diff --git a/script/main.js b/script/main.js index 7927d37d..f56a4278 100644 --- 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 index 7efd1e43..65e0490e 100644 --- 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 index 2b874edc..b7d85970 100644 --- 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 index a692a5c9..51efdcd7 100644 --- a/template/canada_covid19/reference.html +++ b/template/canada_covid19/reference.html @@ -1191,7 +1191,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission 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 - None + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access', 'Indeterminate'] @@ -1218,7 +1218,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission 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 - None + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access', 'Indeterminate'] @@ -1245,7 +1245,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission 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 - None + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access', 'Indeterminate']