new wastewater templates; GRDI 9.0; CanCoGeN 2.3.4

Author: ddooley

web/templates/canada_covid19/schema.json

@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ""
-version: 2.2.3
+version: 2.3.4
 imports:
 - 'linkml:types'
 prefixes:

web/templates/canada_covid19/schema.yaml

@@ -145,6 +145,7 @@ NML submitted specimen type menu	OBI:0002600	Swab
 
 
 Related specimen relationship type menu	HP:0011009	Acute										
+	GENEPIO:0101016	Chronic (prolonged) infection investigation										
 		Convalescent										
 		Familial										
 	EFO:0009642	Follow-up										
@@ -379,6 +380,7 @@ anatomical part menu	UBERON:0001245	Anus
 	UBERON:0005922			Inferior Nasal Turbinate								
 	UBERON:0001728		Nasopharynx (NP)									
 	UBERON:0001729		Oropharynx (OP)									
+	UBERON:0000341		Pharynx (throat)									
 
 
 body product menu	UBERON:0001913	Breast Milk										
@@ -568,6 +570,7 @@ purpose of sequencing menu	GENEPIO:0100005	Baseline surveillance (random samplin
 	GENEPIO:0100273				Sample has epidemiological link to Variant of Concern (VoC)							
 	GENEPIO:0100274					Sample has epidemiological link to Omicron Variant 						
 	GENEPIO:0100009			Longitudinal surveillance (repeat sampling of individuals) 								
+	GENEPIO:0100842				Chronic (prolonged) infection surveillance							
 	GENEPIO:0100010			Re-infection surveillance 								
 	GENEPIO:0100011			Vaccine escape surveillance								
 	GENEPIO:0100012			Travel-associated surveillance								
@@ -898,7 +901,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		Thunder Bay Regional Health Sciences Centre										
 
 
- sample collected by menu		Alberta Precision Labs (APL)										
+sample collected by menu		Alberta Precision Labs (APL)										
 			Alberta ProvLab North (APLN)									
 			Alberta ProvLab South (APLS)									
 		BCCDC Public Health Laboratory										
@@ -1204,4 +1207,6 @@ geo_loc_name (country) menu	GAZ:00006882	Afghanistan
 	GAZ:00000564	Western Sahara										
 	GAZ:00005284	Yemen										
 	GAZ:00001107	Zambia										
-	GAZ:00001106	Zimbabwe										
+	GAZ:00001106	Zimbabwe										
+												
+					

web/templates/canada_covid19/schema_core.yaml

@@ -158,4 +158,5 @@ CanCOGeN Covid-19		GENEPIO:0001122	Database Identifiers
 
 		GENEPIO:0001516	Contributor acknowledgement																			
 	Contributor acknowledgement	GENEPIO:0001517	authors		WhitespaceMinimizedString					TRUE					Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.	Include the first and last names of all individuals that should be attributed, separated by a comma.	Tejinder Singh, Fei Hu, Joe Blogs	Authors	Authors	PH_CANCOGEN_AUTHORS		
-	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		
+	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		
+