bccdc name, and example changes

cidgoh · Dec 2, 2020 · dfe3f0d · dfe3f0d
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diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js
@@ -297,7 +297,7 @@ var DATA = [
         },
         "vocabulary": {
           "National Microbiology Laboratory (NML)": {},
-          "BC Centre for Disease Control (BCCDC)": {},
+          "BCCDC Public Health Laboratory": {},
           "Alberta Precision Labs (APL)": {
             "Alberta ProvLab North (APLN)": {},
             "Alberta ProvLab South (APLS)": {}
@@ -918,7 +918,7 @@ var DATA = [
         "requirement": "",
         "description": "The relationship of the related specimen to the previous submission.",
         "guidance": "Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system.",
-        "examples": "swab",
+        "examples": "Follow-up",
         "exportField": {
           "CNPHI": [
             {
@@ -1168,7 +1168,7 @@ var DATA = [
         "requirement": "required",
         "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.",
         "guidance": "Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. ",
-        "examples": "Building floor",
+        "examples": "Production Facility",
         "exportField": {
           "GISAID": [
             {
@@ -1924,7 +1924,7 @@ var DATA = [
         "requirement": "",
         "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician.",
         "guidance": "Select all of the symptoms experienced by the host from the pick list.",
-        "examples": "Cough; Fever; Chills",
+        "examples": "Chills (sudden cold sensation); Cough; Fever",
         "exportField": {
           "CNPHI": [
             {
@@ -2055,7 +2055,7 @@ var DATA = [
         "requirement": "",
         "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.",
         "guidance": "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.",
-        "examples": "Asthma; Pregnancy; Smoker",
+        "examples": "Asthma; Pregnancy; Smoking",
         "vocabulary": {
           "Age 60+": {},
           "Anemia": {},
@@ -2489,7 +2489,7 @@ var DATA = [
         "requirement": "",
         "description": "Event leading to exposure.",
         "guidance": "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team.",
-        "examples": "Mass gathering (convention)",
+        "examples": "Convention",
         "exportField": {
           "GISAID": [
             {

diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv
@@ -28,12 +28,12 @@ ID	SC %
 	Sample collection and processing	purpose of sampling	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The reason that the sample was collected.	The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. 	Diagnostic testing		Reason for Sampling
 	Sample collection and processing	purpose of sampling details	xs:token		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The description of why the sample was collected providing specific details.	Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. 	The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. 		
 	Sample collection and processing	NML submitted specimen type	select							The type of specimen submitted to the NML for testing.	Select the specimen type from the pick list provided.	swab		Specimen Type
-	Sample collection and processing	NML related specimen relationship type	select							The relationship of the related specimen to the previous submission.	Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system.	swab		Related Specimen ID|Related Specimen Relationship Type
+	Sample collection and processing	NML related specimen relationship type	select							The relationship of the related specimen to the previous submission.	Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system.	Follow-up		Related Specimen ID|Related Specimen Relationship Type
 	Sample collection and processing	anatomical material	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				A substance obtained from an anatomical part of an organism e.g. tissue, blood.	Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Blood	Specimen source	Anatomical Material
 	Sample collection and processing	anatomical part	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				An anatomical part of an organism e.g. oropharynx.	Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Nasopharynx (NP)	Specimen source	Anatomical Site
 	Sample collection and processing	body product	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				A substance excreted/secreted from an organism e.g. feces, urine, sweat.	Provide a descriptor if a body product was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Feces	Specimen source	Body Product
 	Sample collection and processing	environmental material	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				A substance obtained from the natural or man-made environment e.g. soil, water, sewage.	Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Face mask	Specimen source	Environmental Material
-	Sample collection and processing	environmental site	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.	Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Building floor	Specimen source	Environmental Site
+	Sample collection and processing	environmental site	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.	Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Production Facility	Specimen source	Environmental Site
 	Sample collection and processing	collection device	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The instrument or container used to collect the sample e.g. swab.	Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Swab	Specimen source	Specimen Collection Matrix
 	Sample collection and processing	collection method	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The process used to collect the sample e.g. phlebotamy, necropsy.	Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. 	Bronchoalveolar lavage (BAL)	Specimen source	Collection Method
 	Sample collection and processing	collection protocol	xs:token							The name and version of a particular protocol used for sampling.	Free text.	BCRonaSamplingProtocol v. 1.2		
@@ -56,10 +56,10 @@ ID	SC %
 	Host Information	host origin geo_loc name (country)	select	geo_loc_name (country)	Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The country of residence of the host.	Select the country name from pick list provided in the template.	United Kingdom		
 	Host Information	host subject ID	xs:token							A unique identifier by which each host can be referred to e.g. #131	Provide the host identifier. Should be a unique, user-defined identifier.	BCxy123		
 	Host Information	symptom onset date	xs:date		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The date on which the symptoms began or were first noted.	ISO 8601 standard "YYYY-MM-DD".	2020-03-16		Symptoms Onset Date
-	Host Information	signs and symptoms	multiple		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician.	Select all of the symptoms experienced by the host from the pick list.	Cough; Fever; Chills		Symptoms
+	Host Information	signs and symptoms	multiple		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician.	Select all of the symptoms experienced by the host from the pick list.	Chills (sudden cold sensation); Cough; Fever		Symptoms
 	Host Information	pre-existing conditions and risk factors	multiple		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					"Patient pre-existing conditions and risk factors.
 Pre-existing condition: A medical condition that existed prior to the current infection.
-Risk Factor: A variable associated with an increased risk of disease or infection."	Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.	Asthma; Pregnancy; Smoker		
+Risk Factor: A variable associated with an increased risk of disease or infection."	Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.	Asthma; Pregnancy; Smoking		
 	Host Information	complications	multiple		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					Patient medical complications that are believed to have occurred as a result of host disease.	Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team.	Acute Respiratory Failure; Coma; Septicemia		
 		Host exposure information												
 	Host exposure information	location of exposure geo_loc name (country)	select	geo_loc_name (country)	Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The country where the host was likely exposed to the causative agent of the illness.	Select the country name from pick list provided in the template.	Canada		
@@ -69,7 +69,7 @@ Risk Factor: A variable associated with an increased risk of disease or infectio
 	Host exposure information	most recent travel departure date	xs:date		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.	Provide the travel departure date.	2020-03-16		Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date
 	Host exposure information	most recent travel return date	xs:date		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The date of a person's most recent return to some residence from a journey originating at that residence.	Provide the travel return date.	2020-04-26		Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date
 	Host exposure information	travel history	xs:token							Travel outside the country in last six months.	Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first.	Canada, Vancouver; USA, Seattle; Italy, Milan		
-	Host exposure information	exposure event	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					Event leading to exposure.	Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team.	Mass gathering (convention)	Additional location information	Exposure Event
+	Host exposure information	exposure event	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					Event leading to exposure.	Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team.	Convention	Additional location information	Exposure Event
 	Host exposure information	direct/indirect exposure	select							The exposure transmission contact type.	Select direct or indirect exposure from the pick-list.	Direct		
 	Host exposure information	host role	multiple							The role of the host in relation to the exposure setting.	Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team.	Patient		
 	Host exposure information	exposure setting	multiple							The setting leading to exposure.	Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team.	Healthcare Setting		
@@ -893,7 +893,7 @@ PR:A0A663DJA2	gene name 1	ORF10
 
 
 	sequence submitted by	National Microbiology Laboratory (NML)												
-	sequence submitted by	BC Centre for Disease Control (BCCDC)												
+	sequence submitted by	BCCDC Public Health Laboratory												
 	sequence submitted by	Alberta Precision Labs (APL)												
 	Alberta Precision Labs (APL)	Alberta ProvLab North (APLN)												
 	Alberta Precision Labs (APL)	Alberta ProvLab South (APLS)												

diff --git a/template/canada_covid19/reference.html b/template/canada_covid19/reference.html
@@ -276,7 +276,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td class="label">NML related specimen relationship type</td>
 							<td>The relationship of the related specimen to the previous submission.</td>
 							<td>Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system.</td>
-							<td>swab</td>
+							<td>Follow-up</td>
 							<td>None</td>
 						</tr>
 
@@ -321,7 +321,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td class="label">environmental site</td>
 							<td>An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.</td>
 							<td>Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. </td>
-							<td>Building floor</td>
+							<td>Production Facility</td>
 							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access']</td>
 						</tr>
 
@@ -523,7 +523,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td class="label">signs and symptoms</td>
 							<td>A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician.</td>
 							<td>Select all of the symptoms experienced by the host from the pick list.</td>
-							<td>Cough; Fever; Chills</td>
+							<td>Chills (sudden cold sensation); Cough; Fever</td>
 							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access']</td>
 						</tr>
 
@@ -534,7 +534,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 Pre-existing condition: A medical condition that existed prior to the current infection.
 Risk Factor: A variable associated with an increased risk of disease or infection.</td>
 							<td>Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.</td>
-							<td>Asthma; Pregnancy; Smoker</td>
+							<td>Asthma; Pregnancy; Smoking</td>
 							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access']</td>
 						</tr>
 
@@ -619,7 +619,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td class="label">exposure event</td>
 							<td>Event leading to exposure.</td>
 							<td>Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team.</td>
-							<td>Mass gathering (convention)</td>
+							<td>Convention</td>
 							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access']</td>
 						</tr>