diff --git a/script/main.js b/script/main.js index 20a45494..e0ba4c33 100644 --- a/script/main.js +++ b/script/main.js @@ -11,7 +11,7 @@ * main.html?template=test_template * */ -const VERSION = '0.14.5'; +const VERSION = '0.14.6'; 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 c37f66fb..8de3ce4b 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -92,28 +92,28 @@ var DATA = [ } }, { - "fieldName": "NML submitted specimen primary ID", + "fieldName": "case ID", "capitalize": "", - "ontology_id": "GENEPIO:0001125", - "datatype": "xs:token", + "ontology_id": "GENEPIO:0100281", + "datatype": "xs:unique", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "", - "description": "The primary ID of the specimen submitted thorough the National Microbiology Laboratory (NML) LaSER.", - "guidance": "Store the identifier for the specimen submitted through the NML LaSER system.", - "examples": "SR20-12345", + "requirement": "recommended", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "guidance": "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing.", + "examples": "ABCD1234", "exportField": { "NML_LIMS": [ { - "field": "NML submitted specimen primary ID" + "field": "case ID" } ] } }, { - "fieldName": "NML related specimen primary ID", + "fieldName": "Related specimen primary ID", "capitalize": "", "ontology_id": "GENEPIO:0001128", "datatype": "xs:token", @@ -128,8 +128,8 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "The primary ID of the related specimen previously submitted thorough the National Microbiology Laboratory (NML) LaSER.", - "guidance": "Store the primary ID of the related specimen previously submitted thorough LaSER", + "description": "The primary ID of a related specimen previously submitted to the repository.", + "guidance": "Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system.", "examples": "SR20-12345", "exportField": { "CNPHI": [ @@ -396,6 +396,7 @@ var DATA = [ } }, "BCCDC Public Health Laboratory": {}, + "Dynacare": {}, "Dynacare (Manitoba)": {}, "Dynacare (Brampton)": {}, "Eastern Ontario Regional Laboratory Association": {}, @@ -526,6 +527,8 @@ var DATA = [ "BCCDC Public Health Laboratory": {}, "Canadore College": {}, "The Centre for Applied Genomics (TCAG)": {}, + "Dynacare": {}, + "Dynacare (Brampton)": {}, "Dynacare (Manitoba)": {}, "The Hospital for Sick Children (SickKids)": {}, "Laboratoire de sant\u00e9 publique du Qu\u00e9bec (LSPQ)": {}, @@ -1922,7 +1925,7 @@ var DATA = [ } }, { - "fieldName": "NML related specimen relationship type", + "fieldName": "Related specimen relationship type", "capitalize": "", "ontology_id": "GENEPIO:0001209", "datatype": "select", @@ -1931,9 +1934,9 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "The relationship of the related specimen to the previous National Microbiology Laboratory (NML) 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": "Follow-up", + "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", + "guidance": "Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system.", + "examples": "Specimen sampling methods testing", "exportField": { "CNPHI": [ { @@ -1951,9 +1954,14 @@ var DATA = [ "Convalescent": {}, "Familial": {}, "Follow-up": { - "ontology_id": "EFO:0009642" + "ontology_id": "EFO:0009642", + "schema:ItemList": { + "Reinfection testing": {} + } }, - "Previously Submitted": {} + "Previously Submitted": {}, + "Sequencing/bioinformatics methods development/validation": {}, + "Specimen sampling methods testing": {} } }, { @@ -3619,10 +3627,10 @@ var DATA = [ "Non-binary gender": { "ontology_id": "GSSO:000132" }, - "Transgender (Male to Female)": { + "Transgender (assigned male at birth)": { "ontology_id": "GSSO:004004" }, - "Transgender (Female to Male)": { + "Transgender (assigned female at birth)": { "ontology_id": "GSSO:004005" }, "Undeclared": {}, @@ -5454,29 +5462,9 @@ var DATA = [ } } }, - "Funeral Home": { - "ontology_id": "ECTO NTR" - }, - "Place of Worship": { - "ontology_id": "ECTO NTR", - "schema:ItemList": { - "Church": { - "ontology_id": "ECTO NTR" - }, - "Mosque": { - "ontology_id": "ECTO NTR" - }, - "Temple": { - "ontology_id": "ECTO NTR" - } - } - }, "Nursery": { "ontology_id": "ECTO NTR" }, - "Household": { - "ontology_id": "ECTO NTR" - }, "Community Service Centre": { "ontology_id": "ECTO NTR" }, @@ -5492,6 +5480,9 @@ var DATA = [ "First Nations Reserve": { "ontology_id": "ECTO NTR" }, + "Funeral Home": { + "ontology_id": "ECTO NTR" + }, "Group Home": { "ontology_id": "ECTO NTR" }, @@ -5538,6 +5529,9 @@ var DATA = [ } } }, + "Household": { + "ontology_id": "ECTO NTR" + }, "Insecure Housing (Homeless)": { "ontology_id": "ECTO NTR" }, @@ -5572,6 +5566,20 @@ var DATA = [ "Petting zoo": { "ontology_id": "ECTO:5000008" }, + "Place of Worship": { + "ontology_id": "ECTO NTR", + "schema:ItemList": { + "Church": { + "ontology_id": "ECTO NTR" + }, + "Mosque": { + "ontology_id": "ECTO NTR" + }, + "Temple": { + "ontology_id": "ECTO NTR" + } + } + }, "Restaurant": { "ontology_id": "ECTO:1000040" }, @@ -5675,9 +5683,8 @@ var DATA = [ ] }, "schema:ItemList": { - "Yes": {}, - "No": {}, - "Unknown": {} + "Prior antiviral treatment": {}, + "No prior antiviral treatment": {} } }, { @@ -6947,7 +6954,8 @@ var DATA = [ }, "Variant of Interest (VOI)": { "ontology_id": "GENEPIO" - } + }, + "Variant Under Monitoring": {} } }, { diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index bcce30f5..b5444b6b 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -4,8 +4,8 @@ GENEPIO:0001122 Database Identifiers GENEPIO:0001123 Database Identifiers specimen collector sample ID xs:unique Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID GENEPIO:0001202 Database Identifiers third party lab service provider name xs:token The name of the third party company or laboratory that provided services. Store the sample identifier supplied by the third party services provider. Switch Health HC_TEXT5 GENEPIO:0001149 Database Identifiers third party lab sample ID xs:token The identifier assigned to a sample by a third party service provider. SHK123456 PH_ID_NUMBER_PRIMARY -GENEPIO:0001125 Database Identifiers NML submitted specimen primary ID xs:token The primary ID of the specimen submitted thorough the National Microbiology Laboratory (NML) LaSER. Store the identifier for the specimen submitted through the NML LaSER system. SR20-12345 NML submitted specimen primary ID -GENEPIO:0001128 Database Identifiers NML related specimen primary ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The primary ID of the related specimen previously submitted thorough the National Microbiology Laboratory (NML) LaSER. Store the primary ID of the related specimen previously submitted thorough LaSER SR20-12345 Related Specimen ID;Related Specimen Relationship Type NML related specimen primary ID +GENEPIO:0100281 Database Identifiers case ID xs:unique recommended The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 case ID +GENEPIO:0001128 Database Identifiers Related specimen primary ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type NML related specimen primary ID GENEPIO:0001131 Database Identifiers IRIDA sample name xs:token The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name GENEPIO:0001133 Database Identifiers umbrella bioproject accession select UPPER The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession GENEPIO:0001136 Database Identifiers bioproject accession xs:token UPPER The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession @@ -31,7 +31,7 @@ GENEPIO:0001195 Sample collection and processing isolate xs:token Not Applicab 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 -GENEPIO:0001209 Sample collection and processing NML related specimen relationship type select The relationship of the related specimen to the previous National Microbiology Laboratory (NML) 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 +GENEPIO:0001209 Sample collection and processing Related specimen relationship type select The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Specimen sampling methods testing Related Specimen ID;Related Specimen Relationship Type GENEPIO:0001211 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 PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material GENEPIO:0001214 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 PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part GENEPIO:0001216 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 PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product @@ -293,11 +293,14 @@ OBI:0001010 NML submitted specimen type Nucleic acid GENEPIO:0001619 NML submitted specimen type Not Applicable -HP:0011009 NML related specimen relationship type Acute - NML related specimen relationship type Convalescent - NML related specimen relationship type Familial -EFO:0009642 NML related specimen relationship type Follow-up - NML related specimen relationship type Previously Submitted +HP:0011009 Related specimen relationship type Acute + Related specimen relationship type Convalescent + Related specimen relationship type Familial +EFO:0009642 Related specimen relationship type Follow-up + Follow-up Reinfection testing + Related specimen relationship type Previously Submitted + Related specimen relationship type Sequencing/bioinformatics methods development/validation + Related specimen relationship type Specimen sampling methods testing VO:0004925 pre-existing conditions and risk factors Age 60+ @@ -394,6 +397,7 @@ NCIT:C157332 Transplant Kidney transplant GENEPIO variant designation Variant of Concern (VOC) GENEPIO variant designation Variant of Interest (VOI) + variant designation Variant Under Monitoring CIDO:0000019 variant evidence RT-qPCR CIDO:0000027 variant evidence Sequencing @@ -530,9 +534,8 @@ UBERON:0001827 body product Tear UBERON:0006530 body product Fluid (seminal) UBERON:0001913 body product Breast Milk - prior SARS-CoV-2 infection Yes - prior SARS-CoV-2 infection No - prior SARS-CoV-2 infection Unknown + prior SARS-CoV-2 infection Prior antiviral treatment + prior SARS-CoV-2 infection No prior antiviral treatment ENVO:03501208 environmental material Air vent @@ -762,8 +765,8 @@ GENEPIO NTR host age bin 100+ 90+ NCIT:C46110 host gender Female NCIT:C46109 host gender Male GSSO:000132 host gender Non-binary gender -GSSO:004004 host gender Transgender (Male to Female) -GSSO:004005 host gender Transgender (Female to Male) +GSSO:004004 host gender Transgender (assigned male at birth) +GSSO:004005 host gender Transgender (assigned female at birth) host gender Undeclared host gender Unknown @@ -849,18 +852,13 @@ ECTO:1000033 Occupational, Residency or Patronage Exposure Abbatoir ECTO NTR Occupational, Residency or Patronage Exposure Animal Rescue ECTO NTR Occupational, Residency or Patronage Exposure Childcare ECTO NTR Childcare Daycare -ECTO NTR Occupational, Residency or Patronage Exposure Funeral Home -ECTO NTR Occupational, Residency or Patronage Exposure Place of Worship -ECTO NTR Place of Worship Church -ECTO NTR Place of Worship Mosque -ECTO NTR Place of Worship Temple -ECTO NTR Occupational, Residency or Patronage Exposure Nursery -ECTO NTR Occupational, Residency or Patronage Exposure Household +ECTO NTR Occupational, Residency or Patronage Exposure Nursery ECTO NTR Occupational, Residency or Patronage Exposure Community Service Centre ECTO NTR Occupational, Residency or Patronage Exposure Correctional Facility ECTO NTR Occupational, Residency or Patronage Exposure Dormitory ECTO:1000034 Occupational, Residency or Patronage Exposure Farm ECTO NTR Occupational, Residency or Patronage Exposure First Nations Reserve +ECTO NTR Occupational, Residency or Patronage Exposure Funeral Home ECTO NTR Occupational, Residency or Patronage Exposure Group Home ECTO NTR Occupational, Residency or Patronage Exposure Healthcare Setting ECTO NTR Healthcare Setting Ambulance @@ -875,6 +873,7 @@ ECTO:1000036 Healthcare Setting Laboratory ECTO NTR Healthcare Setting Long-Term Care Facility ECTO NTR Healthcare Setting Pharmacy ECTO NTR Healthcare Setting Physician's Office +ECTO NTR Occupational, Residency or Patronage Exposure Household ECTO NTR Occupational, Residency or Patronage Exposure Insecure Housing (Homeless) ECTO NTR Occupational, Residency or Patronage Exposure Occupational Exposure ECTO NTR Occupational Exposure Worksite @@ -885,6 +884,10 @@ ECTO NTR Outdoors Hiking Trail ECTO:6000030 Outdoors Hunting Ground ECTO NTR Outdoors Ski Resort ECTO:5000008 Occupational, Residency or Patronage Exposure Petting zoo +ECTO NTR Occupational, Residency or Patronage Exposure Place of Worship +ECTO NTR Place of Worship Church +ECTO NTR Place of Worship Mosque +ECTO NTR Place of Worship Temple ECTO:1000040 Occupational, Residency or Patronage Exposure Restaurant ECTO:1000041 Occupational, Residency or Patronage Exposure Retail Store ECTO NTR Occupational, Residency or Patronage Exposure School @@ -991,6 +994,8 @@ PR NTR? gene name 1 orf14 orf14 sequence submitted by BCCDC Public Health Laboratory sequence submitted by Canadore College sequence submitted by The Centre for Applied Genomics (TCAG) + sequence submitted by Dynacare + sequence submitted by Dynacare (Brampton) sequence submitted by Dynacare (Manitoba) sequence submitted by The Hospital for Sick Children (SickKids) sequence submitted by Laboratoire de santé publique du Québec (LSPQ) @@ -1014,6 +1019,7 @@ PR NTR? gene name 1 orf14 orf14 Alberta Precision Labs (APL) Alberta ProvLab North (APLN) Alberta Precision Labs (APL) Alberta ProvLab South (APLS) sample collected by BCCDC Public Health Laboratory + sample collected by Dynacare sample collected by Dynacare (Manitoba) sample collected by Dynacare (Brampton) sample collected by Eastern Ontario Regional Laboratory Association diff --git a/template/canada_covid19/reference.html b/template/canada_covid19/reference.html index 13c9573c..9503ec2c 100644 --- a/template/canada_covid19/reference.html +++ b/template/canada_covid19/reference.html @@ -62,18 +62,18 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission - NML submitted specimen primary ID - The primary ID of the specimen submitted thorough the National Microbiology Laboratory (NML) LaSER. - Store the identifier for the specimen submitted through the NML LaSER system. - SR20-12345 + case ID + The identifier used to specify an epidemiologically detected case of disease. + Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. + ABCD1234 None - NML related specimen primary ID - The primary ID of the related specimen previously submitted thorough the National Microbiology Laboratory (NML) LaSER. - Store the primary ID of the related specimen previously submitted thorough LaSER + Related specimen primary ID + The primary ID of a related specimen previously submitted to the repository. + Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] @@ -300,10 +300,10 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission - NML related specimen relationship type - The relationship of the related specimen to the previous National Microbiology Laboratory (NML) 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 relationship type + The relationship of the current specimen to the specimen/sample previously submitted to the repository. + Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. + Specimen sampling methods testing None