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

Table 2 Universal SARS-CoV-2 Canadian case report form data items and the equivalent cancogen specification values

Generalized Data Field / Category	Generalized Picklist Term	CanCOGeN Equivalent	Ontology Identifier
Case Identifier		Case ID	GENEPIO:0100281
Name (First & Last)		N/A	N/A
Date of Birth		N/A	N/A
Phone Number		N/A	N/A
Gender		Host Gender	GENEPIO:0001395
Symptom Onset Date ^a		Symptom Onset Date ^b	GENEPIO:0001399
Signs & Symptoms		Signs and Symptoms	GENEPIO:0001400
	Cough	Cough	HP:0012735
	Fever ^c	Fever Fever ( > = 38 °C)	HP:0001945 GENEPIO:0100066
	Headache	Headache	HP:0002315
	Sore Throat	Pharyngitis (Sore Throat)	HP:0025439
Pre-existing Conditions and Risk Factors		Pre-existing Conditions and Risk Factors	GENEPIO:0001401
	Cardiac Disease	Cardiac Disease	MONDO:0005267
	Diabetes	Diabetes Mellitus (diabetes)	HP:0000819
	Pregnancy	Pregnancy	NCIT: C25742
	Respiratory Disease	Respiratory Disorder	MONDO:0005087
Complications		Complications	GENEPIO:0001402
	Altered Mental Status	Altered Mental Status	HP:0011446
	Encephalitis	Encephalitis (Brain Inflammation)	HP:0002383

^a Significant variation in the recommended date format across case report forms: DD/MM/YYYY, MM/DD/YYYY, YYYY/MM/DD, YYYY/MMM/DD, and Unspecified
^b ISO 8601 standard “YYYY-MM-DD”
^c Minimum temperature that defines a fever has some variation between forms or is not defined
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 would be of value to local and provincial levels. Ontology identifiers can be looked up online for more data item information

ISSN: 2049-3258