SARS-CoV-2 genomic contextual data harmonization: recommendations from a mixed methods analysis of COVID-19 case report forms across Canada

Cameron, Rhiannon; Savić Kallesøe, Sarah; Griffiths, Emma J.; Dooley, Damion; Sridhar, Aishwarya; Sehar, Anoosha; Tindale, Lauren C.; Hsiao, William W.L.

doi:10.1186/s13690-025-01604-5

Archives of Public Health

Table 3 SARS-CoV-2 cancogen specification values, submission requirements, and the equivalent Canadian case report form data fields

From: SARS-CoV-2 genomic contextual data harmonization: recommendations from a mixed methods analysis of COVID-19 case report forms across Canada

Generalized Data Field	CanCOGeN Field Equivalent	Ontology Identifier	CanCOGeN Requirement
Database Identifiers
Case Identifier	Case ID	GENEPIO:0100281	Required
Host Information
Complications	Complications	GENEPIO:0001402	Optional
Date of Birth	Host Age ^a	GENEPIO:0001392	Required
Gender	Host Gender	GENEPIO:0001395	Required
Host Health Outcome	Host Health Outcome	GENEPIO:0001390	Optional
Host Health State	Host Health State	GENEPIO:0001388	Optional
Host Health Status Details	Host Health Status Details	GENEPIO:0001389	Optional
Host Resident Information			N/A
Indigenous Identification			N/A ^b
Name (First & Last)			N/A
Personal Health Number			N/A
Phone Number			N/A
Pre-existing Conditions and Risk Factors	Pre-Existing Conditions And Risk Factors	GENEPIO:0001401	Optional
Signs & Symptoms	Signs And Symptoms	GENEPIO:0001400	Optional
Symptom Onset Date	Symptom Onset Date	GENEPIO:0001399	Optional
Host Exposure Information
Exposure Additional Information / History Details	Exposure Details	GENEPIO:0001431	Optional
Exposure Event	Exposure Event	GENEPIO:0001417	Optional
Exposure Setting	Exposure Setting	GENEPIO:0001428	Optional
Exposures - Close, Direct, & Indirect Contact	Exposure Contact Level	GENEPIO:0001418	Optional
Host Role	Host Role	GENEPIO:0001419	Optional
Location of Exposure - Country	Location Of Exposure Geo_loc Name (Country)	GENEPIO:0001410	Optional
Location of Exposure - Travel History	Travel History	GENEPIO:0001416	Optional
Location of Exposure - Most Recent Travel - Destination City	Destination Of Most Recent Travel (City)	GENEPIO:0001411	Optional
Location of Exposure - Most Recent Travel - Destination State/Province/Territory	Destination Of Most Recent Travel (State/Province/Territory)	GENEPIO:0001412	Optional
Location of Exposure - Most Recent Travel - Destination Country	Destination Of Most Recent Travel (Country)	GENEPIO:0001413	Optional
Location of Exposure - Most Recent Travel - Departure Date	Most Recent Travel Departure Date	GENEPIO:0001414	Optional
Location of Exposure - Most Recent Travel - Return Date	Most Recent Travel Return Date	GENEPIO:0001415	Optional

^a “Host Age” is not an exact match for “Date of Birth”; it was used in the specification because it is less identifiable than “Date of Birth” and the age value was what is needed for CanCOGeN objectives
^b This field was deemed of high importance but is not currently under the custodianship of CanCOGeN data collection
Case report form data items have been generalized to a single label for this table. Not Applicable (N/A) values occur because they were not appropriate for privacy protections of user data at the national level, but could be of value to local and provincial levels. Ontology identifiers can be looked up online for more information. This table includes only a subset of CanCOGeN specification fields; the comprehensive specification is available online

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ISSN: 2049-3258

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