diff --git a/script/main.js b/script/main.js index 9e71f7ba..32a651e1 100644 --- a/script/main.js +++ b/script/main.js @@ -11,7 +11,7 @@ * main.html?template=test_template * */ -const VERSION = '0.13.21'; +const VERSION = '0.13.22'; const TEMPLATES = { 'CanCOGeN Covid-19': {'folder': 'canada_covid19', 'status': 'published'}, 'PHAC Dexa (ALPHA)': {'folder': 'phac_dexa', 'status': 'draft'}, diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index 166be732..c7dcb05d 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -5,7 +5,7 @@ var DATA = [ { "fieldName": "specimen collector sample ID", "capitalize": "", - "ontology_id": "", + "ontology_id": "GENEPIO_0001123", "datatype": "xs:unique", "source": "", "dataStatus": [ @@ -33,9 +33,6 @@ var DATA = [ } ], "NML_LIMS": [ - { - "field": "VD_LAB_NUMBER" - }, { "field": "TEXT_ID" } @@ -47,24 +44,45 @@ var DATA = [ ] } }, + { + "fieldName": "Switch Health ID", + "capitalize": "", + "ontology_id": "GENEPIO_0001149", + "datatype": "xs:token", + "source": "", + "dataStatus": null, + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "The identifier assigned to a sample by Switch Health.", + "guidance": "Store the identifier supplied by Seitch Health for the sample.", + "examples": "SHK123456", + "exportField": { + "NML_LIMS": [ + { + "field": "VD_LAB_NUMBER" + } + ] + } + }, { "fieldName": "NML submitted specimen primary ID", "capitalize": "", - "ontology_id": "", + "ontology_id": "GENEPIO_0001125", "datatype": "xs:token", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "The primary ID of the specimen submitted thorough LaSER.", + "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" }, { "fieldName": "NML related specimen primary ID", "capitalize": "", - "ontology_id": "", + "ontology_id": "GENEPIO_0001128", "datatype": "xs:token", "source": "", "dataStatus": [ @@ -77,7 +95,7 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "The primary ID of the related specimen previously submitted thorough LaSER", + "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", "examples": "SR20-12345", "exportField": { @@ -94,7 +112,7 @@ var DATA = [ { "fieldName": "IRIDA sample name", "capitalize": "", - "ontology_id": "", + "ontology_id": "GENEPIO_0001131", "datatype": "xs:token", "source": "", "dataStatus": null, @@ -108,7 +126,7 @@ var DATA = [ { "fieldName": "umbrella bioproject accession", "capitalize": "UPPER", - "ontology_id": "", + "ontology_id": "GENEPIO_0001133", "datatype": "select", "source": "", "dataStatus": null, @@ -125,7 +143,7 @@ var DATA = [ { "fieldName": "bioproject accession", "capitalize": "UPPER", - "ontology_id": "", + "ontology_id": "GENEPIO_0001136", "datatype": "xs:token", "source": "", "dataStatus": null, @@ -156,7 +174,7 @@ var DATA = [ { "fieldName": "biosample accession", "capitalize": "UPPER", - "ontology_id": "", + "ontology_id": "GENEPIO_0001139", "datatype": "xs:token", "source": "", "dataStatus": null, @@ -182,7 +200,7 @@ var DATA = [ { "fieldName": "SRA accession", "capitalize": "UPPER", - "ontology_id": "", + "ontology_id": "GENEPIO_0001142", "datatype": "xs:token", "source": "", "dataStatus": null, @@ -208,7 +226,7 @@ var DATA = [ { "fieldName": "GenBank accession", "capitalize": "UPPER", - "ontology_id": "", + "ontology_id": "GENEPIO_0001145", "datatype": "xs:token", "source": "", "dataStatus": null, @@ -229,7 +247,7 @@ var DATA = [ { "fieldName": "GISAID accession", "capitalize": "UPPER", - "ontology_id": "", + "ontology_id": "GENEPIO_0001147", "datatype": "xs:token", "source": "", "dataStatus": null, @@ -1580,7 +1598,7 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "required", - "description": "The type of specimen submitted to the NML for testing.", + "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "guidance": "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 \u201cNot Applicable\u201d.", "examples": "swab", "exportField": { @@ -1649,7 +1667,7 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "The relationship of the related specimen to the previous submission.", + "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", "exportField": { @@ -5613,6 +5631,13 @@ var DATA = [ "description": "The role of the host in relation to the exposure setting.", "guidance": "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.", "examples": "Patient", + "exportField": { + "NML_LIMS": [ + { + "field": "PH_HOST_ROLE" + } + ] + }, "schema:ItemList": { "Attendee": { "schema:ItemList": { @@ -5649,6 +5674,7 @@ var DATA = [ "Laboratory Worker": {}, "Rotational Worker": {}, "Seasonal Worker": {}, + "Transport Truck Driver": {}, "Veterinarian": {} } }, diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index 30fce117..a69790af 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -1,16 +1,17 @@ Ontology ID parent class label datatype source data status requirement min value max value capitalize description guidance examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE ID SC % - Database Identifiers - 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 VD_LAB_NUMBER;TEXT_ID sample_name - Database Identifiers NML submitted specimen primary ID xs:token The primary ID of the specimen submitted thorough LaSER. Store the identifier for the specimen submitted through the NML LaSER system. SR20-12345 - 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 LaSER Store the primary ID of the related specimen previously submitted thorough LaSER SR20-12345 Related Specimen ID;Related Specimen Relationship Type - 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 - 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 - 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 - Database Identifiers biosample accession xs:token UPPER The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers SRA accession xs:token UPPER The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers GenBank accession xs:token UPPER The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession - Database Identifiers GISAID accession xs:token UPPER The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession +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 +GENEPIO_0001149 Database Identifiers Switch Health ID xs:token The identifier assigned to a sample by Switch Health. Store the identifier supplied by Seitch Health for the sample. SHK123456 VD_LAB_NUMBER +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 +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 +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 +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 +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 +GENEPIO_0001139 Database Identifiers biosample accession xs:token UPPER The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION +GENEPIO_0001142 Database Identifiers SRA accession xs:token UPPER The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION +GENEPIO_0001145 Database Identifiers GenBank accession xs:token UPPER The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession +GENEPIO_0001147 Database Identifiers GISAID accession xs:token UPPER The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession Sample collection and processing Sample collection and processing sample collected by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name collected_by Sample collection and processing sample collector contact email xs:token The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca @@ -28,8 +29,8 @@ ID SC % 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/xxxxx/2020”. hCov-19/CANADA/prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name 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 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 description - Sample collection and processing NML submitted specimen type select required The type of specimen submitted to the 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 - 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 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 + 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 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 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 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 @@ -77,7 +78,7 @@ ID SC % Host exposure information travel history xs:token Travel history 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. Convention Additional location information Exposure Event PH_EXPOSURE Host exposure information exposure contact level select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access 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 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 PH_HOST_ROLE 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 PH_EXPOSURE Host exposure information exposure details xs:token Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver PH_EXPOSURE_DETAILS @@ -810,6 +811,7 @@ OMRSE:00000008? host gender Male Work Laboratory Worker Work Rotational Worker Work Seasonal Worker + Work Transport Truck Driver Work Veterinarian host role Social role Social role Acquaintance of case diff --git a/template/canada_covid19/reference.html b/template/canada_covid19/reference.html index a4dece34..1a690d28 100644 --- a/template/canada_covid19/reference.html +++ b/template/canada_covid19/reference.html @@ -43,9 +43,18 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission + + Switch Health ID + The identifier assigned to a sample by Switch Health. + Store the identifier supplied by Seitch Health for the sample. + SHK123456 + None + + + NML submitted specimen primary ID - The primary ID of the specimen submitted thorough LaSER. + 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 None @@ -54,7 +63,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission NML related specimen primary ID - The primary ID of the related specimen previously submitted thorough LaSER + 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 ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] @@ -274,7 +283,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission NML submitted specimen type - The type of specimen submitted to the NML for testing. + 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 [''] @@ -283,7 +292,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission NML related specimen relationship type - The relationship of the related specimen to the previous submission. + 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 None