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Welcome to the Data-Ingestion-and-Harmonization wiki!
N3C Data Ingestion and Harmonization V1.0 Specifications
Authors: Davera Gabriel, Stephanie Hong, Dazhi Jiao, Richard Zhu, Tanner Zhang, Tricia Francis, Harold Solbrig, Harold Lehmann, Chris Chute 15 April 2020
This wiki houses all of the documentation for the current work-in-progress version as well as changes added with each mile-stone phases. You can find a pdf added to work-in-progress and pre-release with a historical references. We will keep version of the wiki as it is being defined.
The sidebar to the right links to resources about the ingestion process (sites→Palantir).
A publicly-available record of post-mapping and Palantir-based data characterization is available in this Google Sheet. (The Concept Set Browser and the Knowledge Store, both in the Enclave, are more definitive at the present time.)
- The Enclave API now supports authority property. This property is used to indicate the authority source of the concept set.
DataSet/Manifest Contents and Structures
- CDM minimum required tables
- OMOP Vocabulary Updates
- Process Overview
- DataSet Submission Format
- N3CID Global Domain ID
- Terminology Value Set Mapping Table Structure Explained
- PCORnet terms cross walk table
- ACT term cross walk table
- ACT: Additional Mapping Notes
- TrinetX: Mapping Notes
- Qualitative Results VS Mapping
- Corrected LOINC when COVID test LOINC is missing
- DEMOGRAPHIC VALUSETS
- COVID-19 LOINC corrected
- Safe Harbor Requirement
- type_concept_id default values
- Immunization value-set mappings
- Lab confirmed positive cohort definition
- Long COVID Specialty clinic visit
- Categorical Answer Concept Maps
- BulkImportConceptSetCreation
- Viral Variant Mapping Information
- CMS Data Integration Guidelines
- N3C Data Ingestion
- N3C Data Transformation
- Value Set Mapping table structure
- measurement unit harmonization
- Data Quality Public Worksheet
- PPRL N3C - CMS Release Notes
- N3C Extension
Includes Overview, PreRelease Variable Punchlist, References for creating phenotypes.