diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index edeb5ce9..6db8d2a9 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -2228,7 +2228,9 @@ var DATA = [ "Severe acute respiratory syndrome coronavirus 2": { "ontology_id": "NCBITaxon_2697049" }, - "RaTG13": {}, + "RaTG13": { + "ontology_id": "NCBITaxon_2709072" + }, "RmYN02": {} } }, @@ -2380,9 +2382,7 @@ var DATA = [ "ontology_id": "GENEPIO_0001204", "datatype": "select", "source": "", - "dataStatus": [ - "" - ], + "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "required", @@ -2691,6 +2691,7 @@ var DATA = [ } }, "Buccal mucosa": { + "ontology_id": "UBERON_0006956 ", "exportField": { "NML_LIMS": [ { @@ -2799,6 +2800,7 @@ var DATA = [ } }, "Nasal Cavity": { + "ontology_id": "UBERON_0001707 ", "exportField": { "NML_LIMS": [ { @@ -4508,7 +4510,9 @@ var DATA = [ ] } }, - "Mink": {}, + "Mink": { + "ontology_id": "NCBITaxon_452646" + }, "Pangolin": { "ontology_id": "NCBITaxon_9973", "exportField": { @@ -4672,6 +4676,7 @@ var DATA = [ }, "schema:ItemList": { "Asymptomatic": { + "ontology_id": "NCIT_C3833", "exportField": { "NML_LIMS": [ { @@ -4681,6 +4686,7 @@ var DATA = [ } }, "Deceased": { + "ontology_id": "NCIT_C28554", "exportField": { "NML_LIMS": [ { @@ -4690,6 +4696,7 @@ var DATA = [ } }, "Healthy": { + "ontology_id": "NCIT_C115935", "exportField": { "NML_LIMS": [ { @@ -4899,7 +4906,9 @@ var DATA = [ ] }, "schema:ItemList": { - "COVID-19": {} + "COVID-19": { + "ontology_id": "DOID_0080600" + } } }, { @@ -5106,7 +5115,7 @@ var DATA = [ }, "schema:ItemList": { "Female": { - "ontology_id": "OMRSE:00000009?", + "ontology_id": "NCIT_C46110", "exportField": { "NML_LIMS": [ { @@ -5116,7 +5125,7 @@ var DATA = [ } }, "Male": { - "ontology_id": "OMRSE:00000008?", + "ontology_id": "NCIT_C46109", "exportField": { "NML_LIMS": [ { @@ -7825,7 +7834,7 @@ var DATA = [ "exportField": { "NML_LIMS": [ { - "field": "dehosting method" + "field": "PH_DEHOSTING_METHOD" } ], "VirusSeq_Portal": [ @@ -8274,7 +8283,7 @@ var DATA = [ ], "NML_LIMS": [ { - "field": "bioinformatics protocol" + "field": "PH_BIOINFORMATICS_PROTOCOL" } ], "VirusSeq_Portal": [ @@ -8410,8 +8419,12 @@ var DATA = [ ] }, "schema:ItemList": { - "RT-qPCR": {}, - "Sequencing": {} + "RT-qPCR": { + "ontology_id": "CIDO_0000019" + }, + "Sequencing": { + "ontology_id": "CIDO_0000027" + } } }, { diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index 13d3e43d..a861205c 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -30,7 +30,7 @@ GENEPIO_0001191 Sample collection and processing organism select Not Applicabl 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/xxxxx/2020”. hCov-19/CANADA/prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate 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_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_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 @@ -110,7 +110,7 @@ GENEPIO_0001456 Sequencing amplicon pcr primer scheme xs:token The specif GENEPIO_0001457 Bioinformatics and QC metrics GENEPIO_0001458 Bioinformatics and QC metrics raw sequence data processing method xs:token recommended The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw sequence data processing method raw sequence data processing method -GENEPIO_0001459 Bioinformatics and QC metrics dehosting method xs:token The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting method dehosting method +GENEPIO_0001459 Bioinformatics and QC metrics dehosting method xs:token The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method GENEPIO_0001460 Bioinformatics and QC metrics consensus sequence name xs:token The name of the consensus sequence. Provide the name and version number of the consensus sequence. ncov123assembly3 consensus sequence name GENEPIO_0001461 Bioinformatics and QC metrics consensus sequence filename xs:token The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta consensus sequence filename GENEPIO_0001462 Bioinformatics and QC metrics consensus sequence filepath xs:token The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta consensus sequence filepath @@ -129,7 +129,7 @@ GENEPIO_0001482 Bioinformatics and QC metrics number of base pairs sequenced xs GENEPIO_0001483 Bioinformatics and QC metrics consensus genome length xs:nonNegativeInteger Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 38677 consensus genome length GENEPIO_0001484 Bioinformatics and QC metrics Ns per 100 kbp xs:decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Provide a numerical value (no need to include units). 330 Ns per 100 kbp GENEPIO_0001485 Bioinformatics and QC metrics reference genome accession xs:token A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 reference genome accession reference genome accession -GENEPIO_0001489 Bioinformatics and QC metrics bioinformatics protocol xs:token The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members Bioinformatics Protocol bioinformatics protocol bioinformatics protocol +GENEPIO_0001489 Bioinformatics and QC metrics bioinformatics protocol xs:token The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol GENEPIO_0001498 Lineage and Variant information GENEPIO_0001500 Lineage and Variant information lineage/clade name xs:token The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 PH_LINEAGE_CLADE_NAME GENEPIO_0001501 Lineage and Variant information lineage/clade analysis software name xs:token The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin PH_LINEAGE_CLADE_SOFTWARE @@ -396,8 +396,9 @@ HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated resp variant designation Variant of Concern (VOC) variant designation Variant of Interest (VOI) - variant evidence RT-qPCR - variant evidence Sequencing +CIDO_0000019 variant evidence RT-qPCR +CIDO_0000027 variant evidence Sequencing + complications Abnormal blood oxygen level complications Acute respiratory failure @@ -496,7 +497,7 @@ UBERON_0000479 anatomical material Tissue TISSUE UBERON_0001245 anatomical part Anus ANUS - anatomical part Buccal mucosa BUCCAL_MUCOSA +UBERON_0006956 anatomical part Buccal mucosa BUCCAL_MUCOSA UBERON_0002114 anatomical part Duodenum DUODENUM UBERON_0000970 anatomical part Eye EYE anatomical part Intestine INTESTINE @@ -507,7 +508,7 @@ UBERON_0001557 anatomical part Upper respiratory tract UPPER UBERON_2001427 Upper respiratory tract Anterior Nares ANTERIOR_NARES UBERON_0001043 Upper respiratory tract Esophagus ESOPHAGUS UBERON_0002453 Upper respiratory tract Ethmoid sinus ETHMOID_SINUS - Upper respiratory tract Nasal Cavity NASAL_CAVITY +UBERON_0001707 Upper respiratory tract Nasal Cavity NASAL_CAVITY UBERON_0005921 Nasal Cavity Middle Nasal Turbinate MIDDLE_NASAL UBERON_0005922 Nasal Cavity Inferior Nasal Turbinate INFERIOR_NASAL UBERON_0001728 Upper respiratory tract Nasopharynx (NP) NASOPHARYNX_NP @@ -663,16 +664,16 @@ NCBITaxon_9673 host (common name) Civets CIVETS NCBITaxon_9913 host (common name) Cow bovine NCBITaxon_9615 host (common name) Dog NCBITaxon_9689 host (common name) Lion LION - host (common name) Mink +NCBITaxon_452646 host (common name) Mink NCBITaxon_9973 host (common name) Pangolin PANGOLIN NCBITaxon_9823 host (common name) Pig porcine NCBITaxon_8930 host (common name) Pigeon NCBITaxon_9694 host (common name) Tiger - host health state Asymptomatic ASYMPTOMATIC - host health state Deceased DECEASED - host health state Healthy HEALTHY +NCIT_C3833 host health state Asymptomatic ASYMPTOMATIC +NCIT_C28554 host health state Deceased DECEASED +NCIT_C115935 host health state Healthy HEALTHY host health state Recovered RECOVERED host health state Symptomatic SYMPTOMATIC @@ -691,7 +692,7 @@ NCBITaxon_9694 host (common name) Tiger host health outcome Stable NCBITaxon_2697049 organism Severe acute respiratory syndrome coronavirus 2 - organism RaTG13 +NCBITaxon_2709072 organism RaTG13 organism RmYN02 @@ -744,7 +745,7 @@ BTO_0001444 lab host Vero cell line BTO:0004755 lab host Vero E6 cell line lab host VeroE6/TMPRSS2 cell line - host disease COVID-19 +DOID_0080600 host disease COVID-19 host age bin 0 - 9 host age bin 10 - 19 @@ -758,8 +759,8 @@ BTO:0004755 lab host Vero E6 cell line host age bin 90 - 99 host age bin 100+ -OMRSE:00000009? host gender Female FEMALE -OMRSE:00000008? host gender Male MALE +NCIT_C46110 host gender Female FEMALE +NCIT_C46109 host gender Male MALE host gender Non-binary gender NON_BINARY_GENDER host gender Transgender (Male to Female) TRANSGENDER host gender Transgender (Female to Male) TRANSGENDER @@ -1312,4 +1313,5 @@ GAZ_00009572 geo_loc_name (country) West Bank GAZ_00000564 geo_loc_name (country) Western Sahara GAZ_00005284 geo_loc_name (country) Yemen GAZ_00001107 geo_loc_name (country) Zambia -GAZ_00001106 geo_loc_name (country) Zimbabwe \ No newline at end of file +GAZ_00001106 geo_loc_name (country) Zimbabwe + \ No newline at end of file diff --git a/template/canada_covid19/reference.html b/template/canada_covid19/reference.html index df9a53c3..6a290c70 100644 --- a/template/canada_covid19/reference.html +++ b/template/canada_covid19/reference.html @@ -295,7 +295,7 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission 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 - [''] + None