Volume 53 | July 28, 2022
A program of NIH’s National Center for Advancing Translational Sciences
What the Research Community is Saying about N3C
Justin Reese, PhD
Research Scientist, Lawrence Berkeley National Lab

N3C Teams:
Machine Learning, Diabetes/Obesity, Long COVID, Pharmacoepidemiology, OMOP to OBO
"N3C represents a major step forward in the way that clinical research is conducted. The impressive data harmonization work and the quality biomedical research that the N3C community has done since the start of the pandemic demonstrates that cross-disciplinary teams such as ours can self-organize and address public-health emergencies like COVID-19. 
The massive trove of harmonized, centralized EHR data and the N3C technology stack have made it easier for my group to perform meaningful machine learning (such as prediction and clustering of long COVID patients) and pharmacoepidemiology research, and we look forward to contributing more in the future."
Text Analytics and Natural Language Processing (NLP) Best Practices and the N3C NLP Standard Operating Procedures (Now Available!)

Text Analytics and NLP Best Practices

The OHNLP (Open Health Natural Language Processing), CD2H (Center for Data to Health) NLP (Natural Language Processing) and iEC (Informatics Enterprise Committee) Text Analytics Working Groups have published the Text Analytics and NLP Best Practices (Chapter 9: Best practices of annotating clinical texts for information extraction tasks: https://playbook.biothings.io/en/latest/chapters/chapter_9.html) in the CD2H Informatics Playbook. This covers best practices of annotating clinical texts for information extraction tasks. Investigators and informatics project leads can use the chapter as a guideline for creating gold-standard corpora for clinical information extraction projects. In addition, the chapter presents a recently proposed framework (the Text Retrieval and Use towards Scientific rigor and Transparent process, TRUST) to enhance the data quality of manually curated resources.

N3C NLP Data Enhancements
Standard Operating Procedures (SOP)

The N3C NLP Domain Team and the N3C community developed the N3C NLP Data Enhancements SOP to provide sites with the information needed to submit their N3C NLP data. 
For the teams that would like to contribute to validating the data by annotating the mentions of COVID-19 and PASC-related signs/symptoms from clinical texts, they may reach out to RSTNLP@mayo.edu and follow the N3C NLP Validation and Evaluation Standard Operating Procedures at https://docs.google.com/document/d/1N3SThmfj_7W9whZOFLzVYPad8OeiAKQAYApFV8giIlo/edit?usp=sharing

Questions or Comments:
Join the NLP Slack Channel here.
NLP Office Hours are every other Thursday (Starting August 5th) at 12pm PT/3pm ET.
Please register here for NLP Office Hours: https://washington.zoom.us/meeting/register/tJ0uf-uhpzMqHdWIgYONFyYddPbSpOxUqqdE. After registering, you will receive a confirmation email from no-reply@zoom.us containing information about joining the webinar and an .ics file to add to your calendar.
N3C RECOVER Clinician's Group

The N3C RECOVER Clinician Engagement workgroup serves as a space to integrate clinical expertise and to provide clinical feedback on N3C RECOVER analytical queries and results.
The meetings are held biweekly, on Fridays at 3:00 PM EST (12:00 PM PST). To date, this workgroup has had in-depth conversations on Paxlovid, as well as reviewed and discussed the latest Infection updates data.

For those interested in joining these clinical discussions, contact us at cd2h@cuanschutz.edu, or via Slack at https://paschq.slack.com/archives/C03FL9PFU95.

N3C RECOVER Clinical Engagement Participants
Brian Byrd, MD - University of Michigan
Scott Chapman, MD - University of Minnesota
David Sahner, MD - National Institutes of Health
Mike Liberman, MD - Oregon Community Health Information Network
Adam Dziorny, MD - University of Rochester School of Medicine and Dentistry
Rachel Wong, MD - Stony Brook University
Mary Saltz, MD - Stony Brook University
John Barratta, MD - University of North Carolina
Carole Tucker, MD - University of Texas Medical Branch
Yochai Re-em, MD - University of Pittsburg Liver Research Center
Farrukh Koraishy, MD - SUNY Stony Brook University
Josh Fessel, MD - Division of Clinical Innovation
Thomas Campbell, MD - University of Colorado School of Medicine
Call for AMIA Submissions!

If you have a novel N3C approach or results to share with the medical informatics community, this is your opportunity! Submissions are due Wednesday, September 14, 2022.

CD2H No Cost Extension
The National Center for Data to Health was approved for a 12-month No-Cost Extension (NCE).
Details about the efforts covered during the NCE will be communicated in the coming weeks.

Published works using N3C data are listed on the N3C Cohort Exploration Dashboard. The Publications tab displays titles and links to fully published articles, articles online ahead of print, and published preprints, as well as a list of accepted conference presentations and posters.

Help Us Track N3C Publications!

When you have a research product that is ready for publication or accepted for presentation, please submit it via the N3C Publication Intent Form, which will notify the Publication Committee of N3C output to be registered. (Research products include: manuscripts, posters, conference papers, blogs, press releases, podium presentations, etc.)

Per the N3C Attribution and Publication Principles, all manuscripts using N3C community resources must be reviewed by the Publication Committee. Non-manuscript products do not require review but should be submitted after they have been accepted by the conference to allow for promotion and tracking of collaborator accomplishments.

View the Publication Review web page for more details.
N3C In the News

In a recent study posted to the medRxiv* preprint server, researchers investigated if non-psychiatric PASC-AMs [post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection-associated manifestations] increase the risk of new-onset psychiatric illness diagnosis.

COVID-19 hospitalization is associated with a 45% greater risk of subsequent heart failure (HF), particularly for patients who are younger, White, or previously diagnosed as having heart disease, according to a US study published late last week in Nature Communications.
Sign Up for the Community Forum!

Please register for your Community Forum meeting link. After registering, you will receive a confirmation email from cd2h@uw.edu containing information about joining the meeting and you will also have the ability to download the .ics file to create calendar reminders for future Community Forums.
Register for the Community Forum at https://covid.cd2h.org/forum

N3Community Forum

Presentations take place on select Mondays from 5–6 p.m. ET/2–3 p.m. PT. To attend these and future N3Community Forum presentations, please register here.

Missed an N3Community Forum or want to revisit a past Forum? You can find all the videos on our YouTube page.

N3Community Forum will take a break in August

September 12, 2022

Topic: Clinical, social, and policy factors in COVID-19 cases and deaths: methodological considerations for feature selection and modeling in county-level analyses
Presenter: Charisse Madlock-Brown, PhD
University of Tennessee

September 19, 2022

Topic: COVID-19 patients with documented alcohol use disorder or alcohol-related complications are more likely to be hospitalized and have higher all-cause mortality
Presenter: Kristina Bailey, MD
University of Nebraska

September 26, 2022

Topic: Glycemic Control and Clinical Outcomes in U.S. Patients With COVID-19: Data From the National COVID Cohort Collaborative (N3C) Database
Presenter:  Rachel Wong, MD
Stony Brook University

Important SLACK Update!
Your N3C/CD2H/PASC Slack Access Could be Deactivated

If you receive an email within the next couple of weeks about your Slack access, it means that you have not registered/onboarded with CD2H/N3C and your Slack access will be deactivated.  

If you want to maintain access to the CD2H/N3C/PASC Slack Channels, please go here to onboard by registering (see photo).

Contact cd2h@anschutz.edu for any questions.
No Meeting Weeks - Mark Your Calendars!

To help our community with a positive and productive workload, CD2H-N3C will schedule several “No Meetings Weeks” throughout the year. 

Most meetings will be canceled. Impromptu meetings can still occur to push through action items as needed during no meeting week. Workgroups and Domain Teams should check with their Leads to determine meeting schedules for that week. 

N3C support will continue with regular operations. If you have any trouble logging on to the enclave, please contact NCATSAuthSupport@mail.nih.gov. For all other issues please use the Support Desk.

4th Quarter: November 7-11
No Community Forum during this week
N3Connect Bulletin Break

We are taking a mini break in August. We will see you in September!
We will continue to send out communication as needed to inform the community of important updates and information. Please see our CD2H Slack channel for important information and upcoming events.
N3C Domain Teams

N3C Domain Teams enable researchers with shared interests to analyze data within the N3C Data Enclave and collaborate more efficiently in a team science environment. They include multidisciplinary Clinical Domains composed of subject matter experts, statisticians, informaticists, and machine learning specialists who focus on clinical questions surrounding COVID-19's impact on health. Cross-Cutting Domains have a varied focus that applies to multiple domains. These teams provide an opportunity to collect pilot data for grant submissions, train algorithms on larger datasets, inform clinical trial design, learn how to use tools for large-scale COVID-19 data, and validate results. N3C encourages researchers of all levels to join a Domain Team that represents their interests, or to suggest new clinical areas to explore.


As we have recently crossed the 2-year mark for the COVID-19 pandemic, it is a good inflection point to identify colleagues who have completed their efforts with CD2H/N3C projects and have transitioned to other great opportunities. If this is you, or perhaps your colleague, we would like to ask that you complete this 2-minute form (Bit.ly/cd2h-offboarding-form) to offboard CD2H and or N3C projects. You can continue to just get the newsletter if you wish.

We thank you for your tireless efforts in CD2H/N3C projects and look forward to working with you on many other projects.
Reporting Concerns

In the event that you come across activities that pose misalignment with the principles outlined in the Community Guiding Principles for the National COVID Cohort Collaborative (N3C), you can privately notify us using the Report Conduct Concerns form located on the N3C website under the SUPPORT menu. Your feedback is important and we will take prompt and confidential action to address your concerns. All data management incidents should also be reported to NCATS. Thank you for your contribution!
The National COVID Cohort Collaborative (N3C) is a complementary and synergistic partnership among the Clinical and Translational Science Awards (CTSA) Program hubs, the National Center for Data to Health (CD2H), distributed clinical data networks (PCORnet, OHDSI, ACT, TriNetX), and other partner organizations, with overall stewardship by NIH’s National Center for Advancing Translational Sciences (NCATS). The N3C aims to improve the efficiency and accessibility of analyses using a very large row-level (patient-level) COVID-19 clinical dataset, demonstrate a novel approach for collaborative pandemic data sharing, and speed understanding of and treatments for COVID-19.
CD2H is supported by the National Center for Advancing Translational Sciences (NCATS) 
at the National Institutes of Health
(Grant U24TR002306).