Data Ingestion & Harmonization Workstream

Mission

Ingest data from their native formats—PCORnet, ACT, OMOP, TriNetX—and harmonize the datasets into a common data model (CDM) based on the OMOP 5.3.1 standard to maximize analytics.

View workstream details in the GitHub Repository.

What is the OMOP Common Data Model? The OMOP Common Data Model is a standard for organizing and structuring clinical EHR data. By using a single standard, the N3C is able to accept data from multiple institutions in its original format and harmonize all of the data into a connected resource. Learn more about the harmonization process by watching the N3C Harmonization Webinar on this page, or learn more about the OMOP vocabulary in "OMOP Vocabulary 101" or "OMOP Vocabulary 201".

Office hours are held every other Thursday from 9:00-10:00 am PT/12:00-1:00 pm ET to answer data ingestion questions and address issues. (Regulatory paperwork does not have to be complete to attend.) Register Here.

N3C Data Ingestion Harmonization

Connect with Us:

  1. Onboard to N3C using the link below.
    • In there you will provide your email address. We will add that email address to the CD2H workspace.
  2. Go to our workstream Slack channel directly using the link provided below.
    • Login with your Slack credentials.
Onboard to N3C
Data Ingestion & Harmonization Slack Channel
Data Ingestion & Harmonization Google Group

FAQs

The Phenotype & Data Acquisition team will contact the contributing sites directly if there are concerns with the data ingestion and harmonization process.

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.

Leadership and Administration

Christopher Chute, MD, DrPH
Johns Hopkins University
Usman Sheikh
NCATS
Tricia Francis
Johns Hopkins University

To Cite the N3C: "The analyses described in this [publication/report/presentation] were conducted with data or tools accessed through the NCATS N3C Data Enclave https://covid.cd2h.org and N3C Attribution & Publication Policy v 1.2-2020-08-25b supported by NCATS Contract No. 75N95023D00001 and [insert additional funding agencies or sources and reference numbers as declared by the contributors in their form response above]. This research was possible because of the patients whose information is included within the data and the organizations (https://ncats.nih.gov/n3c/resources/data-contribution/data-transfer-agreement-signatories) and scientists who have contributed to the on-going development of this community resource [https://doi.org/10.1093/jamia/ocaa196]."

For publication submission information, please see the Publication Review Page

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