foundry training course (offered twice a month) to understand core concepts for using the N3C Data Enclave software. Additional resources include live scheduled trainings, written tutorials, interactive tours, official documentation, and a help & support system.
Publicly accessible information about the OMOP Common Data Model (CDM) and OHDSI tools for running analyses against OMOP include the Book of OHDSI and OHDSI tutorial videos and there is free courseware available through EHDEN Academy.The two courses of interest to N3C users would be those covering the CDM and vocabularies and ATLAS.
Contributing site names are masked in the N3C data; however, data can be differentiated, such as by Site A, Site B, etc.
NCATS and the N3C community encourage citation of the N3C Data Enclave. Information on how to cite and acknowledge the N3C Data Enclave can be found in Acknowledging N3C in Publications and Presentations on the NCATS website, as well as in the Attribution & Publication Principles for N3C in the Zenodo database.
The Project Dashboard, which currently can be viewed by anyone with an N3C Data Enclave account, provides a list of approved projects. It includes:
- Project title
- Research project abstract
- Lead Investigator name
- Lead Investigator accessing institution
- Request to join a project as a collaborator
Researchers can use the dashboard to see projects that are using N3C data and can request to join projects open to collaborators by clicking on the “Contact Lead Investigator” button.
The N3C Data Enclave is hosted by NIH; therefore, NIH IT security training is required for users who will be accessing the data. The training is not required for individuals who will not be accessing the data.
Many organizations already require 2-factor authentication (2FA) for secure login. This is a separate security step from the UNA 2FA, so you may be required to perform two verifications. You can mitigate this inconvenience by using the “remember this computer” checkbox on a trusted device. If you already use a 2FA app (e.g., Duo Mobile), you will likely be able to use it by creating a separate account for UNA following the process outlined in this document.
Phenotype & Data Acquisition
The data ingestion and harmonization process will be an iterative process between the Phenotype & Data Acquisition workstream, the Data Ingestion & Harmonization workstream, and contributing sites. First and foremost, the best way to support the data ingestion and harmonization process is to ensure the data payload follows the specifications outlined in the GitHub Wiki documentation. Use of the R or Python Exporter will support consistency while lowering site burden.
The phenotype for COVID-19 continues to evolve as more is learned about the disease and new codes (particularly LOINC) become available. The phenotype is updated approximately every 2 weeks on Fridays, with corresponding code updated by the following Tuesday. The latest version of the phenotype can be found in the Phenotype Github repository.
Data will be transferred to NCATS via SFTP. To obtain SFTP credentials after IRB approval has been granted and the DTA has been signed, please contact Emily Pfaff at epfaff [at] email [dot] unc [dot] edu.
The Wiki documentation outlines the expected data output format, naming conventions, and directory structure. If a site is using the R or Python exporter, all of these steps will be included in those exporter packages. If a site is using the raw SQL, the Wiki should be reviewed for specifications and examples for packaging the data (OMOP, PCORnet, ACT).
Ideally, sites will transmit data to N3C 1-2 times per week. If this refresh rate is not feasible for a site, the Phenotype workstream will provide assistance.
If a site uses its common data model for other purposes (particularly network studies) and follows the guidelines for populating it, it will most likely have the data it needs for the initial phases of N3C. As time goes on, the N3C consortium may agree on additional data elements to add that are not generally found in CDMs, or are infrequently populated.
All sites are strongly encouraged to use the R and Python Exporters that the Phenotype & Data Acquisition workstream has created. This will ensure uniform data exports, which is critical to the data harmonization process. Moreover, the R and Python scripts automate many tasks that would otherwise be manual.
Alternatively, sites may choose to use the raw SQL scripts. If a site chooses this option, they should closely review and follow the export specifications outlined in the documentation (OMOP, PCORnet, ACT).
If you are working with TriNetX, TriNetX will export your site’s data on your site’s behalf; you will not need to use any of the code (exporters or phenotype).
The Phenotype workstream can provide assistance. If support is needed during any part of the phenotyping, data extraction, or data submission process, communication through the Phenotype & Data Acquisition GitHub repository is the preferred method for communication.
The Phenotype workstream hosts twice weekly Zoom office hours on Mondays and Thursdays from 12:00-1:00 pm ET. Registration details are available on the N3C calendar.
Data Ingestion & Harmonization
Existing OHDSI OMOP data conformance tools and processes are all available in the N3C Data Enclave and are run on the data prior to ingestion into the full dataset. The data quality checks are a hybrid across all data models.
Common data models used by sites are consolidated and harmonized to the OMOP common data model and then ingested into the N3C Data Enclave as a new dataset.
The N3C platform produces synthetic data from the limited dataset (LDS) that a site submits. Comparisons between source limited data and ensuing synthetic data are an essential component of the data quality assurance, verification, and validation processes used by N3C. Therefore, sites are required to submit an LDS to N3C in order to create a synthetic dataset. (See the NCATS webpage for more details on the levels of data access.)