Added Diagnostic PCR Ct Value field null values.

including extra Indeterminate value.
cidgoh · Sep 4, 2021 · bd22758 · bd22758
1 parent 3793b91
commit bd22758
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Showing 4 changed files with 35 additions and 11 deletions.
diff --git a/script/main.js b/script/main.js
@@ -11,7 +11,7 @@
  * main.html?template=test_template
  *
  */
-const VERSION = '0.13.33';
+const VERSION = '0.14.0';
 const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION;
 const TEMPLATES = {
   'CanCOGeN Covid-19': {'folder': 'canada_covid19', 'status': 'published'},

diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js
@@ -2280,6 +2280,9 @@ var DATA = [
           "VirusSeq_Portal": [
             {
               "field": "isolate"
+            },
+            {
+              "field": "fasta header name"
             }
           ]
         }
@@ -8849,7 +8852,14 @@ var DATA = [
         "ontology_id": "GENEPIO_0001509",
         "datatype": "xs:decimal",
         "source": "",
-        "dataStatus": null,
+        "dataStatus": [
+          "Not Applicable",
+          "Missing",
+          "Not Collected",
+          "Not Provided",
+          "Restricted Access",
+          "Indeterminate"
+        ],
         "xs:minInclusive": "",
         "xs:maxInclusive": "",
         "requirement": "",
@@ -8937,7 +8947,14 @@ var DATA = [
         "ontology_id": "GENEPIO_0001512",
         "datatype": "xs:decimal",
         "source": "",
-        "dataStatus": null,
+        "dataStatus": [
+          "Not Applicable",
+          "Missing",
+          "Not Collected",
+          "Not Provided",
+          "Restricted Access",
+          "Indeterminate"
+        ],
         "xs:minInclusive": "",
         "xs:maxInclusive": "",
         "requirement": "",
@@ -9015,7 +9032,14 @@ var DATA = [
         "ontology_id": "GENEPIO_0001515",
         "datatype": "xs:decimal",
         "source": "",
-        "dataStatus": null,
+        "dataStatus": [
+          "Not Applicable",
+          "Missing",
+          "Not Collected",
+          "Not Provided",
+          "Restricted Access",
+          "Indeterminate"
+        ],
         "xs:minInclusive": "",
         "xs:maxInclusive": "",
         "requirement": "",

diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv
@@ -27,7 +27,7 @@ GENEPIO_0001181		Sample collection and processing	geo_loc_name (country)	select
 GENEPIO_0001185		Sample collection and processing	geo_loc_name (state/province/territory)	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The province/territory where the sample was collected.	Provide the province/territory name from the controlled vocabulary provided.	Saskatchewan		Patient Province	HC_PROVINCE	geo_loc_name	geo_loc_name (state/province/territory)
 GENEPIO_0001189		Sample collection and processing	geo_loc_name (city)	xs:token							The city where the sample was collected.	Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz	Medicine Hat		Patient City	geo_loc_name (city)		
 GENEPIO_0001191		Sample collection and processing	organism	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				Taxonomic name of the organism.	Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template.	Severe acute respiratory syndrome coronavirus 2		Pathogen	HC_CURRENT_ID	organism	organism
-GENEPIO_0001195		Sample collection and processing	isolate	xs:token		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				Identifier of the specific isolate.	Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”.	hCov-19/CANADA/BC-prov_rona_99/2020	Virus name	GISAID Virus Name	RESULT - CANCOGEN_SUBMISSIONS	isolate;GISAID_virus_name	isolate
+GENEPIO_0001195		Sample collection and processing	isolate	xs:token		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				Identifier of the specific isolate.	Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”.	hCov-19/CANADA/BC-prov_rona_99/2020	Virus name	GISAID Virus Name	RESULT - CANCOGEN_SUBMISSIONS	isolate;GISAID_virus_name	isolate;fasta header name
 GENEPIO_0001198		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	HC_SAMPLE_CATEGORY	purpose_of_sampling	purpose of sampling
 GENEPIO_0001200		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. 		Details on the Reason for Sampling	PH_SAMPLING_DETAILS	description	purpose of sampling details
 GENEPIO_0001204		Sample collection and processing	NML submitted specimen type	select			required				The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.	This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”.	swab		Specimen Type	PH_SPECIMEN_TYPE		
@@ -140,13 +140,13 @@ GENEPIO_0001505		Lineage and Variant information	variant evidence details	xs:tok
 GENEPIO_0001506			Pathogen diagnostic testing															
 GENEPIO_0001507		Pathogen diagnostic testing	gene name 1	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The name of the gene used in the diagnostic RT-PCR test.	Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI	E gene (orf4)		Gene Target 1	SUBMITTED_RESLT - Gene Target #1	gene_name_1	gene name
 GENEPIO_0001508		Pathogen diagnostic testing	diagnostic pcr protocol 1	xs:token							The name and version number of the protocol used for diagnostic marker amplification.	The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.	EGenePCRTest 2					
-GENEPIO_0001509		Pathogen diagnostic testing	diagnostic pcr Ct value 1	xs:decimal							The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the diagnostic RT-PCR test.	21		Gene Target 1 CT Value	SUBMITTED_RESLT - Gene Target #1 CT Value	diagnostic_PCR_CT_value_1	diagnostic pcr Ct value 
+GENEPIO_0001509		Pathogen diagnostic testing	diagnostic pcr Ct value 1	xs:decimal		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access; Indeterminate					The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the diagnostic RT-PCR test.	21		Gene Target 1 CT Value	SUBMITTED_RESLT - Gene Target #1 CT Value	diagnostic_PCR_CT_value_1	diagnostic pcr Ct value 
 GENEPIO_0001510		Pathogen diagnostic testing	gene name 2	select	gene name 1	Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The name of the gene used in the diagnostic RT-PCR test.	Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI	RdRp gene (nsp12)		Gene Target 2	SUBMITTED_RESLT - Gene Target #2	gene_name_2	
 GENEPIO_0001511		Pathogen diagnostic testing	diagnostic pcr protocol 2	xs:token							The name and version number of the protocol used for diagnostic marker amplification.	The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.	RdRpGenePCRTest 3					
-GENEPIO_0001512		Pathogen diagnostic testing	diagnostic pcr Ct value 2	xs:decimal							The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the second diagnostic RT-PCR test.	36		Gene Target 2 CT Value	SUBMITTED_RESLT - Gene Target #2 CT Value	diagnostic_PCR_CT_value_2	
+GENEPIO_0001512		Pathogen diagnostic testing	diagnostic pcr Ct value 2	xs:decimal		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access; Indeterminate					The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the second diagnostic RT-PCR test.	36		Gene Target 2 CT Value	SUBMITTED_RESLT - Gene Target #2 CT Value	diagnostic_PCR_CT_value_2	
 GENEPIO_0001513		Pathogen diagnostic testing	gene name 3	select	gene name 1	Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The name of the gene used in the diagnostic RT-PCR test.	Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI	RdRp gene (nsp12)		Gene Target 3	SUBMITTED_RESLT - Gene Target #3		
 GENEPIO_0001514		Pathogen diagnostic testing	diagnostic pcr protocol 3	xs:token							The name and version number of the protocol used for diagnostic marker amplification.	The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.	RdRpGenePCRTest 3					
-GENEPIO_0001515		Pathogen diagnostic testing	diagnostic pcr Ct value 3	xs:decimal							The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the second diagnostic RT-PCR test.	30		Gene Target 3 CT Value	SUBMITTED_RESLT - Gene Target #3 CT Value		
+GENEPIO_0001515		Pathogen diagnostic testing	diagnostic pcr Ct value 3	xs:decimal		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access; Indeterminate					The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the second diagnostic RT-PCR test.	30		Gene Target 3 CT Value	SUBMITTED_RESLT - Gene Target #3 CT Value		
 GENEPIO_0001516			Contributor acknowledgement															
 GENEPIO_0001517		Contributor acknowledgement	authors	xs:token			recommended				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		
 GENEPIO_0001518		Contributor acknowledgement	DataHarmonizer provenance	provenance							The DataHarmonizer software version provenance.	The current software 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 provenance: v0.13.21	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		

diff --git a/template/canada_covid19/reference.html b/template/canada_covid19/reference.html
@@ -1191,7 +1191,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td>The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.</td>
 							<td>Provide the CT value of the sample from the diagnostic RT-PCR test.</td>
 							<td>21</td>
-							<td>None</td>
+							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access', 'Indeterminate']</td>
 						</tr>
 
 
@@ -1218,7 +1218,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td>The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.</td>
 							<td>Provide the CT value of the sample from the second diagnostic RT-PCR test.</td>
 							<td>36</td>
-							<td>None</td>
+							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access', 'Indeterminate']</td>
 						</tr>
 
 
@@ -1245,7 +1245,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
 							<td>The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.</td>
 							<td>Provide the CT value of the sample from the second diagnostic RT-PCR test.</td>
 							<td>30</td>
-							<td>None</td>
+							<td>['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access', 'Indeterminate']</td>
 						</tr>