From dd84371dcce3501c9f0109baa4ec0ee6767a8e7c Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 12 Oct 2021 01:06:59 -0700 Subject: [PATCH] implementing regular expression pattern As well as some updates to CanCoGen vocabulary template --- script/main.js | 107 +- script/make_data.py | 3 + template/canada_covid19/data.js | 1276 +++++++++--- template/canada_covid19/data.tsv | 2623 ++++++++++++------------ template/canada_covid19/reference.html | 6 +- 5 files changed, 2341 insertions(+), 1674 deletions(-) diff --git a/script/main.js b/script/main.js index 3461b1f0..906b0279 100644 --- a/script/main.js +++ b/script/main.js @@ -11,7 +11,7 @@ * main.html?template=test_template * */ -const VERSION = '0.14.1'; +const VERSION = '0.14.2'; const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION; const TEMPLATES = { 'CanCOGeN Covid-19': {'folder': 'canada_covid19', 'status': 'published'}, @@ -275,6 +275,10 @@ const getColumns = (data) => { if (field.requirement) { col.requirement = field.requirement; } + // Compile field's regular expression for quick application. + if (field.pattern) { + field.pattern = new RegExp(field.pattern); + } switch (field.datatype) { case 'xs:date': col.type = 'date'; @@ -1073,7 +1077,8 @@ const getInvalidCells = (hot, data) => { for (let col=0; col { checkProvenance(provenanceChanges, cellVal, row, col); }; if (!cellVal) { - valid = fields[col].requirement !== 'required'; + valid = field.requirement !== 'required'; msg = 'Required cells cannot be empty' } - else switch (datatype) { - // Unique value field (a type of xs:token string) - case 'xs:unique': - // Set up dictionary and count for this column's unique values - if (!uniquefield[col]) { - uniquefield[col] = {}; - for (let keyrow=0; keyrow=0 - valid &= parsedInt.toString()===cellVal; - valid &= testNumericRange(parsedInt, fields[col]); - break; - case 'xs:decimal': - const parsedDec = parseFloat(cellVal); - valid = !isNaN(cellVal) && regexDecimal.test(cellVal); - valid &= testNumericRange(parsedDec, fields[col]); - break; - case 'xs:date': - // moment is a date format addon - valid = moment(cellVal, 'YYYY-MM-DD', true).isValid(); - if (valid) { - valid = testDateRange(cellVal, fields[col]); - } - break; - case 'select': - valid = validateValAgainstVocab(cellVal, fields[col].flatVocabulary); - break; - case 'multiple': - valid = validateValsAgainstVocab(cellVal, fields[col].flatVocabulary); - break; - + // Must be only 1 unique value. Case insensitive comparison + valid = uniquefield[col][cellVal] === 1; + break; + case 'xs:nonNegativeInteger': + const parsedInt = parseInt(cellVal, 10); + valid = !isNaN(cellVal) && parsedInt>=0 + valid &= parsedInt.toString()===cellVal; + valid &= testNumericRange(parsedInt, field); + break; + case 'xs:decimal': + const parsedDec = parseFloat(cellVal); + valid = !isNaN(cellVal) && regexDecimal.test(cellVal); + valid &= testNumericRange(parsedDec, field); + break; + case 'xs:date': + // moment is a date format addon + valid = moment(cellVal, 'YYYY-MM-DD', true).isValid(); + if (valid) { + valid = testDateRange(cellVal, field); + } + break; + case 'select': + valid = validateValAgainstVocab(cellVal, field.flatVocabulary); + break; + case 'multiple': + valid = validateValsAgainstVocab(cellVal, field.flatVocabulary); + break; + + } + // Test regular expression if it is given + if (valid && field.pattern) { + valid = field.pattern.test(cellVal); + } } - - if (!valid && fields[col].dataStatus) { - valid = validateValAgainstVocab(cellVal, fields[col].dataStatus); + if (!valid && field.dataStatus) { + valid = validateValAgainstVocab(cellVal, field.dataStatus); } - if (!valid) { if (!invalidCells.hasOwnProperty(row)) { invalidCells[row] = {}; diff --git a/script/make_data.py b/script/make_data.py index 4ab7d7b4..fc79e0b7 100755 --- a/script/make_data.py +++ b/script/make_data.py @@ -150,6 +150,9 @@ def export_fields (EXPORT_FORMAT, field, row, as_field = False): 'examples': row['examples'] } + if 'pattern' in row and len(row['pattern']) > 0: + field['pattern'] = row['pattern']; + export_fields (EXPORT_FORMAT, field, row, True); reference_html += ''' diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index 65e0490e..a46f267d 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -65,7 +65,7 @@ var DATA = [ "exportField": { "NML_LIMS": [ { - "field": "VD_LAB_NUMBER" + "field": "HC_TEXT5" } ] } @@ -86,7 +86,7 @@ var DATA = [ "exportField": { "NML_LIMS": [ { - "field": "third party lab sample ID" + "field": "PH_ID_NUMBER_PRIMARY" } ] } @@ -642,6 +642,7 @@ var DATA = [ "description": "The email address of the contact responsible for follow-up regarding the sample.", "guidance": "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca", "examples": "RespLab@lab.ca", + "pattern": "^\\S+@\\S+\\.\\S+$", "exportField": { "NML_LIMS": [ { @@ -888,7 +889,7 @@ var DATA = [ }, "schema:ItemList": { "year": { - "ontology_id": "UO:0000035", + "ontology_id": "UO:0000036", "exportField": { "NML_LIMS": [ { @@ -898,7 +899,7 @@ var DATA = [ } }, "month": { - "ontology_id": "UO:0000036", + "ontology_id": "UO:0000035", "exportField": { "NML_LIMS": [ { @@ -1234,7 +1235,7 @@ var DATA = [ "ontology_id": "GAZ_00003762" }, "Curacao": { - "ontology_id": "GAZ_00004021" + "ontology_id": "GAZ:00012582" }, "Cyprus": { "ontology_id": "GAZ_00004006" @@ -1560,7 +1561,7 @@ var DATA = [ "ontology_id": "GAZ_00000584" }, "Malta": { - "ontology_id": "GAZ_00005459" + "ontology_id": "GAZ:00004017" }, "Marshall Islands": { "ontology_id": "GAZ_00007161" @@ -1829,7 +1830,7 @@ var DATA = [ "ontology_id": "GAZ_00233439" }, "Spain": { - "ontology_id": "GAZ_00003936" + "ontology_id": "GAZ:00000591" }, "Spratly Islands": { "ontology_id": "GAZ_00010831" @@ -2231,7 +2232,9 @@ var DATA = [ "RaTG13": { "ontology_id": "NCBITaxon_2709072" }, - "RmYN02": {} + "RmYN02": { + "ontology_id": "NCBITaxon NTR" + } } }, { @@ -2329,12 +2332,18 @@ var DATA = [ ] }, "schema:ItemList": { - "Cluster/Outbreak investigation": {}, - "Diagnostic testing": {}, + "Cluster/Outbreak investigation": { + "ontology_id": "HSO:0000371" + }, + "Diagnostic testing": { + "ontology_id": "HSO or NCIT NTR?" + }, "Research": { "ontology_id": "NCIT_c15429" }, - "Surveillance": {} + "Surveillance": { + "ontology_id": "HSO:0000268" + } } }, { @@ -3129,6 +3138,7 @@ var DATA = [ }, "schema:ItemList": { "Air vent": { + "ontology_id": "ENVO:03501208", "exportField": { "NML_LIMS": [ { @@ -3148,6 +3158,7 @@ var DATA = [ } }, "Bed rail": { + "ontology_id": "ENVO:03501209", "exportField": { "NML_LIMS": [ { @@ -3177,6 +3188,7 @@ var DATA = [ } }, "Control panel": { + "ontology_id": "ENVO:03501210", "exportField": { "NML_LIMS": [ { @@ -3186,7 +3198,7 @@ var DATA = [ } }, "Door": { - "ontology_id": "NCIT_C48950", + "ontology_id": "ENVO:03501220", "exportField": { "NML_LIMS": [ { @@ -3196,6 +3208,7 @@ var DATA = [ } }, "Door handle": { + "ontology_id": "ENVO:03501211", "exportField": { "NML_LIMS": [ { @@ -3205,6 +3218,7 @@ var DATA = [ } }, "Face mask": { + "ontology_id": "OBI:0002787", "exportField": { "NML_LIMS": [ { @@ -3214,6 +3228,7 @@ var DATA = [ } }, "Face shield": { + "ontology_id": "OBI:0002791", "exportField": { "NML_LIMS": [ { @@ -3253,6 +3268,7 @@ var DATA = [ } }, "Handrail": { + "ontology_id": "ENVO:03501212", "exportField": { "NML_LIMS": [ { @@ -3262,6 +3278,7 @@ var DATA = [ } }, "Hospital gown": { + "ontology_id": "OBI:0002792", "exportField": { "NML_LIMS": [ { @@ -3271,6 +3288,7 @@ var DATA = [ } }, "Light switch": { + "ontology_id": "ENVO:03501213", "exportField": { "NML_LIMS": [ { @@ -3280,6 +3298,7 @@ var DATA = [ } }, "Locker": { + "ontology_id": "ENVO:03501214", "exportField": { "NML_LIMS": [ { @@ -3289,6 +3308,7 @@ var DATA = [ } }, "N95 mask": { + "ontology_id": "OBI:0002790", "exportField": { "NML_LIMS": [ { @@ -3298,6 +3318,7 @@ var DATA = [ } }, "Nurse call button": { + "ontology_id": "ENVO:03501215", "exportField": { "NML_LIMS": [ { @@ -3307,6 +3328,7 @@ var DATA = [ } }, "Paper": { + "ontology_id": "ENVO:03501256", "exportField": { "NML_LIMS": [ { @@ -3336,6 +3358,7 @@ var DATA = [ } }, "PPE gown": { + "ontology_id": "OBI NTR?", "exportField": { "NML_LIMS": [ { @@ -3375,6 +3398,7 @@ var DATA = [ } }, "Stainless steel": { + "ontology_id": "ENVO:03501216", "exportField": { "NML_LIMS": [ { @@ -3384,6 +3408,7 @@ var DATA = [ } }, "Tissue paper": { + "ontology_id": "ENVO:03501217", "exportField": { "NML_LIMS": [ { @@ -3393,6 +3418,7 @@ var DATA = [ } }, "Toilet bowl": { + "ontology_id": "ENVO:03501218", "exportField": { "NML_LIMS": [ { @@ -3412,6 +3438,7 @@ var DATA = [ } }, "Wastewater": { + "ontology_id": "ENVO:00002001", "exportField": { "NML_LIMS": [ { @@ -3421,6 +3448,7 @@ var DATA = [ } }, "Window": { + "ontology_id": "ENVO:03501219", "exportField": { "NML_LIMS": [ { @@ -3492,6 +3520,7 @@ var DATA = [ }, "schema:ItemList": { "Acute care facility": { + "ontology_id": "ENVO:03501135", "exportField": { "NML_LIMS": [ { @@ -3521,6 +3550,7 @@ var DATA = [ } }, "Clinical assessment centre": { + "ontology_id": "ENVO:03501136", "exportField": { "NML_LIMS": [ { @@ -3530,6 +3560,7 @@ var DATA = [ } }, "Conference venue": { + "ontology_id": "ENVO:03501127", "exportField": { "NML_LIMS": [ { @@ -3539,7 +3570,7 @@ var DATA = [ } }, "Corridor": { - "ontology_id": "ENVO REQUEST", + "ontology_id": "ENVO:03501121", "exportField": { "NML_LIMS": [ { @@ -3559,7 +3590,7 @@ var DATA = [ } }, "Emergency room (ER)": { - "ontology_id": "NCIT_C53513", + "ontology_id": "ENVO:03501144", "exportField": { "NML_LIMS": [ { @@ -3569,6 +3600,7 @@ var DATA = [ } }, "Family practice clinic": { + "ontology_id": "ENVO:03501186", "exportField": { "NML_LIMS": [ { @@ -3578,6 +3610,7 @@ var DATA = [ } }, "Group home": { + "ontology_id": "ENVO:03501196", "exportField": { "NML_LIMS": [ { @@ -3587,6 +3620,7 @@ var DATA = [ } }, "Homeless shelter": { + "ontology_id": "ENVO:03501133", "exportField": { "NML_LIMS": [ { @@ -3596,7 +3630,7 @@ var DATA = [ } }, "Hospital": { - "ontology_id": "OBI_0000844", + "ontology_id": "ENVO:00002173", "exportField": { "NML_LIMS": [ { @@ -3606,7 +3640,7 @@ var DATA = [ } }, "Intensive Care Unit (ICU)": { - "ontology_id": "NCIT_C53511", + "ontology_id": "ENVO:03501152", "exportField": { "NML_LIMS": [ { @@ -3616,7 +3650,7 @@ var DATA = [ } }, "Long Term Care Facility": { - "ontology_id": "GENEPIO_0001035", + "ontology_id": "ENVO:03501194", "exportField": { "NML_LIMS": [ { @@ -3626,6 +3660,7 @@ var DATA = [ } }, "Patient room": { + "ontology_id": "ENVO:03501180", "exportField": { "NML_LIMS": [ { @@ -3635,7 +3670,7 @@ var DATA = [ } }, "Prison": { - "ontology_id": "ENVO_01001481", + "ontology_id": "ENVO:03501204", "exportField": { "NML_LIMS": [ { @@ -3655,7 +3690,7 @@ var DATA = [ } }, "School": { - "ontology_id": "NCIT_C17118", + "ontology_id": "ENVO:03501130", "exportField": { "NML_LIMS": [ { @@ -3665,6 +3700,7 @@ var DATA = [ } }, "Sewage Plant": { + "ontology_id": "ENVO:00003043", "exportField": { "NML_LIMS": [ { @@ -3674,6 +3710,7 @@ var DATA = [ } }, "Subway train": { + "ontology_id": "ENVO:03501109", "exportField": { "NML_LIMS": [ { @@ -3683,6 +3720,7 @@ var DATA = [ } }, "Wet market": { + "ontology_id": "ENVO:03501198", "exportField": { "NML_LIMS": [ { @@ -3744,6 +3782,7 @@ var DATA = [ }, "schema:ItemList": { "Air filter": { + "ontology_id": "ENVO:00003968", "exportField": { "NML_LIMS": [ { @@ -3753,7 +3792,7 @@ var DATA = [ } }, "Blood Collection Tube": { - "ontology_id": "NCIT:C113122", + "ontology_id": "OBI:0002859", "exportField": { "NML_LIMS": [ { @@ -3763,7 +3802,7 @@ var DATA = [ } }, "Bronchoscope": { - "ontology_id": "NCIT:C17611 ", + "ontology_id": "OBI:0002826", "exportField": { "NML_LIMS": [ { @@ -3773,6 +3812,7 @@ var DATA = [ } }, "Collection Container": { + "ontology_id": "OBI:0002088", "exportField": { "NML_LIMS": [ { @@ -3782,6 +3822,7 @@ var DATA = [ } }, "Collection Cup": { + "ontology_id": "OBI NTR?", "exportField": { "NML_LIMS": [ { @@ -3791,6 +3832,7 @@ var DATA = [ } }, "Fibrobronchoscope Brush": { + "ontology_id": "OBI:0002825", "exportField": { "NML_LIMS": [ { @@ -3800,6 +3842,7 @@ var DATA = [ } }, "Filter": { + "ontology_id": "ENVO NTR", "exportField": { "NML_LIMS": [ { @@ -3809,6 +3852,7 @@ var DATA = [ } }, "Fine Needle": { + "ontology_id": "OBI:0002827", "exportField": { "NML_LIMS": [ { @@ -3818,6 +3862,7 @@ var DATA = [ } }, "Microcapillary tube": { + "ontology_id": "OBI:0002858", "exportField": { "NML_LIMS": [ { @@ -3847,7 +3892,7 @@ var DATA = [ } }, "Serum Collection Tube": { - "ontology_id": "NCIT:C113675 ", + "ontology_id": "OBI:0002860", "exportField": { "NML_LIMS": [ { @@ -3857,6 +3902,7 @@ var DATA = [ } }, "Sputum Collection Tube": { + "ontology_id": "OBI:0002861", "exportField": { "NML_LIMS": [ { @@ -3866,6 +3912,7 @@ var DATA = [ } }, "Suction Catheter": { + "ontology_id": "OBI:0002831", "exportField": { "NML_LIMS": [ { @@ -3875,7 +3922,7 @@ var DATA = [ } }, "Swab": { - "ontology_id": "NCIT:c17627", + "ontology_id": "OBI NTR?", "exportField": { "NML_LIMS": [ { @@ -3885,6 +3932,7 @@ var DATA = [ } }, "Urine Collection Tube": { + "ontology_id": "OBI:0002862", "exportField": { "NML_LIMS": [ { @@ -3894,6 +3942,7 @@ var DATA = [ } }, "Virus Transport Medium": { + "ontology_id": "OBI:0002866", "exportField": { "NML_LIMS": [ { @@ -3955,7 +4004,7 @@ var DATA = [ }, "schema:ItemList": { "Amniocentesis": { - "ontology_id": "NCIT:C52009", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -3965,7 +4014,7 @@ var DATA = [ } }, "Aspiration": { - "ontology_id": "NCIT:C15631", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -3975,6 +4024,7 @@ var DATA = [ }, "schema:ItemList": { "Suprapubic Aspiration": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -3984,6 +4034,7 @@ var DATA = [ } }, "Tracheal aspiration": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -3993,6 +4044,7 @@ var DATA = [ } }, "Vacuum Aspiration": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4026,6 +4078,7 @@ var DATA = [ } }, "Filtration": { + "ontology_id": "OBI:0302885", "exportField": { "NML_LIMS": [ { @@ -4035,6 +4088,7 @@ var DATA = [ }, "schema:ItemList": { "Air filtration": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4056,7 +4110,7 @@ var DATA = [ }, "schema:ItemList": { "Bronchoalveolar lavage (BAL)": { - "ontology_id": "BTO:0000155", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4066,6 +4120,7 @@ var DATA = [ } }, "Gastric Lavage": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4077,7 +4132,7 @@ var DATA = [ } }, "Lumbar Puncture": { - "ontology_id": "NCIT:C15327", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4087,7 +4142,7 @@ var DATA = [ } }, "Necropsy": { - "ontology_id": "MMO:0000344", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4097,7 +4152,7 @@ var DATA = [ } }, "Phlebotomy": { - "ontology_id": "NCIT:c28221", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4107,7 +4162,7 @@ var DATA = [ } }, "Rinsing": { - "ontology_id": "GENEPIO:0002116", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4116,10 +4171,13 @@ var DATA = [ ] }, "schema:ItemList": { - "Saline gargle (mouth rinse and gargle)": {} + "Saline gargle (mouth rinse and gargle)": { + "ontology_id": "OBI NTR" + } } }, "Scraping": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4129,7 +4187,7 @@ var DATA = [ } }, "Swabbing": { - "ontology_id": "GENEPIO:0002117", + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4139,6 +4197,7 @@ var DATA = [ }, "schema:ItemList": { "Finger Prick": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4150,6 +4209,7 @@ var DATA = [ } }, "Wash": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4159,6 +4219,7 @@ var DATA = [ } }, "Washout Tear Collection": { + "ontology_id": "OBI NTR", "exportField": { "NML_LIMS": [ { @@ -4222,9 +4283,15 @@ var DATA = [ ] }, "schema:ItemList": { - "Virus passage": {}, - "RNA re-extraction (post RT-PCR)": {}, - "Specimens pooled": {} + "Virus passage": { + "ontology_id": "OBI NTR?" + }, + "RNA re-extraction (post RT-PCR)": { + "ontology_id": "OBI NTR?" + }, + "Specimens pooled": { + "ontology_id": "OBI:0600016" + } } }, { @@ -4264,18 +4331,24 @@ var DATA = [ ] }, "schema:ItemList": { - "293/ACE2 cell line": {}, + "293/ACE2 cell line": { + "ontology_id": "BTO NTR" + }, "Caco2 cell line": { "ontology_id": "BTO_0000195 " }, "Calu3 cell line": { "ontology_id": "BTO_0002750" }, - "EFK3B cell line": {}, + "EFK3B cell line": { + "ontology_id": "BTO NTR" + }, "HEK293T cell line": { "ontology_id": "BTO_0002181" }, - "HRCE cell line": {}, + "HRCE cell line": { + "ontology_id": "BTO NTR" + }, "Huh7 cell line": { "ontology_id": "BTO_0001950" }, @@ -4285,7 +4358,6 @@ var DATA = [ "MDBK cell line": { "ontology_id": "BTO_0000836 " }, - "Mv1Lu cell line": {}, "NHBE cell line": { "ontology_id": "BTO_0002924" }, @@ -4304,7 +4376,9 @@ var DATA = [ "Vero E6 cell line": { "ontology_id": "BTO:0004755" }, - "VeroE6/TMPRSS2 cell line": {} + "VeroE6/TMPRSS2 cell line": { + "ontology_id": "BTO NTR" + } } }, { @@ -4527,7 +4601,7 @@ var DATA = [ } }, "Pig": { - "ontology_id": "NCBITaxon_9823", + "ontology_id": "NCBITaxon_9825", "exportField": { "CNPHI": [ { @@ -4910,7 +4984,7 @@ var DATA = [ }, "schema:ItemList": { "COVID-19": { - "ontology_id": "DOID_0080600" + "ontology_id": "MONDO:0100096" } } }, @@ -5057,17 +5131,53 @@ var DATA = [ ] }, "schema:ItemList": { - "0 - 9": {}, - "10 - 19": {}, - "20 - 29": {}, - "30 - 39": {}, - "40 - 49": {}, - "50 - 59": {}, - "60 - 69": {}, - "70 - 79": {}, - "80 - 89": {}, - "90 - 99": {}, - "100+": {} + "0 - 9": { + "ontology_id": "GENEPIO NTR" + }, + "10 - 19": { + "ontology_id": "GENEPIO NTR" + }, + "20 - 29": { + "ontology_id": "GENEPIO NTR" + }, + "30 - 39": { + "ontology_id": "GENEPIO NTR" + }, + "40 - 49": { + "ontology_id": "GENEPIO NTR" + }, + "50 - 59": { + "ontology_id": "GENEPIO NTR" + }, + "60 - 69": { + "ontology_id": "GENEPIO NTR" + }, + "70 - 79": { + "ontology_id": "GENEPIO NTR" + }, + "80 - 89": { + "ontology_id": "GENEPIO NTR" + }, + "90 - 99": { + "ontology_id": "GENEPIO NTR", + "exportField": { + "VirusSeq_Portal": [ + { + "value": "90+" + } + ] + } + }, + "100+": { + "ontology_id": "GENEPIO NTR", + "exportField": { + "VirusSeq_Portal": [ + { + "value": "90+" + } + ] + } + } } }, { @@ -5138,6 +5248,7 @@ var DATA = [ } }, "Non-binary gender": { + "ontology_id": "GSSO:000132", "exportField": { "NML_LIMS": [ { @@ -5147,6 +5258,7 @@ var DATA = [ } }, "Transgender (Male to Female)": { + "ontology_id": "GSSO:004004", "exportField": { "NML_LIMS": [ { @@ -5156,6 +5268,7 @@ var DATA = [ } }, "Transgender (Female to Male)": { + "ontology_id": "GSSO:004005", "exportField": { "NML_LIMS": [ { @@ -5330,7 +5443,9 @@ var DATA = [ ] }, "schema:ItemList": { - "Abnormal lung auscultation": {}, + "Abnormal lung auscultation": { + "ontology_id": "HP REQUEST" + }, "Abnormality of taste sensation": { "ontology_id": "HP:0000223", "exportField": { @@ -5468,6 +5583,7 @@ var DATA = [ } }, "Inability to arouse (inability to stay awake)": { + "ontology_id": "HP REQUEST", "exportField": { "NML_LIMS": [ { @@ -5632,6 +5748,7 @@ var DATA = [ } }, "Cyanotic face (bluish face)": { + "ontology_id": "HP REQUEST", "exportField": { "NML_LIMS": [ { @@ -5643,8 +5760,10 @@ var DATA = [ } }, "Central Cyanosis": { + "ontology_id": "HP REQUEST", "schema:ItemList": { "Cyanotic lips (bluish lips)": { + "ontology_id": "HP REQUEST", "exportField": { "NML_LIMS": [ { @@ -5655,7 +5774,9 @@ var DATA = [ } } }, - "Peripheral Cyanosis": {} + "Peripheral Cyanosis": { + "ontology_id": "HP REQUEST" + } } }, "Dyspnea (breathing difficulty)": { @@ -5719,6 +5840,9 @@ var DATA = [ ] } }, + "Prostration (complete exhaustion)": { + "ontology_id": "HP REQUEST" + }, "Fever": { "ontology_id": "HP_0001945 ", "exportField": { @@ -5730,6 +5854,7 @@ var DATA = [ }, "schema:ItemList": { "Fever (>=38\u00b0C)": { + "ontology_id": "HP REQUEST", "exportField": { "CNPHI": [ { @@ -5750,7 +5875,9 @@ var DATA = [ ] } }, - "Ground Glass Opacities (GGO)": {}, + "Ground Glass Opacities (GGO)": { + "ontology_id": "HP REQUEST" + }, "Headache": { "ontology_id": "HP_0002315", "exportField": { @@ -5794,7 +5921,9 @@ var DATA = [ ] }, "schema:ItemList": { - "Silent hypoxemia": {} + "Silent hypoxemia": { + "ontology_id": "HP REQUEST" + } } }, "Internal hemorrhage (internal bleeding)": { @@ -5873,7 +6002,9 @@ var DATA = [ "Nose bleed": { "ontology_id": "HP_0000421" }, - "Otitis": {}, + "Otitis": { + "ontology_id": "HP REQUEST" + }, "Pain": { "ontology_id": "HP:0012531", "schema:ItemList": { @@ -5934,18 +6065,20 @@ var DATA = [ ] } }, - "Pharyngeal exudate": {}, + "Pharyngeal exudate": { + "ontology_id": "HP REQUEST" + }, "Pleural effusion": { "ontology_id": "HP:0002202" }, "Pneumonia": { "ontology_id": "HP:0002090" }, - "Prostration": {}, "Pseudo-chilblains": { "ontology_id": "HP:0033696", "schema:ItemList": { "Pseudo-chilblains on fingers (covid fingers)": { + "ontology_id": "HP REQUEST", "exportField": { "NML_LIMS": [ { @@ -5955,6 +6088,7 @@ var DATA = [ } }, "Pseudo-chilblains on toes (covid toes)": { + "ontology_id": "HP REQUEST", "exportField": { "NML_LIMS": [ { @@ -6099,39 +6233,69 @@ var DATA = [ }, "schema:ItemList": { "Age 60+": {}, - "Anemia": {}, - "Anorexia": {}, - "Birthing labor": {}, - "Bone marrow failure": {}, + "Anemia": { + "ontology_id": "HP:0001903" + }, + "Anorexia": { + "ontology_id": "HP:0002039" + }, + "Birthing labor": { + "ontology_id": "NCIT:C92743" + }, + "Bone marrow failure": { + "ontology_id": "NCIT_C80693" + }, "Cancer": { + "ontology_id": "MONDO:0004992", "schema:ItemList": { - "Breast cancer": {}, - "Colorectal cancer": {}, - "Hematologic malignancy": {}, - "Lung cancer": {}, - "Metastatic disease": {} + "Breast cancer": { + "ontology_id": "MONDO:0007254" + }, + "Colorectal cancer": { + "ontology_id": "MONDO:0005575" + }, + "Hematologic malignancy (cancer of the blood)": { + "ontology_id": "DOID:2531" + }, + "Lung cancer": { + "ontology_id": "MONDO:0008903" + }, + "Metastatic disease": { + "ontology_id": "MONDO:0024880" + } } }, "Cancer treatment": { + "ontology_id": "NCIT:C16212", "schema:ItemList": { - "Cancer surgery": {}, + "Cancer surgery": { + "ontology_id": "NCIT:C157740" + }, "Chemotherapy": { + "ontology_id": "NCIT:C15632", "schema:ItemList": { - "Adjuvant chemotherapy": {} + "Adjuvant chemotherapy": { + "ontology_id": "NCIT:C15360" + } } } } }, "Cardiac disorder": { + "ontology_id": "NCIT:C3079", "schema:ItemList": { "Arrhythmia": { "ontology_id": "HP:0011675" }, - "Cardiac disease": {}, + "Cardiac disease": { + "ontology_id": "MONDO:0005267" + }, "Cardiomyopathy": { "ontology_id": "HP:0001638" }, - "Cardiac injury": {}, + "Cardiac injury": { + "ontology_id": "NCIT:C45430" + }, "Hypertension (high blood pressure)": { "ontology_id": "HP_0000822" }, @@ -6140,64 +6304,119 @@ var DATA = [ } } }, - "Cesarean section": {}, - "Chronic cough": {}, - "Chronic gastrointestinal disease": {}, - "Chronic lung disease": {}, - "Corticosteroids": {}, + "Cesarean section": { + "ontology_id": "HP:0011410" + }, + "Chronic cough": { + "ontology_id": "HP REQUEST" + }, + "Chronic gastrointestinal disease": { + "ontology_id": "HP REQUEST" + }, + "Chronic lung disease": { + "ontology_id": "HP:0006528" + }, + "Corticosteroids": { + "ontology_id": "NCIT:C211" + }, "Diabetes mellitus (diabetes)": { + "ontology_id": "HP:0000819", "schema:ItemList": { - "Type I diabetes mellitus (T1D)": {}, - "Type II diabetes mellitus (T2D)": {} + "Type I diabetes mellitus (T1D)": { + "ontology_id": "HP:0100651" + }, + "Type II diabetes mellitus (T2D)": { + "ontology_id": "HP:0005978" + } } }, - "Eczema": {}, + "Eczema": { + "ontology_id": "HP:0000964" + }, "Electrolyte disturbance": { + "ontology_id": "HP:0003111", "schema:ItemList": { - "Hypocalcemia": {}, - "Hypokalemia": {}, - "Hypomagnesemia": {} + "Hypocalcemia": { + "ontology_id": "HP:0002901" + }, + "Hypokalemia": { + "ontology_id": "HP:0002900" + }, + "Hypomagnesemia": { + "ontology_id": "HP:0002917" + } } }, "Encephalitis (brain inflammation)": { "ontology_id": "HP:0002383" }, - "Epilepsy": {}, - "Hemodialysis": {}, - "Hemoglobinopathy": {}, + "Epilepsy": { + "ontology_id": "MONDO:0005027" + }, + "Hemodialysis": { + "ontology_id": "NCIT:C15248" + }, + "Hemoglobinopathy": { + "ontology_id": "MONDO:0044348" + }, "Human immunodeficiency virus (HIV)": { + "ontology_id": "MONDO:0005109", "schema:ItemList": { - "Acquired immunodeficiency syndrome (AIDS)": {}, - "HIV and antiretroviral therapy (ART)": {} + "Acquired immunodeficiency syndrome (AIDS)": { + "ontology_id": "MONDO:0012268" + }, + "HIV and antiretroviral therapy (ART)": { + "ontology_id": "NCIT:C16118" + } } }, "Immunocompromised": { + "ontology_id": "NCIT:C14139", "schema:ItemList": { - "Lupus": {} + "Lupus": { + "ontology_id": "MONDO:0004670" + } } }, "Inflammatory bowel disease (IBD)": { + "ontology_id": "MONDO:0005265", "schema:ItemList": { "Colitis": { + "ontology_id": "HP:0002583", "schema:ItemList": { - "Ulcerative colitis": {} + "Ulcerative colitis": { + "ontology_id": "HP:0100279" + } } }, - "Crohn's disease": {} + "Crohn's disease": { + "ontology_id": "HP:0100280" + } } }, "Renal disorder": { + "ontology_id": "NCIT:C3149", "schema:ItemList": { - "Renal disease": {}, - "Chronic renal disease": {}, - "Renal failure": {} + "Renal disease": { + "ontology_id": "MONDO:0005240" + }, + "Chronic renal disease": { + "ontology_id": "HP:0012622" + }, + "Renal failure": { + "ontology_id": "HP:0000084" + } } }, "Liver disease": { + "ontology_id": "MONDO:0005154", "schema:ItemList": { "Chronic liver disease": { + "ontology_id": "NCIT:C113609", "schema:ItemList": { - "Fatty liver disease (FLD)": {} + "Fatty liver disease (FLD)": { + "ontology_id": "HP:0001397" + } } } } @@ -6205,70 +6424,120 @@ var DATA = [ "Myalgia (muscle pain)": { "ontology_id": "HP:0003326" }, - "Myalgic encephalomyelitis (ME)": {}, + "Myalgic encephalomyelitis (ME)": { + "ontology_id": "MONDO:0005404" + }, "Neurological disorder": { + "ontology_id": "MONDO:0005071", "schema:ItemList": { - "Neuromuscular disorder": {} + "Neuromuscular disorder": { + "ontology_id": "MONDO:0019056" + } } }, "Obesity": { + "ontology_id": "HP:0001513", "schema:ItemList": { - "Severe obesity": {} + "Severe obesity": { + "ontology_id": "MONDO:0005139" + } } }, "Respiratory disorder": { + "ontology_id": "MONDO:0005087", "schema:ItemList": { - "Asthma": {}, - "Chronic bronchitis": {}, + "Asthma": { + "ontology_id": "HP:0002099" + }, + "Chronic bronchitis": { + "ontology_id": "HP:0004469" + }, "Chronic pulmonary disease": { + "ontology_id": "HP:0006528", "schema:ItemList": { - "Chronic obstructive pulmonary disease": {} + "Chronic obstructive pulmonary disease": { + "ontology_id": "HP:0006510" + } } }, - "Emphysema": {}, + "Emphysema": { + "ontology_id": "HP:0002097" + }, "Lung disease": { + "ontology_id": "MONDO:0005275", "schema:ItemList": { - "Chronic lung disease": {}, - "Pulmonary fibrosis": {} + "Chronic lung disease": { + "ontology_id": "HP:0006528" + }, + "Pulmonary fibrosis": { + "ontology_id": "HP:0002206" + } } }, "Pneumonia": { "ontology_id": "HP:0002090" }, "Respiratory failure": { + "ontology_id": "HP:0002878", "schema:ItemList": { - "Adult respiratory distress syndrome": {}, - "Newborn respiratory distress syndrome": {} + "Adult respiratory distress syndrome": { + "ontology_id": "HP:0033677" + }, + "Newborn respiratory distress syndrome": { + "ontology_id": "MONDO:0009971" + } } }, - "Tuberculosis": {} + "Tuberculosis": { + "ontology_id": "MONDO:0018076" + } } }, "Postpartum (\u22646 weeks)": {}, - "Pregnancy": {}, - "Rheumatic disease": {}, - "Sickle cell disease": {}, + "Pregnancy": { + "ontology_id": "NCIT:C25742" + }, + "Rheumatic disease": { + "ontology_id": "MONDO:0005554" + }, + "Sickle cell disease": { + "ontology_id": "MONDO:0011382" + }, "Substance use": { + "ontology_id": "NBO:0001845", "schema:ItemList": { - "Alcohol abuse": {}, + "Alcohol abuse": { + "ontology_id": "MONDO:0002046" + }, "Drug abuse": { "schema:ItemList": { "Injection drug abuse": {} } }, - "Smoking": {}, - "Vaping": {} + "Smoking": { + "ontology_id": "NBO:0015005" + }, + "Vaping": { + "ontology_id": "NBO NTR" + } } }, "Tachypnea (accelerated respiratory rate)": { "ontology_id": "HP:0002789" }, "Transplant": { + "ontology_id": "NCIT:C159659", "schema:ItemList": { - "Bone marrow transplant": {}, + "Bone marrow transplant": { + "ontology_id": "NCIT:C131759" + }, "Cardiac transplant": {}, - "Hematopoietic stem cell transplant (HSCT)": {}, - "Kidney transplant": {}, + "Hematopoietic stem cell transplant (HSCT)": { + "ontology_id": "NCIT:C126836" + }, + "Kidney transplant": { + "ontology_id": "NCIT:C157332" + }, "Liver transplant": {} } } @@ -6301,128 +6570,247 @@ var DATA = [ ] }, "schema:ItemList": { - "Abnormal blood oxygen level": {}, - "Acute respiratory failure": {}, + "Abnormal blood oxygen level": { + "ontology_id": "HP:0500165" + }, + "Acute respiratory failure": { + "ontology_id": "MONDO:0001208" + }, "Arrhythmia (complication)": { "ontology_id": "HP:0011675", "schema:ItemList": { "Tachycardia": { + "ontology_id": "HP:0001649", "schema:ItemList": { - "Polymorphic ventricular tachycardia (VT)": {}, - "Tachyarrhythmia": {} + "Polymorphic ventricular tachycardia (VT)": { + "ontology_id": "HP:0031677" + }, + "Tachyarrhythmia": { + "ontology_id": "HP NTR" + } } } } }, "Noncardiogenic pulmonary edema": { + "ontology_id": "HP NTR", "schema:ItemList": { "Acute respiratory distress syndrome (ARDS)": { + "ontology_id": "HP:0033677", "schema:ItemList": { - "COVID-19 associated ARDS (CARDS)": {}, - "Neurogenic pulmonary edema (NPE)": {} + "COVID-19 associated ARDS (CARDS)": { + "ontology_id": "HP NTR" + }, + "Neurogenic pulmonary edema (NPE)": { + "ontology_id": "HP NTR" + } } } } }, - "Cardiac injury": {}, - "Cardiac arrest": {}, - "Cardiogenic shock": {}, + "Cardiac injury": { + "ontology_id": "NCIT:C45430" + }, + "Cardiac arrest": { + "ontology_id": "HP:0001695" + }, + "Cardiogenic shock": { + "ontology_id": "HP:0030149" + }, "Blood clot": { + "ontology_id": "UBERON:0010210", "schema:ItemList": { - "Arterial clot": {}, - "Deep vein thrombosis (DVT)": {}, - "Pulmonary embolism (PE)": {} + "Arterial clot": { + "ontology_id": "HP:0004420" + }, + "Deep vein thrombosis (DVT)": { + "ontology_id": "HP:0002625" + }, + "Pulmonary embolism (PE)": { + "ontology_id": "HP:0002204" + } } }, "Cardiomyopathy": { "ontology_id": "HP:0001638" }, - "Central nervous system invasion": {}, + "Central nervous system invasion": { + "ontology_id": "MONDO:0024619" + }, "Stroke (complication)": { + "ontology_id": "HP:0001297", "schema:ItemList": { - "Central Nervous System Vasculitis": {}, + "Central Nervous System Vasculitis": { + "ontology_id": "MONDO:0003346" + }, "Ischemic stroke": { "schema:ItemList": { - "Acute ischemic stroke": {} + "Acute ischemic stroke": { + "ontology_id": "HP:0002140" + } } } } }, - "Coma": {}, - "Convulsions": {}, - "COVID-19 associated coagulopathy (CAC)": {}, - "Cystic fibrosis": {}, - "Cytokine release syndrome": {}, - "Disseminated intravascular coagulation (DIC)": {}, - "Encephalopathy": {}, - "Fulminant myocarditis": {}, - "Guillain-Barr\u00e9 syndrome": {}, + "Coma": { + "ontology_id": "HP:0001259" + }, + "Convulsions": { + "ontology_id": "HP:0011097" + }, + "COVID-19 associated coagulopathy (CAC)": { + "ontology_id": "HP NTR" + }, + "Cystic fibrosis": { + "ontology_id": "MONDO:0009061" + }, + "Cytokine release syndrome": { + "ontology_id": "MONDO:0600008" + }, + "Disseminated intravascular coagulation (DIC)": { + "ontology_id": "HP NTR" + }, + "Encephalopathy": { + "ontology_id": "HP:0001298" + }, + "Fulminant myocarditis": { + "ontology_id": "HP NTR" + }, + "Guillain-Barr\u00e9 syndrome": { + "ontology_id": "MONDO:0016218" + }, "Internal hemorrhage (complication; internal bleeding)": { + "ontology_id": "HP:0011029", "schema:ItemList": { - "Intracerebral haemorrhage": {} + "Intracerebral haemorrhage": { + "ontology_id": "MONDO:0013792" + } } }, "Kawasaki disease": { + "ontology_id": "HP NTR", "schema:ItemList": { - "Typical Kawasaki disease": {}, - "Incomplete Kawasaki disease": {} + "Typical Kawasaki disease": { + "ontology_id": "HP NTR" + }, + "Incomplete Kawasaki disease": { + "ontology_id": "HP NTR" + } } }, "Kidney injury": { "schema:ItemList": { - "Acute kidney injury": {} + "Acute kidney injury": { + "ontology_id": "HP:0001919" + } } }, - "Liver dysfunction": {}, + "Long COVID-19": { + "ontology_id": "MONDO:0100233" + }, + "Liver dysfunction": { + "ontology_id": "HP:0001410" + }, "Liver injury": { "schema:ItemList": { - "Acute liver injury": {} + "Acute liver injury": { + "ontology_id": "HP NTR" + } } }, "Lung injury": { "schema:ItemList": { - "Acute lung injury": {} + "Acute lung injury": { + "ontology_id": "MONDO:0015796" + }, + "Ventilation induced lung injury (VILI)": { + "ontology_id": "HP NTR" + } } }, - "Meningitis": {}, - "Migraine": {}, - "Miscarriage": {}, - "Multisystem inflammatory syndrome in children (MIS-C)": {}, - "Muscle injury": {}, - "Myalgic encephalomyelitis (ME)": {}, + "Meningitis": { + "ontology_id": "HP:0001287" + }, + "Migraine": { + "ontology_id": "HP:0002076" + }, + "Miscarriage": { + "ontology_id": "HP:0005268" + }, + "Multisystem inflammatory syndrome in children (MIS-C)": { + "ontology_id": "MONDO:0100163" + }, + "Muscle injury": { + "ontology_id": "HP NTR" + }, + "Myalgic encephalomyelitis (ME)": { + "ontology_id": "MONDO:0005404" + }, "Myocardial infarction (heart attack)": { + "ontology_id": "MONDO:0005068", "schema:ItemList": { - "Acute myocardial infarction": {}, - "Elevation myocardial infarction": {}, - "ST-segment elevation myocardial infarction": {} + "Acute myocardial infarction": { + "ontology_id": "MONDO:0004781" + }, + "ST-segment elevation myocardial infarction": { + "ontology_id": "MONDO:0041656" + } } }, - "Myocardial injury": {}, - "Neonatal complications": {}, + "Myocardial injury": { + "ontology_id": "HP NTR" + }, + "Neonatal complications": { + "ontology_id": "NCIT:C168498" + }, "Organ failure": { + "ontology_id": "HP NTR", "schema:ItemList": { - "Heart failure": {}, - "Liver failure": {} + "Heart failure": { + "ontology_id": "HP:0002878" + }, + "Liver failure": { + "ontology_id": "HP:0001399" + } } }, - "Paralysis": {}, + "Paralysis": { + "ontology_id": "HP:0003470" + }, "Pneumothorax (collapsed lung)": { + "ontology_id": "HP:0002107", "schema:ItemList": { - "Spontaneous pneumothorax": {}, - "Spontaneous tension pneymothorax": {} + "Spontaneous pneumothorax": { + "ontology_id": "HP:0002108" + }, + "Spontaneous tension pneumothorax": { + "ontology_id": "MONDO:0002075" + } } }, "Pneumonia (complication)": { + "ontology_id": "HP:0002090", "schema:ItemList": { - "COVID-19 pneumonia": {} + "COVID-19 pneumonia": { + "ontology_id": "HP NTR" + } } }, - "Pregancy complications": {}, - "Rhabdomyolysis": {}, + "Pregancy complications": { + "ontology_id": "HP:0001197" + }, + "Rhabdomyolysis": { + "ontology_id": "HP:0003201" + }, "Secondary infection": { + "ontology_id": "IDO:0000567", "schema:ItemList": { - "Secondary staph infection": {}, - "Secondary strep infection": {} + "Secondary staph infection": { + "ontology_id": "IDO NTR" + }, + "Secondary strep infection": { + "ontology_id": "IDO NTR" + } } }, "Seizure (complication)": { @@ -6433,18 +6821,32 @@ var DATA = [ } } }, - "Sepsis": {}, - "Septicemia": {}, + "Sepsis": { + "ontology_id": "HP:0100806" + }, + "Septicemia": { + "ontology_id": "HP NTR" + }, "Shock": { + "ontology_id": "HP:0031273", "schema:ItemList": { - "Hyperinflammatory shock": {}, - "Refractory cardiogenic shock": {}, - "Refractory cardiogenic plus vasoplegic shock": {}, - "Septic shock": {} + "Hyperinflammatory shock": { + "ontology_id": "HP NTR" + }, + "Refractory cardiogenic shock": { + "ontology_id": "HP NTR" + }, + "Refractory cardiogenic plus vasoplegic shock": { + "ontology_id": "HP NTR" + }, + "Septic shock": { + "ontology_id": "HP NTR" + } } }, - "Vasculitis": {}, - "Ventilation induced lung injury (VILI)": {} + "Vasculitis": { + "ontology_id": "HP:0002633" + } } } ] @@ -6809,9 +7211,13 @@ var DATA = [ }, "schema:ItemList": { "Mass Gathering": { + "ontology_id": "PCO NTR", "schema:ItemList": { - "Agricultural Event": {}, + "Agricultural Event": { + "ontology_id": "PCO NTR" + }, "Convention": { + "ontology_id": "PCO NTR", "exportField": { "NML_LIMS": [ { @@ -6820,16 +7226,24 @@ var DATA = [ ] } }, - "Convocation": {}, + "Convocation": { + "ontology_id": "PCO NTR" + }, "Recreational Event": { + "ontology_id": "PCO NTR", "schema:ItemList": { - "Concert": {}, - "Sporting Event": {} + "Concert": { + "ontology_id": "PCO NTR" + }, + "Sporting Event": { + "ontology_id": "PCO NTR" + } } } } }, "Religious Gathering": { + "ontology_id": "PCO NTR", "exportField": { "NML_LIMS": [ { @@ -6838,10 +7252,13 @@ var DATA = [ ] }, "schema:ItemList": { - "Mass": {} + "Mass": { + "ontology_id": "PCO NTR" + } } }, "Social Gathering": { + "ontology_id": "PCO:0000033", "exportField": { "NML_LIMS": [ { @@ -6850,20 +7267,37 @@ var DATA = [ ] }, "schema:ItemList": { - "Baby Shower": {}, - "Community Event": {}, + "Baby Shower": { + "ontology_id": "PCO:0000039" + }, + "Community Event": { + "ontology_id": "PCO:0000034" + }, "Family Gathering": { + "ontology_id": "PCO NTR", "schema:ItemList": { - "Family Reunion": {} + "Family Reunion": { + "ontology_id": "PCO NTR" + } } }, - "Funeral": {}, - "Party": {}, - "Potluck": {}, - "Wedding": {} + "Funeral": { + "ontology_id": "PCO NTR" + }, + "Party": { + "ontology_id": "PCO:0000035" + }, + "Potluck": { + "ontology_id": "PCO:0000037" + }, + "Wedding": { + "ontology_id": "PCO:0000038" + } } }, - "Other exposure event": {} + "Other exposure event": { + "ontology_id": "NCIT:C168623" + } } }, { @@ -6894,12 +7328,20 @@ var DATA = [ }, "schema:ItemList": { "Contact with infected individual": { + "ontology_id": "NCIT NTR?", "schema:ItemList": { - "Direct contact (direct human-to-human contact)": {}, + "Direct contact (direct human-to-human contact)": { + "ontology_id": "NCIT NTR?" + }, "Indirect contact": { + "ontology_id": "NCIT NTR?", "schema:ItemList": { - "Close contact (face-to-face, no direct contact)": {}, - "Casual contact": {} + "Close contact (face-to-face, no direct contact)": { + "ontology_id": "NCIT NTR?" + }, + "Casual contact": { + "ontology_id": "NCIT:C102606" + } } } } @@ -6928,66 +7370,141 @@ var DATA = [ }, "schema:ItemList": { "Attendee": { + "ontology_id": "OMRSE NTR", "schema:ItemList": { - "Student": {} + "Student": { + "ontology_id": "OMRSE:00000058" + } } }, "Patient": { + "ontology_id": "OMRSE:00000030", "schema:ItemList": { - "Inpatient": {}, - "Outpatient": {} + "Inpatient": { + "ontology_id": "OMRSE NTR" + }, + "Outpatient": { + "ontology_id": "OMRSE NTR" + } } }, - "Passenger": {}, - "Resident": {}, - "Visitor": {}, - "Volunteer": {}, + "Passenger": { + "ontology_id": "OMRSE NTR" + }, + "Resident": { + "ontology_id": "OMRSE NTR" + }, + "Visitor": { + "ontology_id": "OMRSE NTR" + }, + "Volunteer": { + "ontology_id": "OMRSE NTR" + }, "Work": { + "ontology_id": "OMRSE NTR", "schema:ItemList": { - "Administrator": {}, + "Administrator": { + "ontology_id": "OMRSE NTR" + }, "First Responder": { + "ontology_id": "OMRSE NTR", + "schema:ItemList": { + "Firefighter": { + "ontology_id": "OMRSE NTR" + }, + "Paramedic": { + "ontology_id": "OMRSE NTR" + }, + "Police Officer": { + "ontology_id": "OMRSE NTR" + } + } + }, + "Child Care/Education Worker": { + "ontology_id": "OMRSE NTR" + }, + "Essential Worker": { + "ontology_id": "OMRSE NTR" + }, + "Healthcare Worker": { + "ontology_id": "OMRSE NTR", "schema:ItemList": { - "Firefighter": {}, - "Paramedic": {}, - "Police Officer": {} - } - }, - "Child Care/Education Worker": {}, - "Essential Worker": {}, - "Healthcare Worker": {}, - "Nurse": {}, - "Personal Care Aid": {}, - "Pharmacist": {}, - "Physician": {}, - "Housekeeper": {}, - "International worker": {}, - "Kitchen Worker": {}, - "Laboratory Worker": {}, - "Rotational Worker": {}, - "Seasonal Worker": {}, + "Nurse": { + "ontology_id": "OMRSE:00000014" + }, + "Personal Care Aid": { + "ontology_id": "OMRSE NTR" + }, + "Pharmacist": { + "ontology_id": "OMRSE NTR" + }, + "Physician": { + "ontology_id": "OMRSE:00000050" + } + } + }, + "Housekeeper": { + "ontology_id": "OMRSE NTR" + }, + "International worker": { + "ontology_id": "OMRSE NTR" + }, + "Kitchen Worker": { + "ontology_id": "OMRSE NTR" + }, + "Laboratory Worker": { + "ontology_id": "OMRSE NTR" + }, + "Rotational Worker": { + "ontology_id": "OMRSE NTR" + }, + "Seasonal Worker": { + "ontology_id": "OMRSE NTR" + }, "Transport Worker": { + "ontology_id": "OMRSE NTR", "schema:ItemList": { - "Transport Truck Driver": {} + "Transport Truck Driver": { + "ontology_id": "OMRSE NTR" + } } }, - "Veterinarian": {} + "Veterinarian": { + "ontology_id": "OMRSE NTR" + } } }, "Social role": { + "ontology_id": "OMRSE:00000001", "schema:ItemList": { - "Acquaintance of case": {}, + "Acquaintance of case": { + "ontology_id": "OMRSE NTR" + }, "Relative of case": { + "ontology_id": "OMRSE NTR", "schema:ItemList": { - "Child of case": {}, - "Parent of case": {}, - "Father of case": {}, - "Mother of case": {} + "Child of case": { + "ontology_id": "OMRSE NTR" + }, + "Parent of case": { + "ontology_id": "OMRSE NTR" + }, + "Father of case": { + "ontology_id": "OMRSE NTR" + }, + "Mother of case": { + "ontology_id": "OMRSE NTR" + } } }, - "Spouse of case": {} + "Spouse of case": { + "ontology_id": "OMRSE NTR" + } } }, - "Other Host Role": {} + "Other Host Role": { + "ontology_id": "OMRSE NTR" + } } }, { @@ -7014,84 +7531,156 @@ var DATA = [ "Human Exposure": { "ontology_id": "ECTO_3000005", "schema:ItemList": { - "Contact with Known COVID-19 Case": {}, - "Contact with Patient": {}, - "Contact with Probable COVID-19 Case": {}, - "Contact with Person with Acute Respiratory Illness": {}, - "Contact with Person with Fever and/or Cough": {}, - "Contact with Person who Recently Travelled": {} + "Contact with Known COVID-19 Case": { + "ontology_id": "ECTO NTR" + }, + "Contact with Patient": { + "ontology_id": "ECTO NTR" + }, + "Contact with Probable COVID-19 Case": { + "ontology_id": "ECTO NTR" + }, + "Contact with Person with Acute Respiratory Illness": { + "ontology_id": "ECTO NTR" + }, + "Contact with Person with Fever and/or Cough": { + "ontology_id": "ECTO NTR" + }, + "Contact with Person who Recently Travelled": { + "ontology_id": "ECTO NTR" + } } }, "Occupational, Residency or Patronage Exposure": { + "ontology_id": "ECTO NTR?", "schema:ItemList": { "Abbatoir": { "ontology_id": "ECTO_1000033" }, - "Animal Rescue": {}, + "Animal Rescue": { + "ontology_id": "ECTO NTR" + }, "Childcare": { + "ontology_id": "ECTO NTR", "schema:ItemList": { - "Daycare": {} + "Daycare": { + "ontology_id": "ECTO NTR" + } } }, - "Funeral Home": {}, + "Funeral Home": { + "ontology_id": "ECTO NTR" + }, "Place of Worship": { + "ontology_id": "ECTO NTR", "schema:ItemList": { - "Church": {}, - "Mosque": {}, - "Temple": {} + "Church": { + "ontology_id": "ECTO NTR" + }, + "Mosque": { + "ontology_id": "ECTO NTR" + }, + "Temple": { + "ontology_id": "ECTO NTR" + } } }, - "Nursery": {}, - "Household": {}, - "Community Service Centre": {}, - "Correctional Facility": {}, - "Dormitory": {}, + "Nursery": { + "ontology_id": "ECTO NTR" + }, + "Household": { + "ontology_id": "ECTO NTR" + }, + "Community Service Centre": { + "ontology_id": "ECTO NTR" + }, + "Correctional Facility": { + "ontology_id": "ECTO NTR" + }, + "Dormitory": { + "ontology_id": "ECTO NTR" + }, "Farm": { "ontology_id": "ECTO_1000034" }, - "First Nations Reserve": {}, - "Group Home": {}, + "First Nations Reserve": { + "ontology_id": "ECTO NTR" + }, + "Group Home": { + "ontology_id": "ECTO NTR" + }, "Healthcare Setting": { - "ontology_id": "ECTO_1000035", + "ontology_id": "ECTO NTR", "schema:ItemList": { - "Ambulance": {}, - "Acute Care Facility": {}, - "Clinic": {}, - "Community Health Centre": {}, + "Ambulance": { + "ontology_id": "ECTO NTR" + }, + "Acute Care Facility": { + "ontology_id": "ECTO NTR" + }, + "Clinic": { + "ontology_id": "ECTO NTR" + }, + "Community Health Centre": { + "ontology_id": "ECTO NTR" + }, "Hospital": { + "ontology_id": "ECTO_1000035", "schema:ItemList": { - "Emergency Department": {}, - "ICU": {}, - "Ward": {} + "Emergency Department": { + "ontology_id": "ECTO NTR" + }, + "ICU": { + "ontology_id": "ECTO NTR" + }, + "Ward": { + "ontology_id": "ECTO NTR" + } } }, "Laboratory": { "ontology_id": "ECTO_1000036" }, - "Long-Term Care Facility": {}, - "Pharmacy": {}, - "Physician's Office": {} + "Long-Term Care Facility": { + "ontology_id": "ECTO NTR" + }, + "Pharmacy": { + "ontology_id": "ECTO NTR" + }, + "Physician's Office": { + "ontology_id": "ECTO NTR" + } } }, - "Insecure Housing (Homeless)": {}, + "Insecure Housing (Homeless)": { + "ontology_id": "ECTO NTR" + }, "Occupational Exposure": { + "ontology_id": "ECTO NTR", "schema:ItemList": { - "Worksite": {}, + "Worksite": { + "ontology_id": "ECTO NTR" + }, "Office": { "ontology_id": "ECTO:1000037" } } }, "Outdoors": { + "ontology_id": "ECTO NTR", "schema:ItemList": { "Camp/camping": { "ontology_id": "ECTO_5000009" }, - "Hiking Trail": {}, + "Hiking Trail": { + "ontology_id": "ECTO NTR" + }, "Hunting Ground": { "ontology_id": "ECTO_6000030" }, - "Ski Resort": {} + "Ski Resort": { + "ontology_id": "ECTO NTR" + } } }, "Petting zoo": { @@ -7103,34 +7692,48 @@ var DATA = [ "Retail Store": { "ontology_id": "ECTO_1000041" }, - "School": {}, + "School": { + "ontology_id": "ECTO NTR" + }, "Temporary Residence": { + "ontology_id": "ECTO NTR", "schema:ItemList": { - "Homeless Shelter": {}, - "Hotel": {} + "Homeless Shelter": { + "ontology_id": "ECTO NTR" + }, + "Hotel": { + "ontology_id": "ECTO NTR" + } } }, - "Veterinary Care Clinic": {} + "Veterinary Care Clinic": { + "ontology_id": "ECTO NTR" + } } }, "Travel Exposure": { + "ontology_id": "ECTO NTR", "schema:ItemList": { - "Travelled": { - "schema:ItemList": { - "Travelled on a Cruise Ship": {}, - "Travelled on a Plane": {}, - "Travelled on Ground Transport": {}, - "Travelled outside Province/Territory": { - "ontology_id": "GENEPIO_0001119" - }, - "Travelled outside Canada": { - "ontology_id": "GENEPIO_0001118" - } - } + "Travelled on a Cruise Ship": { + "ontology_id": "ECTO NTR" + }, + "Travelled on a Plane": { + "ontology_id": "ECTO NTR" + }, + "Travelled on Ground Transport": { + "ontology_id": "ECTO NTR" + }, + "Travelled outside Province/Territory": { + "ontology_id": "GENEPIO_0001119" + }, + "Travelled outside Canada": { + "ontology_id": "GENEPIO_0001118" } } }, - "Other Exposure Setting": {} + "Other Exposure Setting": { + "ontology_id": "GENEPIO NTR?" + } } }, { @@ -7354,7 +7957,9 @@ var DATA = [ ] }, "schema:ItemList": { - "Baseline surveillance (random sampling)": {}, + "Baseline surveillance (random sampling)": { + "ontology_id": "See comment" + }, "Targeted surveillance (non-random sampling)": { "schema:ItemList": { "Priority surveillance project": { @@ -7377,12 +7982,14 @@ var DATA = [ } }, "Cluster/Outbreak investigation": { + "ontology_id": "HSO:0000371", "schema:ItemList": { "Multi-jurisdictional outbreak investigation": {}, "Intra-jurisdictional outbreak investigation": {} } }, "Research": { + "ontology_id": "NCIT_c15429", "schema:ItemList": { "Viral passage experiment": {}, "Protocol testing experiment": {} @@ -7442,14 +8049,14 @@ var DATA = [ ], "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "", + "requirement": "required", "description": "The date the sample was sequenced.", "guidance": "ISO 8601 standard \"YYYY-MM-DD\".", "examples": "2020-06-22", "exportField": { "NML_LIMS": [ { - "field": "sequencing date" + "field": "PH_SEQUENCING_DATE" } ] } @@ -7594,12 +8201,18 @@ var DATA = [ } } }, - "Illumina HiScanSQ": {}, - "Illumina HiSeq": {}, + "Illumina HiScanSQ": { + "ontology_id": "OBI NTR?" + }, + "Illumina HiSeq": { + "ontology_id": "OBI NTR?" + }, "Illumina HiSeq X": { - "ontology_id": "OBI_0002129", + "ontology_id": "OBI NTR?", "schema:ItemList": { - "Illumina HiSeq X Five": {}, + "Illumina HiSeq X Five": { + "ontology_id": "OBI NTR?" + }, "Illumina HiSeq X Ten": { "ontology_id": "OBI_0002129" } @@ -7608,7 +8221,9 @@ var DATA = [ "Illumina HiSeq 1000": { "ontology_id": "OBI_0002022" }, - "Illumina HiSeq 1500": {}, + "Illumina HiSeq 1500": { + "ontology_id": "OBI NTR?" + }, "Illumina HiSeq 2000": { "ontology_id": "OBI_0002001" }, @@ -7622,13 +8237,15 @@ var DATA = [ "ontology_id": "OBI_0002049" }, "Illumina iSeq": { + "ontology_id": "OBI NTR?", "schema:ItemList": { "Illumina iSeq 100": { - "ontology_id": "EFO:0008635" + "ontology_id": "OBI NTR?" } } }, "Illumina NovaSeq": { + "ontology_id": "OBI NTR?", "schema:ItemList": { "Illumina NovaSeq 6000": { "ontology_id": "OBI_0002630" @@ -7636,23 +8253,31 @@ var DATA = [ } }, "Illumina MiniSeq": { - "ontology_id": "EFO_0008636" + "ontology_id": "OBI NTR?" }, "Illumina MiSeq": { "ontology_id": "OBI_0002003" }, - "Illumina NextSeq": {}, + "Illumina NextSeq": { + "ontology_id": "OBI NTR?" + }, "Illumina NextSeq 500": { "ontology_id": "OBI_0002021" }, - "Illumina NextSeq 550": {}, - "Illumina NextSeq 2000": {} + "Illumina NextSeq 550": { + "ontology_id": "OBI NTR?" + }, + "Illumina NextSeq 2000": { + "ontology_id": "OBI NTR?" + } } }, "Pacific Biosciences": { "ontology_id": "OBI_0001856", "schema:ItemList": { - "PacBio RS": {}, + "PacBio RS": { + "ontology_id": "OBI NTR?" + }, "PacBio RS II": { "ontology_id": "OBI_0002012" }, @@ -7665,33 +8290,59 @@ var DATA = [ } }, "Ion Torrent": { + "ontology_id": "OBI NTR?", "schema:ItemList": { "Ion Torrent PGM": { "ontology_id": "GENEPIO_0001935" }, - "Ion Torrent Proton": {}, - "Ion Torrent S5 XL": {}, - "Ion Torrent S5": {} + "Ion Torrent Proton": { + "ontology_id": "OBI NTR?" + }, + "Ion Torrent S5 XL": { + "ontology_id": "OBI NTR?" + }, + "Ion Torrent S5": { + "ontology_id": "OBI NTR?" + } } }, "Oxford Nanopore": { + "ontology_id": "OBI NTR?", "schema:ItemList": { - "Oxford Nanopore GridION": {}, - "Oxford Nanopore MinION": {}, - "Oxford Nanopore PromethION": {} + "Oxford Nanopore GridION": { + "ontology_id": "OBI:0002751" + }, + "Oxford Nanopore MinION": { + "ontology_id": "OBI:0002750" + }, + "Oxford Nanopore PromethION": { + "ontology_id": "OBI:0002752" + } } }, "BGI Genomics": { + "ontology_id": "OBI NTR?", "schema:ItemList": { - "BGI Genomics BGISEQ-500": {} + "BGI Genomics BGISEQ-500": { + "ontology_id": "OBI NTR?" + } } }, "MGI": { + "ontology_id": "OBI NTR?", "schema:ItemList": { - "MGI DNBSEQ-T7": {}, - "MGI DNBSEQ-G400": {}, - "MGI DNBSEQ-G400 FAST": {}, - "MGI DNBSEQ-G50": {} + "MGI DNBSEQ-T7": { + "ontology_id": "OBI NTR?" + }, + "MGI DNBSEQ-G400": { + "ontology_id": "OBI NTR?" + }, + "MGI DNBSEQ-G400 FAST": { + "ontology_id": "OBI NTR?" + }, + "MGI DNBSEQ-G50": { + "ontology_id": "OBI NTR?" + } } } } @@ -7804,14 +8455,14 @@ var DATA = [ "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "recommended", + "requirement": "required", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "guidance": "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3", "examples": "Porechop 0.2.3", "exportField": { "NML_LIMS": [ { - "field": "raw sequence data processing method" + "field": "PH_RAW_SEQUENCE_METHOD" } ], "VirusSeq_Portal": [ @@ -7830,7 +8481,7 @@ var DATA = [ "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "", + "requirement": "required", "description": "The method used to remove host reads from the pathogen sequence.", "guidance": "Provide the name and version number of the software used to remove host reads.", "examples": "Nanostripper", @@ -8274,10 +8925,10 @@ var DATA = [ "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "", - "description": "The name and version number of the bioinformatics protocol used.", - "guidance": "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.", - "examples": "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members", + "requirement": "required", + "description": "A description of the overall bioinformatics strategy used.", + "guidance": "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow.", + "examples": "https://github.com/phac-nml/ncov2019-artic-nf", "exportField": { "CNPHI": [ { @@ -8743,6 +9394,7 @@ var DATA = [ } }, "orf3b": { + "ontology_id": "PR NTR", "exportField": { "BIOSAMPLE": [ { @@ -8802,6 +9454,7 @@ var DATA = [ } }, "orf9c": { + "ontology_id": "PR NTR?", "exportField": { "BIOSAMPLE": [ { @@ -8821,6 +9474,7 @@ var DATA = [ } }, "orf14": { + "ontology_id": "PR NTR?", "exportField": { "BIOSAMPLE": [ { diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index b7d85970..a299f062 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -1,1316 +1,1317 @@ -Ontology ID Meaning (LinkML) 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 EXPORT_VirusSeq_Portal -ID SC % -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 VD_LAB_NUMBER -GENEPIO_0001149 Database Identifiers third party lab sample ID xs:token The identifier assigned to a sample by a third party service provider. SHK123456 third party lab sample ID -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_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 -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 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 GISAID accession -GENEPIO_0001150 Sample collection and processing -GENEPIO_0001153 Sample collection and processing sample collected by select 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 CUSTOMER collected_by sample collected by -GENEPIO_0001156 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 sample collector contact email -GENEPIO_0001158 Sample collection and processing sample collector contact address xs:token The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address -GENEPIO_0001159 Sample collection and processing sequence submitted by select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by -GENEPIO_0001165 Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email -GENEPIO_0001167 Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address -GENEPIO_0001174 Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date -GENEPIO_0001177 Sample collection and processing sample collection date precision select required The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 -GENEPIO_0001179 Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date -GENEPIO_0001181 Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) -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;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 -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 -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 -GENEPIO_0001223 Sample collection and processing environmental material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental 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. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material -GENEPIO_0001232 Sample collection and processing environmental site select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site 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. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site -GENEPIO_0001234 Sample collection and processing collection device select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. 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. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device -GENEPIO_0001241 Sample collection and processing collection method select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. 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. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method -GENEPIO_0001243 Sample collection and processing collection protocol xs:token The name and version of a particular protocol used for sampling. Free text. BCRonaSamplingProtocol v. 1.2 collection protocol -GENEPIO_0001253 Sample collection and processing specimen processing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history specimen processing -GENEPIO_0001255 Sample collection and processing lab host select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Vero E6 cell line Passage details/history lab host lab_host -GENEPIO_0001261 Sample collection and processing passage number xs:nonNegativeInteger Not Applicable recommended Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 Passage details/history passage number passage_history -GENEPIO_0001264 Sample collection and processing passage method xs:token Not Applicable recommended Description of how organism was passaged. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". 0.25% trypsin + 0.02% EDTA Passage details/history passage method passage_method -GENEPIO_0001266 Sample collection and processing biomaterial extracted select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) biomaterial extracted -GENEPIO_0001268 Host Information -GENEPIO_0001386 Host Information host (common name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human Animal Type PH_ANIMAL_TYPE -GENEPIO_0001387 Host Information host (scientific name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) -GENEPIO_0001388 Host Information host health state select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Symptomatic Patient status Host Health State PH_HOST_HEALTH host_health_state -GENEPIO_0001389 Host Information host health status details select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS -GENEPIO_0001390 Host Information host health outcome select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered host health outcome host_disease_outcome -GENEPIO_0001391 Host Information host disease select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease -GENEPIO_0001392 Host Information host age xs:decimal Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age -GENEPIO_0001393 Host Information host age unit select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit -GENEPIO_0001394 Host Information host age bin select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin -GENEPIO_0001395 Host Information host gender select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Title The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". male Gender Patient Sex VD_SEX host_sex host gender -GENEPIO_0001396 Host Information host residence geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country of residence of the host. Select the country name from pick list provided in the template. United Kingdom PH_HOST_COUNTRY -GENEPIO_0001397 Host Information host residence geo_loc name (state/province/territory) select geo_loc_name (state/province/territory) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE -GENEPIO_0001398 Host Information host subject ID xs:token A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host subject ID host_subject_id -GENEPIO_0001399 Host Information symptom onset date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the symptoms began or were first noted. ISO 8601 standard "YYYY-MM-DD". 2020-03-16 Symptoms Onset Date HC_ONSET_DATE -GENEPIO_0001400 Host Information signs and symptoms multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Select all of the symptoms experienced by the host from the pick list. Chills (sudden cold sensation); Cough; Fever Symptoms HC_SYMPTOMS -GENEPIO_0001401 Host Information pre-existing conditions and risk factors multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma; Pregnancy; Smoking pre-existing conditions and risk factors -GENEPIO_0001402 Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Acute Respiratory Failure; Coma; Septicemia complications -GENEPIO_0001403 Host vaccination information -GENEPIO_0001404 Host vaccination information host vaccination status select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated host vaccination status -GENEPIO_0001405 Host vaccination information vaccine name xs:token The name of the vaccine. Free text. Provide the name of the vaccine. Pfizer-BioNTech COVID-19 vaccine vaccine name -GENEPIO_0001406 Host vaccination information number of vaccine doses received xs:nonNegativeInteger The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 number of vaccine doses received -GENEPIO_0001407 Host vaccination information first dose vaccination date xs:date The date the host was first vaccinated. Provide the vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-02-26 first dose vaccination date -GENEPIO_0001408 Host vaccination information last dose vaccination date xs:date The date the host received their last dose of vaccine. Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-09 last dose vaccination date -GENEPIO_0001409 Host exposure information -GENEPIO_0001410 Host exposure information location of exposure geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country where the host was likely exposed to the causative agent of the illness. Select the country name from pick list provided in the template. Canada PH_EXPOSURE_COUNTRY -GENEPIO_0001411 Host exposure information destination of most recent travel (city) xs:token The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL -GENEPIO_0001412 Host exposure information destination of most recent travel (state/province/territory) xs:token The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL -GENEPIO_0001413 Host exposure information destination of most recent travel (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL -GENEPIO_0001414 Host exposure information most recent travel departure date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL -GENEPIO_0001415 Host exposure information most recent travel return date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL -GENEPIO_0001416 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 travel history -GENEPIO_0001417 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 -GENEPIO_0001418 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 exposure contact level -GENEPIO_0001419 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 -GENEPIO_0001428 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 -GENEPIO_0001431 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 - - -GENEPIO_0001434 Host reinfection information -GENEPIO_0001435 Host reinfection information prior SARS-CoV-2 infection select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 infection. If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Yes prior SARS-CoV-2 infection -GENEPIO_0001436 Host reinfection information prior SARS-CoV-2 infection isolate xs:token The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 prior SARS-CoV-2 infection isolate -GENEPIO_0001437 Host reinfection information prior SARS-CoV-2 infection date xs:date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 prior SARS-CoV-2 infection date -GENEPIO_0001438 Host reinfection information prior SARS-CoV-2 antiviral treatment select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. No prior antiviral treatment prior SARS-CoV-2 antiviral treatment -GENEPIO_0001439 Host reinfection information prior SARS-CoV-2 antiviral treatment agent xs:token The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir prior SARS-CoV-2 antiviral treatment agent -GENEPIO_0001440 Host reinfection information prior SARS-CoV-2 antiviral treatment date xs:date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 prior SARS-CoV-2 antiviral treatment date - - -GENEPIO_0001441 Sequencing -GENEPIO_0001445 Sequencing purpose of sequencing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing -GENEPIO_0001446 Sequencing purpose of sequencing details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details -GENEPIO_0001447 Sequencing sequencing date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 sequencing date -GENEPIO_0001448 Sequencing library ID xs:token recommended The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID -GENEPIO_0001449 Sequencing amplicon size xs:token The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size -GENEPIO_0001450 Sequencing library preparation kit xs:token The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library preparation kit -GENEPIO_0001451 Sequencing flow cell barcode xs:token The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 flow cell barcode -GENEPIO_0001452 Sequencing sequencing instrument multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. MinIon Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument -GENEPIO_0001453 Sequencing sequencing protocol name xs:token recommended The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name sequencing protocol name -GENEPIO_0001454 Sequencing sequencing protocol xs:token The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol -GENEPIO_0001455 Sequencing sequencing kit number xs:token The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number -GENEPIO_0001456 Sequencing amplicon pcr primer scheme xs:token The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon pcr primer scheme - - -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 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 -GENEPIO_0001463 Bioinformatics and QC metrics consensus sequence software name xs:token required The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name -GENEPIO_0001469 Bioinformatics and QC metrics consensus sequence software version xs:token required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version -GENEPIO_0001472 Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% breadth of coverage value breadth of coverage value -GENEPIO_0001474 Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage depth of coverage value depth of coverage value -GENEPIO_0001475 Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold -GENEPIO_0001476 Bioinformatics and QC metrics r1 fastq filename xs:token recommended The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename -GENEPIO_0001477 Bioinformatics and QC metrics r2 fastq filename xs:token recommended The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename -GENEPIO_0001478 Bioinformatics and QC metrics r1 fastq filepath xs:token The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath -GENEPIO_0001479 Bioinformatics and QC metrics r2 fastq filepath xs:token The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath -GENEPIO_0001480 Bioinformatics and QC metrics fast5 filename xs:token The user-specified filename of the FAST5 file. Provide the FAST5 filename. rona123assembly.fast5 fast5 filename -GENEPIO_0001481 Bioinformatics and QC metrics fast5 filepath xs:token The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/rona123assembly.fast5 fast5 filepath -GENEPIO_0001482 Bioinformatics and QC metrics number of base pairs sequenced xs:nonNegativeInteger The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 number of base pairs sequenced -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 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 -GENEPIO_0001502 Lineage and Variant information lineage/clade analysis software version xs:token The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION -GENEPIO_0001503 Lineage and Variant information variant designation select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern PH_VARIANT_DESIGNATION -GENEPIO_0001504 Lineage and Variant information variant evidence select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The evidence used to make the variant determination. Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. RT-qPCR PH_VARIANT_EVIDENCE -GENEPIO_0001505 Lineage and Variant information variant evidence details xs:token Details about the evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). PH_VARIANT_EVIDENCE_DETAILS -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 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 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 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 - - - umbrella bioproject accession PRJNA623807 - - - - - - - - -GAZ_00002566 geo_loc_name (state/province/territory) Alberta CA-AB -GAZ_00002562 geo_loc_name (state/province/territory) British Columbia CA-BC -GAZ_00002571 geo_loc_name (state/province/territory) Manitoba CA-MB -GAZ_00002570 geo_loc_name (state/province/territory) New Brunswick CA-NB -GAZ_00002567 geo_loc_name (state/province/territory) Newfoundland and Labrador CA-NL -GAZ_00002575 geo_loc_name (state/province/territory) Northwest Territories CA-NT -GAZ_00002565 geo_loc_name (state/province/territory) Nova Scotia CA-NS -GAZ:00002574 geo_loc_name (state/province/territory) Nunavut CA-NU -GAZ_00002563 geo_loc_name (state/province/territory) Ontario CA-ON -GAZ_00002572 geo_loc_name (state/province/territory) Prince Edward Island CA-PE -GAZ_00002569 geo_loc_name (state/province/territory) Quebec CA-QC -GAZ_00002564 geo_loc_name (state/province/territory) Saskatchewan CA-SK -GAZ_00002576 geo_loc_name (state/province/territory) Yukon CA-YT - -UO:0000035 host age unit month Month -UO:0000036 host age unit year Year - -UO:0000035 sample collection date precision year Year -UO:0000036 sample collection date precision month Month -UO:0000033 sample collection date precision day Day - -OBI:0000895 biomaterial extracted RNA (total) -OBI:0000869 biomaterial extracted RNA (poly-A) -OBI:0002627 biomaterial extracted RNA (ribo-depleted) -OBI REQUEST biomaterial extracted mRNA (messenger RNA) -OBI:0002754 biomaterial extracted mRNA (cDNA) - - - signs and symptoms Abnormal lung auscultation -HP:0000223 signs and symptoms Abnormality of taste sensation SENSE_OF_TASTE -HP:0041051 Abnormality of taste sensation Ageusia (complete loss of taste) AGEUSIA -HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) PARAGEUSIA -HP_0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) HYPOGEUSIA -HP:0004408 signs and symptoms Abnormality of the sense of smell SENSE_OF_SMELL -HP_0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) ANOSMIA -HP_0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) HYPOSMIA -HP:0033677 signs and symptoms Acute Respiratory Distress Syndrome ARDS -HP:0011446 signs and symptoms Altered mental status ALTERED_CONSCIOUS -HP:0011675 signs and symptoms Arrhythmia -HP:0100543 Altered mental status Cognitive impairment COGNITIVE -HP_0001259 Altered mental status Coma COMA -HP_0001289 Altered mental status Confusion CONFUSION -HP_0031258 Confusion Delirium (sudden severe confusion) DELIRIUM - Altered mental status Inability to arouse (inability to stay awake) INABILITY_AWAKE -HP_0000737 Altered mental status Irritability IRRITABILITY -HP_0002371 Altered mental status Loss of speech LOSS_OF_SPEECH -HP_0025406 signs and symptoms Asthenia (generalized weakness) ASTHENIA -HP:0031352 signs and symptoms Chest tightness or pressure CHEST_TIGHT -HP:0025145 Chest tightness or pressure Rigors (fever shakes) RIGORS -HP_0025143 signs and symptoms Chills (sudden cold sensation) Chills CHILLS -HP:0030953 signs and symptoms Conjunctival injection -HP_0000509 signs and symptoms Conjunctivitis (pink eye) Conjunctivitis CONJUNCTIVITIS -MP:0001867 signs and symptoms Coryza (rhinitis) -HP_0012735 signs and symptoms Cough COUGH -HP:0031246 Cough Nonproductive cough (dry cough) NONPRODUCT_COUGH -HP:0031245 Cough Productive cough (wet cough) PRODUCTIVE_COUGH -HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) CYANOSIS -HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis ACROCYANOS -HP:0032556 Acrocyanosis Circumoral cyanosis (bluish around mouth) CIRCUMORAL_CYANOSIS - Acrocyanosis Cyanotic face (bluish face) CYANOTIC_FACE - Cyanosis (blueish skin discolouration) Central Cyanosis - Central Cyanosis Cyanotic lips (bluish lips) CYANOTIC_LIPS - Cyanosis (blueish skin discolouration) Peripheral Cyanosis -HP_0002094 signs and symptoms Dyspnea (breathing difficulty) DYSPNEA -HP_0002014 signs and symptoms Diarrhea (watery stool) Diarrhea, watery DIARRHEA -MP:0031127 signs and symptoms Dry gangrene -HP_0002383 signs and symptoms Encephalitis (brain inflammation) Encephalitis ENCEPHALITIS -HP:0001298 signs and symptoms Encephalopathy -HP_0012378 signs and symptoms Fatigue (tiredness) Fatigue FATIGUE -HP_0001945 signs and symptoms Fever FEVER - Fever Fever (>=38°C) Fever -HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) GLOSSITIS - signs and symptoms Ground Glass Opacities (GGO) -HP_0002315 signs and symptoms Headache HEADACHE -HP_0002105 signs and symptoms Hemoptysis (coughing up blood) HEMOPTYSIS -HP:0012417 signs and symptoms Hypocapnia -HP_0002615 signs and symptoms Hypotension (low blood pressure) HYPOTENSION -HP_0012418 signs and symptoms Hypoxemia (low blood oxygen) HYPOXEMIA - Hypoxemia (low blood oxygen) Silent hypoxemia -HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) INTERNAL_HEMORRHAGE -NCIT:C121416 signs and symptoms Loss of Fine Movements LOSS_OF_FINE_MOVE -HP_0004396 signs and symptoms Low appetite LOW_APPETITE -HP:0033834 signs and symptoms Malaise (general discomfort/unease) MALAISE -HP:0031179 signs and symptoms Meningismus/nuchal rigidity -HP_0001324 signs and symptoms Muscle weakness MUSCLE_WEAK -HP_0001742 signs and symptoms Nasal obstruction (stuffy nose) NASAL_OBSTRUCT -HP_0002018 signs and symptoms Nausea NAUSEA -HP_0000421 signs and symptoms Nose bleed - signs and symptoms Otitis -HP:0012531 signs and symptoms Pain -HP:0002027 Pain Abdominal pain ABDOMINAL -HP_0002829 Pain Arthralgia (painful joints) ARTHRALGIA -HP_0100749 Pain Chest pain CHEST_PAIN -HP:0033771 Chest pain Pleuritic chest pain -HP_0003326 Pain Myalgia (muscle pain) MYALGIA -HP_0025439 signs and symptoms Pharyngitis (sore throat) PHARYNGITIS - signs and symptoms Pharyngeal exudate -HP:0002202 signs and symptoms Pleural effusion -HP:0002090 signs and symptoms Pneumonia - signs and symptoms Prostration -HP:0033696 signs and symptoms Pseudo-chilblains - Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) PSEUDO-CHIBLAINS_F - Pseudo-chilblains Pseudo-chilblains on toes (covid toes) PSEUDO-CHIBLAINS_T -HP_0000988 signs and symptoms Rash RASH -HP_0031417 signs and symptoms Rhinorrhea (runny nose) RHINORRHEA -HP_0001250 signs and symptoms Seizure SEIZURE -HP:0020219 Seizure Motor seizure MOTOR_SEIZURE -HP:0025144 signs and symptoms Shivering (involuntary muscle twitching) SHIVERING -HP_0001350 signs and symptoms Slurred speech SLURRED_SPEECH -HP:0025095 signs and symptoms Sneezing -HP:0033709 signs and symptoms Sputum Production -HP:0001297 signs and symptoms Stroke STROKE -HP:0002716 signs and symptoms Swollen Lymph Nodes -HP_0002789 signs and symptoms Tachypnea (accelerated respiratory rate) TACHYPNEA -HP:0002321 signs and symptoms Vertigo (dizziness) -HP_0002013 signs and symptoms Vomiting (throwing up) VOMITING - - host vaccination status Fully Vaccinated - host vaccination status Partially Vaccinated - host vaccination status Not Vaccinated - - prior SARS-CoV-2 antiviral treatment Prior antivrial treatment - prior SARS-CoV-2 antiviral treatment No prior antivrial treatment - prior SARS-CoV-2 antiviral treatment Unknown - -OBI_0002600 NML submitted specimen type Swab PH_SPECIMEN_TYPE:SWAB -OBI_0000880 NML submitted specimen type RNA PH_SPECIMEN_TYPE:RNA -OBI:0002754 NML submitted specimen type mRNA (cDNA) -OBI:0001010 NML submitted specimen type Nucleic acid PH_SPECIMEN_TYPE:NUCLEIC_ACID -GENEPIO:0001619 NML submitted specimen type Not Applicable PH_SPECIMEN_TYPE:NA - - -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 - - - pre-existing conditions and risk factors Age 60+ - pre-existing conditions and risk factors Anemia - pre-existing conditions and risk factors Anorexia - pre-existing conditions and risk factors Birthing labor - pre-existing conditions and risk factors Bone marrow failure - pre-existing conditions and risk factors Cancer - Cancer Breast cancer - Cancer Colorectal cancer - Cancer Hematologic malignancy - Cancer Lung cancer - Cancer Metastatic disease - pre-existing conditions and risk factors Cancer treatment - Cancer treatment Cancer surgery - Cancer treatment Chemotherapy - Chemotherapy Adjuvant chemotherapy - pre-existing conditions and risk factors Cardiac disorder -HP:0011675 Cardiac disorder Arrhythmia - Cardiac disorder Cardiac disease -HP:0001638 Cardiac disorder Cardiomyopathy - Cardiac disorder Cardiac injury -HP_0000822 Cardiac disorder Hypertension (high blood pressure) -HP:0002615 Cardiac disorder Hypotension (low blood pressure) - pre-existing conditions and risk factors Cesarean section - pre-existing conditions and risk factors Chronic cough - pre-existing conditions and risk factors Chronic gastrointestinal disease - pre-existing conditions and risk factors Chronic lung disease - pre-existing conditions and risk factors Corticosteroids - pre-existing conditions and risk factors Diabetes mellitus (diabetes) - Diabetes mellitus (diabetes) Type I diabetes mellitus (T1D) - Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D) - pre-existing conditions and risk factors Eczema - pre-existing conditions and risk factors Electrolyte disturbance - Electrolyte disturbance Hypocalcemia - Electrolyte disturbance Hypokalemia - Electrolyte disturbance Hypomagnesemia -HP:0002383 pre-existing conditions and risk factors Encephalitis (brain inflammation) - pre-existing conditions and risk factors Epilepsy - pre-existing conditions and risk factors Hemodialysis - pre-existing conditions and risk factors Hemoglobinopathy - pre-existing conditions and risk factors Human immunodeficiency virus (HIV) - Human immunodeficiency virus (HIV) Acquired immunodeficiency syndrome (AIDS) - Human immunodeficiency virus (HIV) HIV and antiretroviral therapy (ART) - pre-existing conditions and risk factors Immunocompromised - Immunocompromised Lupus - pre-existing conditions and risk factors Inflammatory bowel disease (IBD) - Inflammatory bowel disease (IBD) Colitis - Colitis Ulcerative colitis - Inflammatory bowel disease (IBD) Crohn's disease - pre-existing conditions and risk factors Renal disorder - Renal disorder Renal disease - Renal disorder Chronic renal disease - Renal disorder Renal failure - pre-existing conditions and risk factors Liver disease - Liver disease Chronic liver disease - Chronic liver disease Fatty liver disease (FLD) -HP:0003326 pre-existing conditions and risk factors Myalgia (muscle pain) - pre-existing conditions and risk factors Myalgic encephalomyelitis (ME) - pre-existing conditions and risk factors Neurological disorder - Neurological disorder Neuromuscular disorder - pre-existing conditions and risk factors Obesity - Obesity Severe obesity - pre-existing conditions and risk factors Respiratory disorder - Respiratory disorder Asthma - Respiratory disorder Chronic bronchitis - Respiratory disorder Chronic pulmonary disease - Chronic pulmonary disease Chronic obstructive pulmonary disease - Respiratory disorder Emphysema - Respiratory disorder Lung disease - Lung disease Chronic lung disease - Lung disease Pulmonary fibrosis -HP:0002090 Respiratory disorder Pneumonia - Respiratory disorder Respiratory failure - Respiratory failure Adult respiratory distress syndrome - Respiratory failure Newborn respiratory distress syndrome - Respiratory disorder Tuberculosis - pre-existing conditions and risk factors Postpartum (≤6 weeks) - pre-existing conditions and risk factors Pregnancy - pre-existing conditions and risk factors Rheumatic disease - pre-existing conditions and risk factors Sickle cell disease - pre-existing conditions and risk factors Substance use - Substance use Alcohol abuse - Substance use Drug abuse - Drug abuse Injection drug abuse - Substance use Smoking - Substance use Vaping -HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated respiratory rate) - pre-existing conditions and risk factors Transplant - Transplant Bone marrow transplant - Transplant Cardiac transplant - Transplant Hematopoietic stem cell transplant (HSCT) - Transplant Kidney transplant - Transplant Liver transplant - - variant designation Variant of Concern (VOC) - variant designation Variant of Interest (VOI) - -CIDO_0000019 variant evidence RT-qPCR -CIDO_0000027 variant evidence Sequencing - - - complications Abnormal blood oxygen level - complications Acute respiratory failure -HP:0011675 complications Arrhythmia (complication) - Arrhythmia (complication) Tachycardia - Tachycardia Polymorphic ventricular tachycardia (VT) - Tachycardia Tachyarrhythmia - complications Noncardiogenic pulmonary edema - Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) - Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) - Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) - complications Cardiac injury - complications Cardiac arrest - complications Cardiogenic shock - complications Blood clot - Blood clot Arterial clot - Blood clot Deep vein thrombosis (DVT) - Blood clot Pulmonary embolism (PE) -HP:0001638 complications Cardiomyopathy - complications Central nervous system invasion - complications Stroke (complication) - Stroke (complication) Central Nervous System Vasculitis - Stroke (complication) Ischemic stroke - Ischemic stroke Acute ischemic stroke - complications Coma - complications Convulsions - complications COVID-19 associated coagulopathy (CAC) - complications Cystic fibrosis - complications Cytokine release syndrome - complications Disseminated intravascular coagulation (DIC) - complications Encephalopathy - complications Fulminant myocarditis - complications Guillain-Barré syndrome - complications Internal hemorrhage (complication; internal bleeding) - Internal hemorrhage (complication; internal bleeding) Intracerebral haemorrhage - complications Kawasaki disease - Kawasaki disease Typical Kawasaki disease - Kawasaki disease Incomplete Kawasaki disease - complications Kidney injury - Kidney injury Acute kidney injury - complications Liver dysfunction - complications Liver injury - Liver injury Acute liver injury - complications Lung injury - Lung injury Acute lung injury - complications Meningitis - complications Migraine - complications Miscarriage - complications Multisystem inflammatory syndrome in children (MIS-C) - complications Muscle injury - complications Myalgic encephalomyelitis (ME) - complications Myocardial infarction (heart attack) - Myocardial infarction (heart attack) Acute myocardial infarction - Myocardial infarction (heart attack) Elevation myocardial infarction - Myocardial infarction (heart attack) ST-segment elevation myocardial infarction - complications Myocardial injury - complications Neonatal complications - complications Organ failure - Organ failure Heart failure - Organ failure Liver failure - complications Paralysis - complications Pneumothorax (collapsed lung) - Pneumothorax (collapsed lung) Spontaneous pneumothorax - Pneumothorax (collapsed lung) Spontaneous tension pneymothorax - complications Pneumonia (complication) - Pneumonia (complication) COVID-19 pneumonia - complications Pregancy complications - complications Rhabdomyolysis - complications Secondary infection - Secondary infection Secondary staph infection - Secondary infection Secondary strep infection -HP:0001250 complications Seizure (complication) -HP:0020219 Seizure (complication) Motor seizure - complications Sepsis - complications Septicemia - complications Shock - Shock Hyperinflammatory shock - Shock Refractory cardiogenic shock - Shock Refractory cardiogenic plus vasoplegic shock - Shock Septic shock - complications Vasculitis - complications Ventilation induced lung injury (VILI) - - - -UBERON_0000178 anatomical material Blood BLOOD -UBERON_0006314 anatomical material Fluid FLUID -UBERON_0001836 Fluid Saliva SALIVA -UBERON_0001359 Fluid Fluid (cerebrospinal (CSF)) FLUID_CSF -UBERON_0002409 Fluid Fluid (pericardial) FLUID_PERICARDIAL -UBERON_0001087 Fluid Fluid (pleural) FLUID_PLEURAL -UBERON_0036243 Fluid Fluid (vaginal) FLUID_VAGINAL -UBERON_0000173 Fluid Fluid (amniotic) FLUID_AMNIOTIC -UBERON_0000479 anatomical material Tissue TISSUE - - - -UBERON_0001245 anatomical part Anus ANUS -UBERON_0006956 anatomical part Buccal mucosa BUCCAL_MUCOSA -UBERON_0002114 anatomical part Duodenum DUODENUM -UBERON_0000970 anatomical part Eye EYE - anatomical part Intestine INTESTINE -UBERON_0001052 anatomical part Rectum RECTUM -UBERON_0001003 anatomical part Skin SKIN -UBERON_0000945 anatomical part Stomach STOMACH -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 -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 -UBERON_0001729 Upper respiratory tract Oropharynx (OP) OROPHARYNX_OP -UBERON_0001558 anatomical part Lower respiratory tract LOWER -UBERON_0002185 Lower respiratory tract Bronchus BRONCHUS -UBERON_0002048 Lower respiratory tract Lung LUNG -UBERON_0002186 Lung Bronchiole BRONCHIOLE -UBERON_0002169 Lung Alveolar sac ALVEOLAR_SAC -UBERON_0009778 Lower respiratory tract Pleural sac PLEURAL_SAC -UBERON_0002402 Pleural sac Pleural cavity PLEURAL_CAVITY -UBERON_0003126 Lower respiratory tract Trachea TRACHEA - - - - -UBERON_0001988 body product Feces FECES -UBERON_0001088 body product Urine URINE -UBERON_0001089 body product Sweat SWEAT -UBERON_0000912 body product Mucus MUCUS -UBERON_0007311 Mucus Sputum SPUTUM -UBERON_0001827 body product Tear TEAR -UBERON_0006530 body product Fluid (seminal) FLUID_SEMINAL -UBERON_0001913 body product Breast Milk BREAST_MILK - - prior SARS-CoV-2 infection Yes - prior SARS-CoV-2 infection No - prior SARS-CoV-2 infection Unknown - - - environmental material Air vent AIR_VENT -ENVO_00003896 environmental material Banknote BANKNOTE - environmental material Bed rail BED_RAIL -ENVO_01000486 environmental material Building floor BUILDING_FLOOR -ENVO_02000058 environmental material Cloth CLOTH - environmental material Control panel CONTROL_PANEL -NCIT_C48950 environmental material Door DOOR - environmental material Door handle DOOR_HANDLE - environmental material Face mask FACE_MASK - environmental material Face shield FACE_SHIELD -FOODON:00002403 environmental material Food FOOD -FOODON:03490100 environmental material Food packaging FOOD_PACKAGING -ENVO:01000481 environmental material Glass GLASS - environmental material Handrail HANDRAIL - environmental material Hospital gown HOSPITAL_GOWN - environmental material Light switch LIGHT_SWITCH - environmental material Locker LOCKER - environmental material N95 mask N95_MASK - environmental material Nurse call button NURSE_CALL_BUTTON - environmental material Paper PAPER -ENVO:01000060 environmental material Particulate matter PARTICULATE_MATTER -ENVO:01000404 environmental material Plastic PLASTIC - environmental material PPE gown PPE_GOWN -ENVO_00002018 environmental material Sewage SEWAGE -ENVO_01000990 environmental material Sink SINK -ENVO_00001998 environmental material Soil SOIL - environmental material Stainless steel STAINLESS_STEEL - environmental material Tissue paper TISSUE_PAPER - environmental material Toilet bowl TOILET_BOWL -ENVO_00002006 environmental material Water WATER - environmental material Wastewater WASTEWATER - environmental material Window WINDOW -ENVO:00002040 environmental material Wood WOOD - - environmental site Acute care facility ACUTE_CARE_FACILITY -ENVO:00003040 environmental site Animal house ANIMAL_HOUSE -ENVO:01000422 environmental site Bathroom BATHROOM - environmental site Clinical assessment centre CLINICAL_ASSESSMENT_ - environmental site Conference venue CONFERENCE_VENUE -ENVO REQUEST environmental site Corridor CORRIDOR -ENVO_01000927 environmental site Daycare DAYCARE -NCIT_C53513 environmental site Emergency room (ER) EMERGENCY_ROOM_ER - environmental site Family practice clinic FAMILY_PRACTICE_CLIN - environmental site Group home GROUP_HOME - environmental site Homeless shelter HOMELESS_SHELTER -OBI_0000844 environmental site Hospital HOSPITAL -NCIT_C53511 environmental site Intensive Care Unit (ICU) INTENSIVE_CARE_UNIT_ -GENEPIO_0001035 environmental site Long Term Care Facility LONG_TERM_CARE_FACIL - environmental site Patient room PATIENT_ROOM -ENVO_01001481 environmental site Prison PRISON -ENVO_01000536 environmental site Production Facility PRODUCTION_FACILITY -NCIT_C17118 environmental site School SCHOOL - environmental site Sewage Plant SEWAGE_PLANT - environmental site Subway train SUBWAY_TRAIN - environmental site Wet market WET_MARKET - -NCIT:C52009 collection method Amniocentesis AMNIOCENTESIS -NCIT:C15631 collection method Aspiration ASPIRATION - Aspiration Suprapubic Aspiration SUPRAPUBIC_ASPIRATIO - Aspiration Tracheal aspiration TRACHEAL_ASPIRATION - Aspiration Vacuum Aspiration VACUUM_ASPIRATION -OBI:0002650 collection method Biopsy BIOPSY -OBI:0002651 Biopsy Needle Biopsy NEEDLE_BIOPSY - collection method Filtration FILTRATION - Filtration Air filtration AIR_FILTRATION -OBI:0600044 collection method Lavage LAVAGE -BTO:0000155 Lavage Bronchoalveolar lavage (BAL) BAL - Lavage Gastric Lavage GASTRIC_LAVAGE -NCIT:C15327 collection method Lumbar Puncture LUMBAR_PUNCTURE -MMO:0000344 collection method Necropsy NECROPSY -NCIT:c28221 collection method Phlebotomy PHLEBOTOMY -GENEPIO:0002116 collection method Rinsing RINSING - Rinsing Saline gargle (mouth rinse and gargle) - collection method Scraping SCRAPING -GENEPIO:0002117 collection method Swabbing SWABBING - Swabbing Finger Prick FINGER_PRICK - collection method Wash WASH - collection method Washout Tear Collection WASHOUT - - - collection device Air filter AIR_FILTER -NCIT:C113122 collection device Blood Collection Tube BLOOD_TUBE -NCIT:C17611 collection device Bronchoscope BRONCHOSCOPE - collection device Collection Container CONTAINER - collection device Collection Cup CUP - collection device Fibrobronchoscope Brush BRUSH - collection device Filter FILTER - collection device Fine Needle FINE_NEEDLE - collection device Microcapillary tube MICROCAPILLARY_TUBE -OBI:0001128 collection device Micropipette MICROPIPETTE -OBI:0000436 collection device Needle NEEDLE -NCIT:C113675 collection device Serum Collection Tube SERUM_TUBE - collection device Sputum Collection Tube SPUTUM_TUBE - collection device Suction Catheter SUCTION_CATHETER -NCIT:c17627 collection device Swab SWAB - collection device Urine Collection Tube URINE_TUBE - collection device Virus Transport Medium TRANSPORT_MEDIUM - - -NCBITaxon_9606 host (scientific name) Homo sapiens -NCBITaxon_9913 host (scientific name) Bos taurus -NCBITaxon_9615 host (scientific name) Canis lupus familiaris -NCBITaxon_9397 host (scientific name) Chiroptera -NCBITaxon_8930 host (scientific name) Columbidae -NCBITaxon_9685 host (scientific name) Felis catus -NCBITaxon_9031 host (scientific name) Gallus gallus -NCBITaxon_9973 host (scientific name) Manis -NCBITaxon_9974 host (scientific name) Manis javanica -NCBITaxon_452646 host (scientific name) Neovison vison -NCBITaxon_9689 host (scientific name) Panthera leo -NCBITaxon_9694 host (scientific name) Panthera tigris -NCBITaxon_58055 host (scientific name) Rhinolophidae -NCBITaxon_59477 host (scientific name) Rhinolophus affinis -NCBITaxon_9825 host (scientific name) Sus scrofa domesticus -NCBITaxon_9673 host (scientific name) Viverridae - - -NCBITaxon_9606 host (common name) Human HUMAN -NCBITaxon_9397 host (common name) Bat BAT -NCBITaxon_9685 host (common name) Cat -NCBITaxon_9031 host (common name) Chicken -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 -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 - - -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 - - - host health status details Hospitalized HOSPITALIZED - Hospitalized Hospitalized (Non-ICU) NON_ICU - Hospitalized Hospitalized (ICU) ICU - host health status details Mechanical Ventilation VENTILATION - host health status details Medically Isolated ISOLATED - Medically Isolated Medically Isolated (Negative Pressure) ISOLATED_NEGATIVE_PR - host health status details Self-quarantining SELF_QUARANTINING - - host health outcome Deceased - host health outcome Deteriorating - host health outcome Recovered - host health outcome Stable - -NCBITaxon_2697049 organism Severe acute respiratory syndrome coronavirus 2 -NCBITaxon_2709072 organism RaTG13 - organism RmYN02 - - - purpose of sampling Cluster/Outbreak investigation - purpose of sampling Diagnostic testing -NCIT_c15429 purpose of sampling Research - purpose of sampling Surveillance - - - purpose of sequencing Baseline surveillance (random sampling) - purpose of sequencing Targeted surveillance (non-random sampling) - Targeted surveillance (non-random sampling) Priority surveillance project - Priority surveillance project Screening for Variants of Concern (VoC) - Priority surveillance project Longitudinal surveillance (repeat sampling of individuals) - Priority surveillance project Re-infection surveillance - Priority surveillance project Vaccine escape surveillance - Priority surveillance project Travel-associated surveillance - Travel-associated surveillance Domestic travel surveillance - Travel-associated surveillance International travel surveillance - Travel-associated surveillance Surveillance of international border crossing by air travel - Travel-associated surveillance Surveillance of international border crossing by ground transport - Travel-associated surveillance Surveillance from international worker testing - purpose of sequencing Cluster/Outbreak investigation - Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation - Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation - purpose of sequencing Research - Research Viral passage experiment - Research Protocol testing experiment - - - specimen processing Virus passage - specimen processing RNA re-extraction (post RT-PCR) - specimen processing Specimens pooled - - lab host 293/ACE2 cell line -BTO_0000195 lab host Caco2 cell line -BTO_0002750 lab host Calu3 cell line - lab host EFK3B cell line -BTO_0002181 lab host HEK293T cell line - lab host HRCE cell line -BTO_0001950 lab host Huh7 cell line -CLO_0007330 lab host LLCMk2 cell line -BTO_0000836 lab host MDBK cell line - lab host Mv1Lu cell line -BTO_0002924 lab host NHBE cell line -BTO_0001865 lab host PK-15 cell line -BTO_0002909 lab host RK-13 cell line -BTO_0002035 lab host U251 cell line -BTO_0001444 lab host Vero cell line -BTO:0004755 lab host Vero E6 cell line - lab host VeroE6/TMPRSS2 cell line - -DOID_0080600 host disease COVID-19 - - host age bin 0 - 9 - host age bin 10 - 19 - host age bin 20 - 29 - host age bin 30 - 39 - host age bin 40 - 49 - host age bin 50 - 59 - host age bin 60 - 69 - host age bin 70 - 79 - host age bin 80 - 89 - host age bin 90 - 99 - host age bin 100+ - -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 - host gender Undeclared REFUSED - host gender Unknown UNKNOWN - - exposure event Mass Gathering - Mass Gathering Agricultural Event - Mass Gathering Convention CONVENTION - Mass Gathering Convocation - Mass Gathering Recreational Event - Recreational Event Concert - Recreational Event Sporting Event - exposure event Religious Gathering RELIGIOUS - Religious Gathering Mass - exposure event Social Gathering SOCIAL - Social Gathering Baby Shower - Social Gathering Community Event - Social Gathering Family Gathering - Family Gathering Family Reunion - Social Gathering Funeral - Social Gathering Party - Social Gathering Potluck - Social Gathering Wedding - exposure event Other exposure event - - exposure contact level Contact with infected individual - Contact with infected individual Direct contact (direct human-to-human contact) - Contact with infected individual Indirect contact - Indirect contact Close contact (face-to-face, no direct contact) - Indirect contact Casual contact - - - host role Attendee - Attendee Student - host role Patient - Patient Inpatient - Patient Outpatient - host role Passenger - host role Resident - host role Visitor - host role Volunteer - host role Work - Work Administrator - Work First Responder - First Responder Firefighter - First Responder Paramedic - First Responder Police Officer - Work Child Care/Education Worker - Work Essential Worker - Work Healthcare Worker - Work Nurse - Work Personal Care Aid - Work Pharmacist - Work Physician - Work Housekeeper - Work International worker - Work Kitchen Worker - Work Laboratory Worker - Work Rotational Worker - Work Seasonal Worker - Work Transport Worker - Transport Worker Transport Truck Driver - Work Veterinarian - host role Social role - Social role Acquaintance of case - Social role Relative of case - Relative of case Child of case - Relative of case Parent of case - Relative of case Father of case - Relative of case Mother of case - Social role Spouse of case - host role Other Host Role - -ECTO_3000005 exposure setting Human Exposure - Human Exposure Contact with Known COVID-19 Case - Human Exposure Contact with Patient - Human Exposure Contact with Probable COVID-19 Case - Human Exposure Contact with Person with Acute Respiratory Illness - Human Exposure Contact with Person with Fever and/or Cough - Human Exposure Contact with Person who Recently Travelled - exposure setting Occupational, Residency or Patronage Exposure -ECTO_1000033 Occupational, Residency or Patronage Exposure Abbatoir - Occupational, Residency or Patronage Exposure Animal Rescue - Occupational, Residency or Patronage Exposure Childcare - Childcare Daycare - Occupational, Residency or Patronage Exposure Funeral Home - Occupational, Residency or Patronage Exposure Place of Worship - Place of Worship Church - Place of Worship Mosque - Place of Worship Temple - Occupational, Residency or Patronage Exposure Nursery - Occupational, Residency or Patronage Exposure Household - Occupational, Residency or Patronage Exposure Community Service Centre - Occupational, Residency or Patronage Exposure Correctional Facility - Occupational, Residency or Patronage Exposure Dormitory -ECTO_1000034 Occupational, Residency or Patronage Exposure Farm - Occupational, Residency or Patronage Exposure First Nations Reserve - Occupational, Residency or Patronage Exposure Group Home -ECTO_1000035 Occupational, Residency or Patronage Exposure Healthcare Setting - Healthcare Setting Ambulance - Healthcare Setting Acute Care Facility - Healthcare Setting Clinic - Healthcare Setting Community Health Centre - Healthcare Setting Hospital - Hospital Emergency Department - Hospital ICU - Hospital Ward -ECTO_1000036 Healthcare Setting Laboratory - Healthcare Setting Long-Term Care Facility - Healthcare Setting Pharmacy - Healthcare Setting Physician's Office - Occupational, Residency or Patronage Exposure Insecure Housing (Homeless) - Occupational, Residency or Patronage Exposure Occupational Exposure - Occupational Exposure Worksite -ECTO:1000037 Occupational Exposure Office - Occupational, Residency or Patronage Exposure Outdoors -ECTO_5000009 Outdoors Camp/camping - Outdoors Hiking Trail -ECTO_6000030 Outdoors Hunting Ground - Outdoors Ski Resort -ECTO_5000008 Occupational, Residency or Patronage Exposure Petting zoo -ECTO_1000040 Occupational, Residency or Patronage Exposure Restaurant -ECTO_1000041 Occupational, Residency or Patronage Exposure Retail Store - Occupational, Residency or Patronage Exposure School - Occupational, Residency or Patronage Exposure Temporary Residence - Temporary Residence Homeless Shelter - Temporary Residence Hotel - Occupational, Residency or Patronage Exposure Veterinary Care Clinic - exposure setting Travel Exposure - Travel Exposure Travelled - Travelled Travelled on a Cruise Ship - Travelled Travelled on a Plane - Travelled Travelled on Ground Transport -GENEPIO_0001119 Travelled Travelled outside Province/Territory -GENEPIO_0001118 Travelled Travelled outside Canada - exposure setting Other Exposure Setting - - - -OBI_0000759 sequencing instrument Illumina -OBI_0002128 Illumina Illumina Genome Analyzer -OBI_0000703 Illumina Genome Analyzer Illumina Genome Analyzer II -OBI_0002000 Illumina Genome Analyzer Illumina Genome Analyzer IIx - Illumina Illumina HiScanSQ - Illumina Illumina HiSeq -OBI_0002129 Illumina Illumina HiSeq X - Illumina HiSeq X Illumina HiSeq X Five -OBI_0002129 Illumina HiSeq X Illumina HiSeq X Ten -OBI_0002022 Illumina Illumina HiSeq 1000 - Illumina Illumina HiSeq 1500 -OBI_0002001 Illumina Illumina HiSeq 2000 -OBI_0002002 Illumina Illumina HiSeq 2500 -OBI_0002048 Illumina Illumina HiSeq 3000 -OBI_0002049 Illumina Illumina HiSeq 4000 - Illumina Illumina iSeq -EFO:0008635 Illumina iSeq Illumina iSeq 100 - Illumina Illumina NovaSeq -OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 -EFO_0008636 Illumina Illumina MiniSeq -OBI_0002003 Illumina Illumina MiSeq - Illumina Illumina NextSeq -OBI_0002021 Illumina Illumina NextSeq 500 - Illumina Illumina NextSeq 550 - Illumina Illumina NextSeq 2000 -OBI_0001856 sequencing instrument Pacific Biosciences - Pacific Biosciences PacBio RS -OBI_0002012 Pacific Biosciences PacBio RS II -OBI_0002632 Pacific Biosciences PacBio Sequel -OBI_0002633 Pacific Biosciences PacBio Sequel II - sequencing instrument Ion Torrent -GENEPIO_0001935 Ion Torrent Ion Torrent PGM - Ion Torrent Ion Torrent Proton - Ion Torrent Ion Torrent S5 XL - Ion Torrent Ion Torrent S5 - sequencing instrument Oxford Nanopore - Oxford Nanopore Oxford Nanopore GridION - Oxford Nanopore Oxford Nanopore MinION - Oxford Nanopore Oxford Nanopore PromethION - sequencing instrument BGI Genomics - BGI Genomics BGI Genomics BGISEQ-500 - sequencing instrument MGI - MGI MGI DNBSEQ-T7 - MGI MGI DNBSEQ-G400 - MGI MGI DNBSEQ-G400 FAST - MGI MGI DNBSEQ-G50 - - -PR:P0DTC4 gene name 1 E gene (orf4) E gene E gene E (orf4) -PR:P0DTC5 gene name 1 M gene (orf5) M (orf5) -PR:P0DTC9 gene name 1 N gene (orf9) N (orf9) -PR:P0DTC2 gene name 1 Spike gene (orf2) S (orf2) -PR:000050281 gene name 1 orf1ab (rep) orf1ab (rep) -PR:P0DTC1-1 orf1ab (rep) orf1a (pp1a) orf1a (pp1a) -PR:000050280 orf1a (pp1a) nsp11 nsp11 -PR:000050270 orf1ab (rep) nsp1 nsp1 -PR:000050271 orf1ab (rep) nsp2 nsp2 -PR:000050272 orf1ab (rep) nsp3 nsp3 -PR:000050273 orf1ab (rep) nsp4 nsp4 -PR:000050274 orf1ab (rep) nsp5 nsp5 -PR:000050275 orf1ab (rep) nsp6 nsp6 -PR:000050276 orf1ab (rep) nsp7 nsp7 -PR:000050277 orf1ab (rep) nsp8 nsp8 -PR:000050278 orf1ab (rep) nsp9 nsp9 -PR:000050279 orf1ab (rep) nsp10 nsp10 -PR:000050284 orf1ab (rep) RdRp gene (nsp12) nsp12 (RdRp) -PR:000050285 orf1ab (rep) hel gene (nsp13) nsp13 (Hel) -PR:000050286 orf1ab (rep) exoN gene (nsp14) nsp14 (ExoN) -PR:000050287 orf1ab (rep) nsp15 nsp15 -PR:000050288 orf1ab (rep) nsp16 nsp16 -PR:P0DTC3 gene name 1 orf3a orf3a - gene name 1 orf3b orf3b -PR:P0DTC6 gene name 1 orf6 (ns6) orf6 (ns6) -PR:P0DTC7 gene name 1 orf7a orf7a -PR:P0DTD8 gene name 1 orf7b (ns7b) orf7b (ns7b) -PR:P0DTC8 gene name 1 orf8 (ns8) orf8 (ns8) -PR:P0DTD2 gene name 1 orf9b orf9b - gene name 1 orf9c orf9c -PR:A0A663DJA2 gene name 1 orf10 orf10 - gene name 1 orf14 orf14 - gene name 1 SARS-COV-2 5' UTR - - - sequence submitted by Alberta Precision Labs (APL) - Alberta Precision Labs (APL) Alberta ProvLab North (APLN) - Alberta Precision Labs (APL) Alberta ProvLab South (APLS) - 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 (Manitoba) Dynacare Manitoba - sequence submitted by The Hospital for Sick Children (SickKids) CANCOGEN_SICK_KIDS_HOSPITAL - sequence submitted by Laboratoire de santé publique du Québec (LSPQ) - sequence submitted by Manitoba Cadham Provincial Laboratory - sequence submitted by McMaster University - sequence submitted by McGill University - sequence submitted by National Microbiology Laboratory (NML) - sequence submitted by New Brunswick - Vitalité Health Network - sequence submitted by Newfoundland and Labrador - Eastern Health - sequence submitted by Nova Scotia Health Authority - sequence submitted by Ontario Institute for Cancer Research (OICR) - sequence submitted by Prince Edward Island - Health PEI - sequence submitted by Public Health Ontario (PHO) - sequence submitted by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - sequence submitted by Sunnybrook Health Sciences Centre - sequence submitted by Thunder Bay Regional Health Sciences Centre - sequence submitted by Queen's University / Kingston Health Sciences Centre - - - sample collected by Alberta Precision Labs (APL) - Alberta Precision Labs (APL) Alberta ProvLab North (APLN) CANCOGEN_EDMONTON_PROV_LAB - Alberta Precision Labs (APL) Alberta ProvLab South (APLS) CANCOGEN_CALGARY_PROV_LAB - sample collected by BCCDC Public Health Laboratory CANCOGEN_BCCDC - sample collected by Dynacare (Manitoba) Dynacare Manitoba - sample collected by Eastern Ontario Regional Laboratory Association CANCOGEN_EORLA - sample collected by Hamilton Health Sciences " +Ontology ID Meaning (LinkML) parent class label datatype source data status requirement min value max value capitalize pattern description guidance examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +ID SC % +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_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 +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 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 GISAID accession +GENEPIO_0001150 Sample collection and processing +GENEPIO_0001153 Sample collection and processing sample collected by select 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 CUSTOMER collected_by sample collected by +GENEPIO_0001156 Sample collection and processing sample collector contact email xs:token ^\S+@\S+\.\S+$ 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 sample collector contact email +GENEPIO_0001158 Sample collection and processing sample collector contact address xs:token The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address +GENEPIO_0001159 Sample collection and processing sequence submitted by select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by +GENEPIO_0001165 Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email +GENEPIO_0001167 Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address +GENEPIO_0001174 Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date +GENEPIO_0001177 Sample collection and processing sample collection date precision select required The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 +GENEPIO_0001179 Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date +GENEPIO_0001181 Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) +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;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 +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 +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 +GENEPIO_0001223 Sample collection and processing environmental material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental 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. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material +GENEPIO_0001232 Sample collection and processing environmental site select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site 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. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site +GENEPIO_0001234 Sample collection and processing collection device select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. 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. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device +GENEPIO_0001241 Sample collection and processing collection method select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. 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. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method +GENEPIO_0001243 Sample collection and processing collection protocol xs:token The name and version of a particular protocol used for sampling. Free text. BCRonaSamplingProtocol v. 1.2 collection protocol +GENEPIO_0001253 Sample collection and processing specimen processing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history specimen processing +GENEPIO_0001255 Sample collection and processing lab host select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Vero E6 cell line Passage details/history lab host lab_host +GENEPIO_0001261 Sample collection and processing passage number xs:nonNegativeInteger Not Applicable recommended Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 Passage details/history passage number passage_history +GENEPIO_0001264 Sample collection and processing passage method xs:token Not Applicable recommended Description of how organism was passaged. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". 0.25% trypsin + 0.02% EDTA Passage details/history passage method passage_method +GENEPIO_0001266 Sample collection and processing biomaterial extracted select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) biomaterial extracted +GENEPIO_0001268 Host Information +GENEPIO_0001386 Host Information host (common name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human Animal Type PH_ANIMAL_TYPE +GENEPIO_0001387 Host Information host (scientific name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) +GENEPIO_0001388 Host Information host health state select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Symptomatic Patient status Host Health State PH_HOST_HEALTH host_health_state +GENEPIO_0001389 Host Information host health status details select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS +GENEPIO_0001390 Host Information host health outcome select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered host health outcome host_disease_outcome +GENEPIO_0001391 Host Information host disease select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease +GENEPIO_0001392 Host Information host age xs:decimal Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age +GENEPIO_0001393 Host Information host age unit select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit +GENEPIO_0001394 Host Information host age bin select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin +GENEPIO_0001395 Host Information host gender select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Title The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". male Gender Patient Sex VD_SEX host_sex host gender +GENEPIO_0001396 Host Information host residence geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country of residence of the host. Select the country name from pick list provided in the template. United Kingdom PH_HOST_COUNTRY +GENEPIO_0001397 Host Information host residence geo_loc name (state/province/territory) select geo_loc_name (state/province/territory) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE +GENEPIO_0001398 Host Information host subject ID xs:token A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host subject ID host_subject_id +GENEPIO_0001399 Host Information symptom onset date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the symptoms began or were first noted. ISO 8601 standard "YYYY-MM-DD". 2020-03-16 Symptoms Onset Date HC_ONSET_DATE +GENEPIO_0001400 Host Information signs and symptoms multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Select all of the symptoms experienced by the host from the pick list. Chills (sudden cold sensation); Cough; Fever Symptoms HC_SYMPTOMS +GENEPIO_0001401 Host Information pre-existing conditions and risk factors multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma; Pregnancy; Smoking pre-existing conditions and risk factors +GENEPIO_0001402 Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Acute Respiratory Failure; Coma; Septicemia complications +GENEPIO_0001403 Host vaccination information +GENEPIO_0001404 Host vaccination information host vaccination status select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated host vaccination status +GENEPIO_0001405 Host vaccination information vaccine name xs:token The name of the vaccine. Free text. Provide the name of the vaccine. Pfizer-BioNTech COVID-19 vaccine vaccine name +GENEPIO_0001406 Host vaccination information number of vaccine doses received xs:nonNegativeInteger The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 number of vaccine doses received +GENEPIO_0001407 Host vaccination information first dose vaccination date xs:date The date the host was first vaccinated. Provide the vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-02-26 first dose vaccination date +GENEPIO_0001408 Host vaccination information last dose vaccination date xs:date The date the host received their last dose of vaccine. Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-09 last dose vaccination date +GENEPIO_0001409 Host exposure information +GENEPIO_0001410 Host exposure information location of exposure geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country where the host was likely exposed to the causative agent of the illness. Select the country name from pick list provided in the template. Canada PH_EXPOSURE_COUNTRY +GENEPIO_0001411 Host exposure information destination of most recent travel (city) xs:token The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL +GENEPIO_0001412 Host exposure information destination of most recent travel (state/province/territory) xs:token The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL +GENEPIO_0001413 Host exposure information destination of most recent travel (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL +GENEPIO_0001414 Host exposure information most recent travel departure date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL +GENEPIO_0001415 Host exposure information most recent travel return date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL +GENEPIO_0001416 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 travel history +GENEPIO_0001417 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 +GENEPIO_0001418 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 exposure contact level +GENEPIO_0001419 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 +GENEPIO_0001428 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 +GENEPIO_0001431 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 + + +GENEPIO_0001434 Host reinfection information +GENEPIO_0001435 Host reinfection information prior SARS-CoV-2 infection select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 infection. If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Yes prior SARS-CoV-2 infection +GENEPIO_0001436 Host reinfection information prior SARS-CoV-2 infection isolate xs:token The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 prior SARS-CoV-2 infection isolate +GENEPIO_0001437 Host reinfection information prior SARS-CoV-2 infection date xs:date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 prior SARS-CoV-2 infection date +GENEPIO_0001438 Host reinfection information prior SARS-CoV-2 antiviral treatment select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. No prior antiviral treatment prior SARS-CoV-2 antiviral treatment +GENEPIO_0001439 Host reinfection information prior SARS-CoV-2 antiviral treatment agent xs:token The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir prior SARS-CoV-2 antiviral treatment agent +GENEPIO_0001440 Host reinfection information prior SARS-CoV-2 antiviral treatment date xs:date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 prior SARS-CoV-2 antiviral treatment date + + +GENEPIO_0001441 Sequencing +GENEPIO_0001445 Sequencing purpose of sequencing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing +GENEPIO_0001446 Sequencing purpose of sequencing details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details +GENEPIO_0001447 Sequencing sequencing date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE +GENEPIO_0001448 Sequencing library ID xs:token recommended The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID +GENEPIO_0001449 Sequencing amplicon size xs:token The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size +GENEPIO_0001450 Sequencing library preparation kit xs:token The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library preparation kit +GENEPIO_0001451 Sequencing flow cell barcode xs:token The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 flow cell barcode +GENEPIO_0001452 Sequencing sequencing instrument multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. MinIon Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument +GENEPIO_0001453 Sequencing sequencing protocol name xs:token recommended The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name sequencing protocol name +GENEPIO_0001454 Sequencing sequencing protocol xs:token The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol +GENEPIO_0001455 Sequencing sequencing kit number xs:token The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number +GENEPIO_0001456 Sequencing amplicon pcr primer scheme xs:token The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon pcr primer scheme + + +GENEPIO_0001457 Bioinformatics and QC metrics +GENEPIO_0001458 Bioinformatics and QC metrics raw sequence data processing method xs:token required 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 PH_RAW_SEQUENCE_METHOD raw sequence data processing method +GENEPIO_0001459 Bioinformatics and QC metrics dehosting method xs:token required 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 +GENEPIO_0001463 Bioinformatics and QC metrics consensus sequence software name xs:token required The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name +GENEPIO_0001469 Bioinformatics and QC metrics consensus sequence software version xs:token required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version +GENEPIO_0001472 Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% breadth of coverage value breadth of coverage value +GENEPIO_0001474 Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage depth of coverage value depth of coverage value +GENEPIO_0001475 Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold +GENEPIO_0001476 Bioinformatics and QC metrics r1 fastq filename xs:token recommended The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename +GENEPIO_0001477 Bioinformatics and QC metrics r2 fastq filename xs:token recommended The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename +GENEPIO_0001478 Bioinformatics and QC metrics r1 fastq filepath xs:token The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath +GENEPIO_0001479 Bioinformatics and QC metrics r2 fastq filepath xs:token The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath +GENEPIO_0001480 Bioinformatics and QC metrics fast5 filename xs:token The user-specified filename of the FAST5 file. Provide the FAST5 filename. rona123assembly.fast5 fast5 filename +GENEPIO_0001481 Bioinformatics and QC metrics fast5 filepath xs:token The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/rona123assembly.fast5 fast5 filepath +GENEPIO_0001482 Bioinformatics and QC metrics number of base pairs sequenced xs:nonNegativeInteger The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 number of base pairs sequenced +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 required A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf 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 +GENEPIO_0001502 Lineage and Variant information lineage/clade analysis software version xs:token The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION +GENEPIO_0001503 Lineage and Variant information variant designation select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern PH_VARIANT_DESIGNATION +GENEPIO_0001504 Lineage and Variant information variant evidence select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The evidence used to make the variant determination. Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. RT-qPCR PH_VARIANT_EVIDENCE +GENEPIO_0001505 Lineage and Variant information variant evidence details xs:token Details about the evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). PH_VARIANT_EVIDENCE_DETAILS +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 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 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 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 + + + umbrella bioproject accession PRJNA623807 + + + + + + + + +GAZ_00002566 geo_loc_name (state/province/territory) Alberta CA-AB +GAZ_00002562 geo_loc_name (state/province/territory) British Columbia CA-BC +GAZ_00002571 geo_loc_name (state/province/territory) Manitoba CA-MB +GAZ_00002570 geo_loc_name (state/province/territory) New Brunswick CA-NB +GAZ_00002567 geo_loc_name (state/province/territory) Newfoundland and Labrador CA-NL +GAZ_00002575 geo_loc_name (state/province/territory) Northwest Territories CA-NT +GAZ_00002565 geo_loc_name (state/province/territory) Nova Scotia CA-NS +GAZ:00002574 geo_loc_name (state/province/territory) Nunavut CA-NU +GAZ_00002563 geo_loc_name (state/province/territory) Ontario CA-ON +GAZ_00002572 geo_loc_name (state/province/territory) Prince Edward Island CA-PE +GAZ_00002569 geo_loc_name (state/province/territory) Quebec CA-QC +GAZ_00002564 geo_loc_name (state/province/territory) Saskatchewan CA-SK +GAZ_00002576 geo_loc_name (state/province/territory) Yukon CA-YT + +UO:0000035 host age unit month Month +UO:0000036 host age unit year Year + +UO:0000036 sample collection date precision year Year +UO:0000035 sample collection date precision month Month +UO:0000033 sample collection date precision day Day + +OBI:0000895 biomaterial extracted RNA (total) +OBI:0000869 biomaterial extracted RNA (poly-A) +OBI:0002627 biomaterial extracted RNA (ribo-depleted) +OBI REQUEST biomaterial extracted mRNA (messenger RNA) +OBI:0002754 biomaterial extracted mRNA (cDNA) + + +HP REQUEST signs and symptoms Abnormal lung auscultation +HP:0000223 signs and symptoms Abnormality of taste sensation SENSE_OF_TASTE +HP:0041051 Abnormality of taste sensation Ageusia (complete loss of taste) AGEUSIA +HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) PARAGEUSIA +HP_0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) HYPOGEUSIA +HP:0004408 signs and symptoms Abnormality of the sense of smell SENSE_OF_SMELL +HP_0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) ANOSMIA +HP_0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) HYPOSMIA +HP:0033677 signs and symptoms Acute Respiratory Distress Syndrome ARDS +HP:0011446 signs and symptoms Altered mental status ALTERED_CONSCIOUS +HP:0011675 signs and symptoms Arrhythmia +HP:0100543 Altered mental status Cognitive impairment COGNITIVE +HP_0001259 Altered mental status Coma COMA +HP_0001289 Altered mental status Confusion CONFUSION +HP_0031258 Confusion Delirium (sudden severe confusion) DELIRIUM +HP REQUEST Altered mental status Inability to arouse (inability to stay awake) INABILITY_AWAKE +HP_0000737 Altered mental status Irritability IRRITABILITY +HP_0002371 Altered mental status Loss of speech LOSS_OF_SPEECH +HP_0025406 signs and symptoms Asthenia (generalized weakness) ASTHENIA +HP:0031352 signs and symptoms Chest tightness or pressure CHEST_TIGHT +HP:0025145 Chest tightness or pressure Rigors (fever shakes) RIGORS +HP_0025143 signs and symptoms Chills (sudden cold sensation) Chills CHILLS +HP:0030953 signs and symptoms Conjunctival injection +HP_0000509 signs and symptoms Conjunctivitis (pink eye) Conjunctivitis CONJUNCTIVITIS +MP:0001867 signs and symptoms Coryza (rhinitis) +HP_0012735 signs and symptoms Cough COUGH +HP:0031246 Cough Nonproductive cough (dry cough) NONPRODUCT_COUGH +HP:0031245 Cough Productive cough (wet cough) PRODUCTIVE_COUGH +HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) CYANOSIS +HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis ACROCYANOS +HP:0032556 Acrocyanosis Circumoral cyanosis (bluish around mouth) CIRCUMORAL_CYANOSIS +HP REQUEST Acrocyanosis Cyanotic face (bluish face) CYANOTIC_FACE +HP REQUEST Cyanosis (blueish skin discolouration) Central Cyanosis +HP REQUEST Central Cyanosis Cyanotic lips (bluish lips) CYANOTIC_LIPS +HP REQUEST Cyanosis (blueish skin discolouration) Peripheral Cyanosis +HP_0002094 signs and symptoms Dyspnea (breathing difficulty) DYSPNEA +HP_0002014 signs and symptoms Diarrhea (watery stool) Diarrhea, watery DIARRHEA +MP:0031127 signs and symptoms Dry gangrene +HP_0002383 signs and symptoms Encephalitis (brain inflammation) Encephalitis ENCEPHALITIS +HP:0001298 signs and symptoms Encephalopathy +HP_0012378 signs and symptoms Fatigue (tiredness) Fatigue FATIGUE +HP REQUEST signs and symptoms Prostration (complete exhaustion) +HP_0001945 signs and symptoms Fever FEVER +HP REQUEST Fever Fever (>=38°C) Fever +HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) GLOSSITIS +HP REQUEST signs and symptoms Ground Glass Opacities (GGO) +HP_0002315 signs and symptoms Headache HEADACHE +HP_0002105 signs and symptoms Hemoptysis (coughing up blood) HEMOPTYSIS +HP:0012417 signs and symptoms Hypocapnia +HP_0002615 signs and symptoms Hypotension (low blood pressure) HYPOTENSION +HP_0012418 signs and symptoms Hypoxemia (low blood oxygen) HYPOXEMIA +HP REQUEST Hypoxemia (low blood oxygen) Silent hypoxemia +HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) INTERNAL_HEMORRHAGE +NCIT:C121416 signs and symptoms Loss of Fine Movements LOSS_OF_FINE_MOVE +HP_0004396 signs and symptoms Low appetite LOW_APPETITE +HP:0033834 signs and symptoms Malaise (general discomfort/unease) MALAISE +HP:0031179 signs and symptoms Meningismus/nuchal rigidity +HP_0001324 signs and symptoms Muscle weakness MUSCLE_WEAK +HP_0001742 signs and symptoms Nasal obstruction (stuffy nose) NASAL_OBSTRUCT +HP_0002018 signs and symptoms Nausea NAUSEA +HP_0000421 signs and symptoms Nose bleed +HP REQUEST signs and symptoms Otitis +HP:0012531 signs and symptoms Pain +HP:0002027 Pain Abdominal pain ABDOMINAL +HP_0002829 Pain Arthralgia (painful joints) ARTHRALGIA +HP_0100749 Pain Chest pain CHEST_PAIN +HP:0033771 Chest pain Pleuritic chest pain +HP_0003326 Pain Myalgia (muscle pain) MYALGIA +HP_0025439 signs and symptoms Pharyngitis (sore throat) PHARYNGITIS +HP REQUEST signs and symptoms Pharyngeal exudate +HP:0002202 signs and symptoms Pleural effusion +HP:0002090 signs and symptoms Pneumonia +HP:0033696 signs and symptoms Pseudo-chilblains +HP REQUEST Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) PSEUDO-CHIBLAINS_F +HP REQUEST Pseudo-chilblains Pseudo-chilblains on toes (covid toes) PSEUDO-CHIBLAINS_T +HP_0000988 signs and symptoms Rash RASH +HP_0031417 signs and symptoms Rhinorrhea (runny nose) RHINORRHEA +HP_0001250 signs and symptoms Seizure SEIZURE +HP:0020219 Seizure Motor seizure MOTOR_SEIZURE +HP:0025144 signs and symptoms Shivering (involuntary muscle twitching) SHIVERING +HP_0001350 signs and symptoms Slurred speech SLURRED_SPEECH +HP:0025095 signs and symptoms Sneezing +HP:0033709 signs and symptoms Sputum Production +HP:0001297 signs and symptoms Stroke STROKE +HP:0002716 signs and symptoms Swollen Lymph Nodes +HP_0002789 signs and symptoms Tachypnea (accelerated respiratory rate) TACHYPNEA +HP:0002321 signs and symptoms Vertigo (dizziness) +HP_0002013 signs and symptoms Vomiting (throwing up) VOMITING + + host vaccination status Fully Vaccinated + host vaccination status Partially Vaccinated + host vaccination status Not Vaccinated + + prior SARS-CoV-2 antiviral treatment Prior antivrial treatment + prior SARS-CoV-2 antiviral treatment No prior antivrial treatment + prior SARS-CoV-2 antiviral treatment Unknown + +OBI_0002600 NML submitted specimen type Swab PH_SPECIMEN_TYPE:SWAB +OBI_0000880 NML submitted specimen type RNA PH_SPECIMEN_TYPE:RNA +OBI:0002754 NML submitted specimen type mRNA (cDNA) +OBI:0001010 NML submitted specimen type Nucleic acid PH_SPECIMEN_TYPE:NUCLEIC_ACID +GENEPIO:0001619 NML submitted specimen type Not Applicable PH_SPECIMEN_TYPE:NA + + +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 + + + pre-existing conditions and risk factors Age 60+ +HP:0001903 pre-existing conditions and risk factors Anemia +HP:0002039 pre-existing conditions and risk factors Anorexia +NCIT:C92743 pre-existing conditions and risk factors Birthing labor +NCIT_C80693 pre-existing conditions and risk factors Bone marrow failure +MONDO:0004992 pre-existing conditions and risk factors Cancer +MONDO:0007254 Cancer Breast cancer +MONDO:0005575 Cancer Colorectal cancer +DOID:2531 Cancer Hematologic malignancy (cancer of the blood) +MONDO:0008903 Cancer Lung cancer +MONDO:0024880 Cancer Metastatic disease +NCIT:C16212 pre-existing conditions and risk factors Cancer treatment +NCIT:C157740 Cancer treatment Cancer surgery +NCIT:C15632 Cancer treatment Chemotherapy +NCIT:C15360 Chemotherapy Adjuvant chemotherapy +NCIT:C3079 pre-existing conditions and risk factors Cardiac disorder +HP:0011675 Cardiac disorder Arrhythmia +MONDO:0005267 Cardiac disorder Cardiac disease +HP:0001638 Cardiac disorder Cardiomyopathy +NCIT:C45430 Cardiac disorder Cardiac injury +HP_0000822 Cardiac disorder Hypertension (high blood pressure) +HP:0002615 Cardiac disorder Hypotension (low blood pressure) +HP:0011410 pre-existing conditions and risk factors Cesarean section +HP REQUEST pre-existing conditions and risk factors Chronic cough +HP REQUEST pre-existing conditions and risk factors Chronic gastrointestinal disease +HP:0006528 pre-existing conditions and risk factors Chronic lung disease +NCIT:C211 pre-existing conditions and risk factors Corticosteroids +HP:0000819 pre-existing conditions and risk factors Diabetes mellitus (diabetes) +HP:0100651 Diabetes mellitus (diabetes) Type I diabetes mellitus (T1D) +HP:0005978 Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D) +HP:0000964 pre-existing conditions and risk factors Eczema +HP:0003111 pre-existing conditions and risk factors Electrolyte disturbance +HP:0002901 Electrolyte disturbance Hypocalcemia +HP:0002900 Electrolyte disturbance Hypokalemia +HP:0002917 Electrolyte disturbance Hypomagnesemia +HP:0002383 pre-existing conditions and risk factors Encephalitis (brain inflammation) +MONDO:0005027 pre-existing conditions and risk factors Epilepsy +NCIT:C15248 pre-existing conditions and risk factors Hemodialysis +MONDO:0044348 pre-existing conditions and risk factors Hemoglobinopathy +MONDO:0005109 pre-existing conditions and risk factors Human immunodeficiency virus (HIV) +MONDO:0012268 Human immunodeficiency virus (HIV) Acquired immunodeficiency syndrome (AIDS) +NCIT:C16118 Human immunodeficiency virus (HIV) HIV and antiretroviral therapy (ART) +NCIT:C14139 pre-existing conditions and risk factors Immunocompromised +MONDO:0004670 Immunocompromised Lupus +MONDO:0005265 pre-existing conditions and risk factors Inflammatory bowel disease (IBD) +HP:0002583 Inflammatory bowel disease (IBD) Colitis +HP:0100279 Colitis Ulcerative colitis +HP:0100280 Inflammatory bowel disease (IBD) Crohn's disease +NCIT:C3149 pre-existing conditions and risk factors Renal disorder +MONDO:0005240 Renal disorder Renal disease +HP:0012622 Renal disorder Chronic renal disease +HP:0000084 Renal disorder Renal failure +MONDO:0005154 pre-existing conditions and risk factors Liver disease +NCIT:C113609 Liver disease Chronic liver disease +HP:0001397 Chronic liver disease Fatty liver disease (FLD) +HP:0003326 pre-existing conditions and risk factors Myalgia (muscle pain) +MONDO:0005404 pre-existing conditions and risk factors Myalgic encephalomyelitis (ME) +MONDO:0005071 pre-existing conditions and risk factors Neurological disorder +MONDO:0019056 Neurological disorder Neuromuscular disorder +HP:0001513 pre-existing conditions and risk factors Obesity +MONDO:0005139 Obesity Severe obesity +MONDO:0005087 pre-existing conditions and risk factors Respiratory disorder +HP:0002099 Respiratory disorder Asthma +HP:0004469 Respiratory disorder Chronic bronchitis +HP:0006528 Respiratory disorder Chronic pulmonary disease +HP:0006510 Chronic pulmonary disease Chronic obstructive pulmonary disease +HP:0002097 Respiratory disorder Emphysema +MONDO:0005275 Respiratory disorder Lung disease +HP:0006528 Lung disease Chronic lung disease +HP:0002206 Lung disease Pulmonary fibrosis +HP:0002090 Respiratory disorder Pneumonia +HP:0002878 Respiratory disorder Respiratory failure +HP:0033677 Respiratory failure Adult respiratory distress syndrome +MONDO:0009971 Respiratory failure Newborn respiratory distress syndrome +MONDO:0018076 Respiratory disorder Tuberculosis + pre-existing conditions and risk factors Postpartum (≤6 weeks) +NCIT:C25742 pre-existing conditions and risk factors Pregnancy +MONDO:0005554 pre-existing conditions and risk factors Rheumatic disease +MONDO:0011382 pre-existing conditions and risk factors Sickle cell disease +NBO:0001845 pre-existing conditions and risk factors Substance use +MONDO:0002046 Substance use Alcohol abuse + Substance use Drug abuse + Drug abuse Injection drug abuse +NBO:0015005 Substance use Smoking +NBO NTR Substance use Vaping +HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated respiratory rate) +NCIT:C159659 pre-existing conditions and risk factors Transplant +NCIT:C131759 Transplant Bone marrow transplant + Transplant Cardiac transplant +NCIT:C126836 Transplant Hematopoietic stem cell transplant (HSCT) +NCIT:C157332 Transplant Kidney transplant + Transplant Liver transplant + + variant designation Variant of Concern (VOC) + variant designation Variant of Interest (VOI) + +CIDO_0000019 variant evidence RT-qPCR +CIDO_0000027 variant evidence Sequencing + + +HP:0500165 complications Abnormal blood oxygen level +MONDO:0001208 complications Acute respiratory failure +HP:0011675 complications Arrhythmia (complication) +HP:0001649 Arrhythmia (complication) Tachycardia +HP:0031677 Tachycardia Polymorphic ventricular tachycardia (VT) +HP NTR Tachycardia Tachyarrhythmia +HP NTR complications Noncardiogenic pulmonary edema +HP:0033677 Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) +HP NTR Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) +HP NTR Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) +NCIT:C45430 complications Cardiac injury +HP:0001695 complications Cardiac arrest +HP:0030149 complications Cardiogenic shock +UBERON:0010210 complications Blood clot +HP:0004420 Blood clot Arterial clot +HP:0002625 Blood clot Deep vein thrombosis (DVT) +HP:0002204 Blood clot Pulmonary embolism (PE) +HP:0001638 complications Cardiomyopathy +MONDO:0024619 complications Central nervous system invasion +HP:0001297 complications Stroke (complication) +MONDO:0003346 Stroke (complication) Central Nervous System Vasculitis + Stroke (complication) Ischemic stroke +HP:0002140 Ischemic stroke Acute ischemic stroke +HP:0001259 complications Coma +HP:0011097 complications Convulsions +HP NTR complications COVID-19 associated coagulopathy (CAC) +MONDO:0009061 complications Cystic fibrosis +MONDO:0600008 complications Cytokine release syndrome +HP NTR complications Disseminated intravascular coagulation (DIC) +HP:0001298 complications Encephalopathy +HP NTR complications Fulminant myocarditis +MONDO:0016218 complications Guillain-Barré syndrome +HP:0011029 complications Internal hemorrhage (complication; internal bleeding) +MONDO:0013792 Internal hemorrhage (complication; internal bleeding) Intracerebral haemorrhage +HP NTR complications Kawasaki disease +HP NTR Kawasaki disease Typical Kawasaki disease +HP NTR Kawasaki disease Incomplete Kawasaki disease + complications Kidney injury +HP:0001919 Kidney injury Acute kidney injury +MONDO:0100233 complications Long COVID-19 +HP:0001410 complications Liver dysfunction + complications Liver injury +HP NTR Liver injury Acute liver injury + complications Lung injury +MONDO:0015796 Lung injury Acute lung injury +HP NTR Lung injury Ventilation induced lung injury (VILI) +HP:0001287 complications Meningitis +HP:0002076 complications Migraine +HP:0005268 complications Miscarriage +MONDO:0100163 complications Multisystem inflammatory syndrome in children (MIS-C) +HP NTR complications Muscle injury +MONDO:0005404 complications Myalgic encephalomyelitis (ME) +MONDO:0005068 complications Myocardial infarction (heart attack) +MONDO:0004781 Myocardial infarction (heart attack) Acute myocardial infarction +MONDO:0041656 Myocardial infarction (heart attack) ST-segment elevation myocardial infarction +HP NTR complications Myocardial injury +NCIT:C168498 complications Neonatal complications +HP NTR complications Organ failure +HP:0002878 Organ failure Heart failure +HP:0001399 Organ failure Liver failure +HP:0003470 complications Paralysis +HP:0002107 complications Pneumothorax (collapsed lung) +HP:0002108 Pneumothorax (collapsed lung) Spontaneous pneumothorax +MONDO:0002075 Pneumothorax (collapsed lung) Spontaneous tension pneumothorax +HP:0002090 complications Pneumonia (complication) +HP NTR Pneumonia (complication) COVID-19 pneumonia +HP:0001197 complications Pregancy complications +HP:0003201 complications Rhabdomyolysis +IDO:0000567 complications Secondary infection +IDO NTR Secondary infection Secondary staph infection +IDO NTR Secondary infection Secondary strep infection +HP:0001250 complications Seizure (complication) +HP:0020219 Seizure (complication) Motor seizure +HP:0100806 complications Sepsis +HP NTR complications Septicemia +HP:0031273 complications Shock +HP NTR Shock Hyperinflammatory shock +HP NTR Shock Refractory cardiogenic shock +HP NTR Shock Refractory cardiogenic plus vasoplegic shock +HP NTR Shock Septic shock +HP:0002633 complications Vasculitis + + + +UBERON_0000178 anatomical material Blood BLOOD +UBERON_0006314 anatomical material Fluid FLUID +UBERON_0001836 Fluid Saliva SALIVA +UBERON_0001359 Fluid Fluid (cerebrospinal (CSF)) FLUID_CSF +UBERON_0002409 Fluid Fluid (pericardial) FLUID_PERICARDIAL +UBERON_0001087 Fluid Fluid (pleural) FLUID_PLEURAL +UBERON_0036243 Fluid Fluid (vaginal) FLUID_VAGINAL +UBERON_0000173 Fluid Fluid (amniotic) FLUID_AMNIOTIC +UBERON_0000479 anatomical material Tissue TISSUE + + + +UBERON_0001245 anatomical part Anus ANUS +UBERON_0006956 anatomical part Buccal mucosa BUCCAL_MUCOSA +UBERON_0002114 anatomical part Duodenum DUODENUM +UBERON_0000970 anatomical part Eye EYE + anatomical part Intestine INTESTINE +UBERON_0001052 anatomical part Rectum RECTUM +UBERON_0001003 anatomical part Skin SKIN +UBERON_0000945 anatomical part Stomach STOMACH +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 +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 +UBERON_0001729 Upper respiratory tract Oropharynx (OP) OROPHARYNX_OP +UBERON_0001558 anatomical part Lower respiratory tract LOWER +UBERON_0002185 Lower respiratory tract Bronchus BRONCHUS +UBERON_0002048 Lower respiratory tract Lung LUNG +UBERON_0002186 Lung Bronchiole BRONCHIOLE +UBERON_0002169 Lung Alveolar sac ALVEOLAR_SAC +UBERON_0009778 Lower respiratory tract Pleural sac PLEURAL_SAC +UBERON_0002402 Pleural sac Pleural cavity PLEURAL_CAVITY +UBERON_0003126 Lower respiratory tract Trachea TRACHEA + + + + +UBERON_0001988 body product Feces FECES +UBERON_0001088 body product Urine URINE +UBERON_0001089 body product Sweat SWEAT +UBERON_0000912 body product Mucus MUCUS +UBERON_0007311 Mucus Sputum SPUTUM +UBERON_0001827 body product Tear TEAR +UBERON_0006530 body product Fluid (seminal) FLUID_SEMINAL +UBERON_0001913 body product Breast Milk BREAST_MILK + + prior SARS-CoV-2 infection Yes + prior SARS-CoV-2 infection No + prior SARS-CoV-2 infection Unknown + + +ENVO:03501208 environmental material Air vent AIR_VENT +ENVO_00003896 environmental material Banknote BANKNOTE +ENVO:03501209 environmental material Bed rail BED_RAIL +ENVO_01000486 environmental material Building floor BUILDING_FLOOR +ENVO_02000058 environmental material Cloth CLOTH +ENVO:03501210 environmental material Control panel CONTROL_PANEL +ENVO:03501220 environmental material Door DOOR +ENVO:03501211 environmental material Door handle DOOR_HANDLE +OBI:0002787 environmental material Face mask FACE_MASK +OBI:0002791 environmental material Face shield FACE_SHIELD +FOODON:00002403 environmental material Food FOOD +FOODON:03490100 environmental material Food packaging FOOD_PACKAGING +ENVO:01000481 environmental material Glass GLASS +ENVO:03501212 environmental material Handrail HANDRAIL +OBI:0002792 environmental material Hospital gown HOSPITAL_GOWN +ENVO:03501213 environmental material Light switch LIGHT_SWITCH +ENVO:03501214 environmental material Locker LOCKER +OBI:0002790 environmental material N95 mask N95_MASK +ENVO:03501215 environmental material Nurse call button NURSE_CALL_BUTTON +ENVO:03501256 environmental material Paper PAPER +ENVO:01000060 environmental material Particulate matter PARTICULATE_MATTER +ENVO:01000404 environmental material Plastic PLASTIC +OBI NTR? environmental material PPE gown PPE_GOWN +ENVO_00002018 environmental material Sewage SEWAGE +ENVO_01000990 environmental material Sink SINK +ENVO_00001998 environmental material Soil SOIL +ENVO:03501216 environmental material Stainless steel STAINLESS_STEEL +ENVO:03501217 environmental material Tissue paper TISSUE_PAPER +ENVO:03501218 environmental material Toilet bowl TOILET_BOWL +ENVO_00002006 environmental material Water WATER +ENVO:00002001 environmental material Wastewater WASTEWATER +ENVO:03501219 environmental material Window WINDOW +ENVO:00002040 environmental material Wood WOOD + +ENVO:03501135 environmental site Acute care facility ACUTE_CARE_FACILITY +ENVO:00003040 environmental site Animal house ANIMAL_HOUSE +ENVO:01000422 environmental site Bathroom BATHROOM +ENVO:03501136 environmental site Clinical assessment centre CLINICAL_ASSESSMENT_ +ENVO:03501127 environmental site Conference venue CONFERENCE_VENUE +ENVO:03501121 environmental site Corridor CORRIDOR +ENVO_01000927 environmental site Daycare DAYCARE +ENVO:03501144 environmental site Emergency room (ER) EMERGENCY_ROOM_ER +ENVO:03501186 environmental site Family practice clinic FAMILY_PRACTICE_CLIN +ENVO:03501196 environmental site Group home GROUP_HOME +ENVO:03501133 environmental site Homeless shelter HOMELESS_SHELTER +ENVO:00002173 environmental site Hospital HOSPITAL +ENVO:03501152 environmental site Intensive Care Unit (ICU) INTENSIVE_CARE_UNIT_ +ENVO:03501194 environmental site Long Term Care Facility LONG_TERM_CARE_FACIL +ENVO:03501180 environmental site Patient room PATIENT_ROOM +ENVO:03501204 environmental site Prison PRISON +ENVO_01000536 environmental site Production Facility PRODUCTION_FACILITY +ENVO:03501130 environmental site School SCHOOL +ENVO:00003043 environmental site Sewage Plant SEWAGE_PLANT +ENVO:03501109 environmental site Subway train SUBWAY_TRAIN +ENVO:03501198 environmental site Wet market WET_MARKET + + +OBI NTR collection method Amniocentesis AMNIOCENTESIS +OBI NTR collection method Aspiration ASPIRATION +OBI NTR Aspiration Suprapubic Aspiration SUPRAPUBIC_ASPIRATIO +OBI NTR Aspiration Tracheal aspiration TRACHEAL_ASPIRATION +OBI NTR Aspiration Vacuum Aspiration VACUUM_ASPIRATION +OBI:0002650 collection method Biopsy BIOPSY +OBI:0002651 Biopsy Needle Biopsy NEEDLE_BIOPSY +OBI:0302885 collection method Filtration FILTRATION +OBI NTR Filtration Air filtration AIR_FILTRATION +OBI:0600044 collection method Lavage LAVAGE +OBI NTR Lavage Bronchoalveolar lavage (BAL) BAL +OBI NTR Lavage Gastric Lavage GASTRIC_LAVAGE +OBI NTR collection method Lumbar Puncture LUMBAR_PUNCTURE +OBI NTR collection method Necropsy NECROPSY +OBI NTR collection method Phlebotomy PHLEBOTOMY +OBI NTR collection method Rinsing RINSING +OBI NTR Rinsing Saline gargle (mouth rinse and gargle) +OBI NTR collection method Scraping SCRAPING +OBI NTR collection method Swabbing SWABBING +OBI NTR Swabbing Finger Prick FINGER_PRICK +OBI NTR collection method Wash WASH +OBI NTR collection method Washout Tear Collection WASHOUT + + +ENVO:00003968 collection device Air filter AIR_FILTER +OBI:0002859 collection device Blood Collection Tube BLOOD_TUBE +OBI:0002826 collection device Bronchoscope BRONCHOSCOPE +OBI:0002088 collection device Collection Container CONTAINER +OBI NTR? collection device Collection Cup CUP +OBI:0002825 collection device Fibrobronchoscope Brush BRUSH +ENVO NTR collection device Filter FILTER +OBI:0002827 collection device Fine Needle FINE_NEEDLE +OBI:0002858 collection device Microcapillary tube MICROCAPILLARY_TUBE +OBI:0001128 collection device Micropipette MICROPIPETTE +OBI:0000436 collection device Needle NEEDLE +OBI:0002860 collection device Serum Collection Tube SERUM_TUBE +OBI:0002861 collection device Sputum Collection Tube SPUTUM_TUBE +OBI:0002831 collection device Suction Catheter SUCTION_CATHETER +OBI NTR? collection device Swab SWAB +OBI:0002862 collection device Urine Collection Tube URINE_TUBE +OBI:0002866 collection device Virus Transport Medium TRANSPORT_MEDIUM + + +NCBITaxon_9606 host (scientific name) Homo sapiens +NCBITaxon_9913 host (scientific name) Bos taurus +NCBITaxon_9615 host (scientific name) Canis lupus familiaris +NCBITaxon_9397 host (scientific name) Chiroptera +NCBITaxon_8930 host (scientific name) Columbidae +NCBITaxon_9685 host (scientific name) Felis catus +NCBITaxon_9031 host (scientific name) Gallus gallus +NCBITaxon_9973 host (scientific name) Manis +NCBITaxon_9974 host (scientific name) Manis javanica +NCBITaxon_452646 host (scientific name) Neovison vison +NCBITaxon_9689 host (scientific name) Panthera leo +NCBITaxon_9694 host (scientific name) Panthera tigris +NCBITaxon_58055 host (scientific name) Rhinolophidae +NCBITaxon_59477 host (scientific name) Rhinolophus affinis +NCBITaxon_9825 host (scientific name) Sus scrofa domesticus +NCBITaxon_9673 host (scientific name) Viverridae + + +NCBITaxon_9606 host (common name) Human HUMAN +NCBITaxon_9397 host (common name) Bat BAT +NCBITaxon_9685 host (common name) Cat +NCBITaxon_9031 host (common name) Chicken +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 +NCBITaxon_452646 host (common name) Mink +NCBITaxon_9973 host (common name) Pangolin PANGOLIN +NCBITaxon_9825 host (common name) Pig porcine +NCBITaxon_8930 host (common name) Pigeon +NCBITaxon_9694 host (common name) Tiger + + +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 + + + host health status details Hospitalized HOSPITALIZED + Hospitalized Hospitalized (Non-ICU) NON_ICU + Hospitalized Hospitalized (ICU) ICU + host health status details Mechanical Ventilation VENTILATION + host health status details Medically Isolated ISOLATED + Medically Isolated Medically Isolated (Negative Pressure) ISOLATED_NEGATIVE_PR + host health status details Self-quarantining SELF_QUARANTINING + + host health outcome Deceased + host health outcome Deteriorating + host health outcome Recovered + host health outcome Stable + +NCBITaxon_2697049 organism Severe acute respiratory syndrome coronavirus 2 +NCBITaxon_2709072 organism RaTG13 +NCBITaxon NTR organism RmYN02 + + +HSO:0000371 purpose of sampling Cluster/Outbreak investigation +HSO or NCIT NTR? purpose of sampling Diagnostic testing +NCIT_c15429 purpose of sampling Research +HSO:0000268 purpose of sampling Surveillance + + +See comment purpose of sequencing Baseline surveillance (random sampling) + purpose of sequencing Targeted surveillance (non-random sampling) + Targeted surveillance (non-random sampling) Priority surveillance project + Priority surveillance project Screening for Variants of Concern (VoC) + Priority surveillance project Longitudinal surveillance (repeat sampling of individuals) + Priority surveillance project Re-infection surveillance + Priority surveillance project Vaccine escape surveillance + Priority surveillance project Travel-associated surveillance + Travel-associated surveillance Domestic travel surveillance + Travel-associated surveillance International travel surveillance + Travel-associated surveillance Surveillance of international border crossing by air travel + Travel-associated surveillance Surveillance of international border crossing by ground transport + Travel-associated surveillance Surveillance from international worker testing +HSO:0000371 purpose of sequencing Cluster/Outbreak investigation + Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation + Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation +NCIT_c15429 purpose of sequencing Research + Research Viral passage experiment + Research Protocol testing experiment + + +OBI NTR? specimen processing Virus passage +OBI NTR? specimen processing RNA re-extraction (post RT-PCR) +OBI:0600016 specimen processing Specimens pooled + +BTO NTR lab host 293/ACE2 cell line +BTO_0000195 lab host Caco2 cell line +BTO_0002750 lab host Calu3 cell line +BTO NTR lab host EFK3B cell line +BTO_0002181 lab host HEK293T cell line +BTO NTR lab host HRCE cell line +BTO_0001950 lab host Huh7 cell line +CLO_0007330 lab host LLCMk2 cell line +BTO_0000836 lab host MDBK cell line +BTO_0002924 lab host NHBE cell line +BTO_0001865 lab host PK-15 cell line +BTO_0002909 lab host RK-13 cell line +BTO_0002035 lab host U251 cell line +BTO_0001444 lab host Vero cell line +BTO:0004755 lab host Vero E6 cell line +BTO NTR lab host VeroE6/TMPRSS2 cell line + +MONDO:0100096 host disease COVID-19 + +GENEPIO NTR host age bin 0 - 9 +GENEPIO NTR host age bin 10 - 19 +GENEPIO NTR host age bin 20 - 29 +GENEPIO NTR host age bin 30 - 39 +GENEPIO NTR host age bin 40 - 49 +GENEPIO NTR host age bin 50 - 59 +GENEPIO NTR host age bin 60 - 69 +GENEPIO NTR host age bin 70 - 79 +GENEPIO NTR host age bin 80 - 89 +GENEPIO NTR host age bin 90 - 99 90+ +GENEPIO NTR host age bin 100+ 90+ + +NCIT_C46110 host gender Female FEMALE +NCIT_C46109 host gender Male MALE +GSSO:000132 host gender Non-binary gender NON_BINARY_GENDER +GSSO:004004 host gender Transgender (Male to Female) TRANSGENDER +GSSO:004005 host gender Transgender (Female to Male) TRANSGENDER + host gender Undeclared REFUSED + host gender Unknown UNKNOWN + +PCO NTR exposure event Mass Gathering +PCO NTR Mass Gathering Agricultural Event +PCO NTR Mass Gathering Convention CONVENTION +PCO NTR Mass Gathering Convocation +PCO NTR Mass Gathering Recreational Event +PCO NTR Recreational Event Concert +PCO NTR Recreational Event Sporting Event +PCO NTR exposure event Religious Gathering RELIGIOUS +PCO NTR Religious Gathering Mass +PCO:0000033 exposure event Social Gathering SOCIAL +PCO:0000039 Social Gathering Baby Shower +PCO:0000034 Social Gathering Community Event +PCO NTR Social Gathering Family Gathering +PCO NTR Family Gathering Family Reunion +PCO NTR Social Gathering Funeral +PCO:0000035 Social Gathering Party +PCO:0000037 Social Gathering Potluck +PCO:0000038 Social Gathering Wedding +NCIT:C168623 exposure event Other exposure event + + +NCIT NTR? exposure contact level Contact with infected individual +NCIT NTR? Contact with infected individual Direct contact (direct human-to-human contact) +NCIT NTR? Contact with infected individual Indirect contact +NCIT NTR? Indirect contact Close contact (face-to-face, no direct contact) +NCIT:C102606 Indirect contact Casual contact + + +OMRSE NTR host role Attendee +OMRSE:00000058 Attendee Student +OMRSE:00000030 host role Patient +OMRSE NTR Patient Inpatient +OMRSE NTR Patient Outpatient +OMRSE NTR host role Passenger +OMRSE NTR host role Resident +OMRSE NTR host role Visitor +OMRSE NTR host role Volunteer +OMRSE NTR host role Work +OMRSE NTR Work Administrator +OMRSE NTR Work First Responder +OMRSE NTR First Responder Firefighter +OMRSE NTR First Responder Paramedic +OMRSE NTR First Responder Police Officer +OMRSE NTR Work Child Care/Education Worker +OMRSE NTR Work Essential Worker +OMRSE NTR Work Healthcare Worker +OMRSE:00000014 Healthcare Worker Nurse +OMRSE NTR Healthcare Worker Personal Care Aid +OMRSE NTR Healthcare Worker Pharmacist +OMRSE:00000050 Healthcare Worker Physician +OMRSE NTR Work Housekeeper +OMRSE NTR Work International worker +OMRSE NTR Work Kitchen Worker +OMRSE NTR Work Laboratory Worker +OMRSE NTR Work Rotational Worker +OMRSE NTR Work Seasonal Worker +OMRSE NTR Work Transport Worker +OMRSE NTR Transport Worker Transport Truck Driver +OMRSE NTR Work Veterinarian +OMRSE:00000001 host role Social role +OMRSE NTR Social role Acquaintance of case +OMRSE NTR Social role Relative of case +OMRSE NTR Relative of case Child of case +OMRSE NTR Relative of case Parent of case +OMRSE NTR Relative of case Father of case +OMRSE NTR Relative of case Mother of case +OMRSE NTR Social role Spouse of case +OMRSE NTR host role Other Host Role + + +ECTO_3000005 exposure setting Human Exposure +ECTO NTR Human Exposure Contact with Known COVID-19 Case +ECTO NTR Human Exposure Contact with Patient +ECTO NTR Human Exposure Contact with Probable COVID-19 Case +ECTO NTR Human Exposure Contact with Person with Acute Respiratory Illness +ECTO NTR Human Exposure Contact with Person with Fever and/or Cough +ECTO NTR Human Exposure Contact with Person who Recently Travelled +ECTO NTR? exposure setting Occupational, Residency or Patronage Exposure +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 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 Group Home +ECTO NTR Occupational, Residency or Patronage Exposure Healthcare Setting +ECTO NTR Healthcare Setting Ambulance +ECTO NTR Healthcare Setting Acute Care Facility +ECTO NTR Healthcare Setting Clinic +ECTO NTR Healthcare Setting Community Health Centre +ECTO_1000035 Healthcare Setting Hospital +ECTO NTR Hospital Emergency Department +ECTO NTR Hospital ICU +ECTO NTR Hospital Ward +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 Insecure Housing (Homeless) +ECTO NTR Occupational, Residency or Patronage Exposure Occupational Exposure +ECTO NTR Occupational Exposure Worksite +ECTO:1000037 Occupational Exposure Office +ECTO NTR Occupational, Residency or Patronage Exposure Outdoors +ECTO_5000009 Outdoors Camp/camping +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_1000040 Occupational, Residency or Patronage Exposure Restaurant +ECTO_1000041 Occupational, Residency or Patronage Exposure Retail Store +ECTO NTR Occupational, Residency or Patronage Exposure School +ECTO NTR Occupational, Residency or Patronage Exposure Temporary Residence +ECTO NTR Temporary Residence Homeless Shelter +ECTO NTR Temporary Residence Hotel +ECTO NTR Occupational, Residency or Patronage Exposure Veterinary Care Clinic +ECTO NTR exposure setting Travel Exposure +ECTO NTR Travel Exposure Travelled on a Cruise Ship +ECTO NTR Travel Exposure Travelled on a Plane +ECTO NTR Travel Exposure Travelled on Ground Transport +GENEPIO_0001119 Travel Exposure Travelled outside Province/Territory +GENEPIO_0001118 Travel Exposure Travelled outside Canada +GENEPIO NTR? exposure setting Other Exposure Setting + + + +OBI_0000759 sequencing instrument Illumina +OBI_0002128 Illumina Illumina Genome Analyzer +OBI_0000703 Illumina Genome Analyzer Illumina Genome Analyzer II +OBI_0002000 Illumina Genome Analyzer Illumina Genome Analyzer IIx +OBI NTR? Illumina Illumina HiScanSQ +OBI NTR? Illumina Illumina HiSeq +OBI NTR? Illumina Illumina HiSeq X +OBI NTR? Illumina HiSeq X Illumina HiSeq X Five +OBI_0002129 Illumina HiSeq X Illumina HiSeq X Ten +OBI_0002022 Illumina Illumina HiSeq 1000 +OBI NTR? Illumina Illumina HiSeq 1500 +OBI_0002001 Illumina Illumina HiSeq 2000 +OBI_0002002 Illumina Illumina HiSeq 2500 +OBI_0002048 Illumina Illumina HiSeq 3000 +OBI_0002049 Illumina Illumina HiSeq 4000 +OBI NTR? Illumina Illumina iSeq +OBI NTR? Illumina iSeq Illumina iSeq 100 +OBI NTR? Illumina Illumina NovaSeq +OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 +OBI NTR? Illumina Illumina MiniSeq +OBI_0002003 Illumina Illumina MiSeq +OBI NTR? Illumina Illumina NextSeq +OBI_0002021 Illumina Illumina NextSeq 500 +OBI NTR? Illumina Illumina NextSeq 550 +OBI NTR? Illumina Illumina NextSeq 2000 +OBI_0001856 sequencing instrument Pacific Biosciences +OBI NTR? Pacific Biosciences PacBio RS +OBI_0002012 Pacific Biosciences PacBio RS II +OBI_0002632 Pacific Biosciences PacBio Sequel +OBI_0002633 Pacific Biosciences PacBio Sequel II +OBI NTR? sequencing instrument Ion Torrent +GENEPIO_0001935 Ion Torrent Ion Torrent PGM +OBI NTR? Ion Torrent Ion Torrent Proton +OBI NTR? Ion Torrent Ion Torrent S5 XL +OBI NTR? Ion Torrent Ion Torrent S5 +OBI NTR? sequencing instrument Oxford Nanopore +OBI:0002751 Oxford Nanopore Oxford Nanopore GridION +OBI:0002750 Oxford Nanopore Oxford Nanopore MinION +OBI:0002752 Oxford Nanopore Oxford Nanopore PromethION +OBI NTR? sequencing instrument BGI Genomics +OBI NTR? BGI Genomics BGI Genomics BGISEQ-500 +OBI NTR? sequencing instrument MGI +OBI NTR? MGI MGI DNBSEQ-T7 +OBI NTR? MGI MGI DNBSEQ-G400 +OBI NTR? MGI MGI DNBSEQ-G400 FAST +OBI NTR? MGI MGI DNBSEQ-G50 + + +PR:P0DTC4 gene name 1 E gene (orf4) E gene E gene E (orf4) +PR:P0DTC5 gene name 1 M gene (orf5) M (orf5) +PR:P0DTC9 gene name 1 N gene (orf9) N (orf9) +PR:P0DTC2 gene name 1 Spike gene (orf2) S (orf2) +PR:000050281 gene name 1 orf1ab (rep) orf1ab (rep) +PR:P0DTC1-1 orf1ab (rep) orf1a (pp1a) orf1a (pp1a) +PR:000050280 orf1a (pp1a) nsp11 nsp11 +PR:000050270 orf1ab (rep) nsp1 nsp1 +PR:000050271 orf1ab (rep) nsp2 nsp2 +PR:000050272 orf1ab (rep) nsp3 nsp3 +PR:000050273 orf1ab (rep) nsp4 nsp4 +PR:000050274 orf1ab (rep) nsp5 nsp5 +PR:000050275 orf1ab (rep) nsp6 nsp6 +PR:000050276 orf1ab (rep) nsp7 nsp7 +PR:000050277 orf1ab (rep) nsp8 nsp8 +PR:000050278 orf1ab (rep) nsp9 nsp9 +PR:000050279 orf1ab (rep) nsp10 nsp10 +PR:000050284 orf1ab (rep) RdRp gene (nsp12) nsp12 (RdRp) +PR:000050285 orf1ab (rep) hel gene (nsp13) nsp13 (Hel) +PR:000050286 orf1ab (rep) exoN gene (nsp14) nsp14 (ExoN) +PR:000050287 orf1ab (rep) nsp15 nsp15 +PR:000050288 orf1ab (rep) nsp16 nsp16 +PR:P0DTC3 gene name 1 orf3a orf3a +PR NTR gene name 1 orf3b orf3b +PR:P0DTC6 gene name 1 orf6 (ns6) orf6 (ns6) +PR:P0DTC7 gene name 1 orf7a orf7a +PR:P0DTD8 gene name 1 orf7b (ns7b) orf7b (ns7b) +PR:P0DTC8 gene name 1 orf8 (ns8) orf8 (ns8) +PR:P0DTD2 gene name 1 orf9b orf9b +PR NTR? gene name 1 orf9c orf9c +PR:A0A663DJA2 gene name 1 orf10 orf10 +PR NTR? gene name 1 orf14 orf14 + gene name 1 SARS-COV-2 5' UTR + + + sequence submitted by Alberta Precision Labs (APL) + Alberta Precision Labs (APL) Alberta ProvLab North (APLN) + Alberta Precision Labs (APL) Alberta ProvLab South (APLS) + 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 (Manitoba) Dynacare Manitoba + sequence submitted by The Hospital for Sick Children (SickKids) CANCOGEN_SICK_KIDS_HOSPITAL + sequence submitted by Laboratoire de santé publique du Québec (LSPQ) + sequence submitted by Manitoba Cadham Provincial Laboratory + sequence submitted by McMaster University + sequence submitted by McGill University + sequence submitted by National Microbiology Laboratory (NML) + sequence submitted by New Brunswick - Vitalité Health Network + sequence submitted by Newfoundland and Labrador - Eastern Health + sequence submitted by Nova Scotia Health Authority + sequence submitted by Ontario Institute for Cancer Research (OICR) + sequence submitted by Prince Edward Island - Health PEI + sequence submitted by Public Health Ontario (PHO) + sequence submitted by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + sequence submitted by Sunnybrook Health Sciences Centre + sequence submitted by Thunder Bay Regional Health Sciences Centre + sequence submitted by Queen's University / Kingston Health Sciences Centre + + + sample collected by Alberta Precision Labs (APL) + Alberta Precision Labs (APL) Alberta ProvLab North (APLN) CANCOGEN_EDMONTON_PROV_LAB + Alberta Precision Labs (APL) Alberta ProvLab South (APLS) CANCOGEN_CALGARY_PROV_LAB + sample collected by BCCDC Public Health Laboratory CANCOGEN_BCCDC + sample collected by Dynacare (Manitoba) Dynacare Manitoba + sample collected by Eastern Ontario Regional Laboratory Association CANCOGEN_EORLA + sample collected by Hamilton Health Sciences " CANCOGEN_HAMILTON_HS" - sample collected by The Hospital for Sick Children (SickKids) CANCOGEN_SICK_KIDS_HOSPITAL - sample collected by Laboratoire de santé publique du Québec (LSPQ) CANCOGEN_LSPQ - sample collected by Lake of the Woods District Hospital - Ontario CANCOGEN_LAKE_OF_THE_WOODS - sample collected by Manitoba Cadham Provincial Laboratory CANCOGEN_CADHAM_LAB - sample collected by McMaster University CANCOGEN_MCMASTER_UNIVERSITY - sample collected by Mount Sinai Hospital " + sample collected by The Hospital for Sick Children (SickKids) CANCOGEN_SICK_KIDS_HOSPITAL + sample collected by Laboratoire de santé publique du Québec (LSPQ) CANCOGEN_LSPQ + sample collected by Lake of the Woods District Hospital - Ontario CANCOGEN_LAKE_OF_THE_WOODS + sample collected by Manitoba Cadham Provincial Laboratory CANCOGEN_CADHAM_LAB + sample collected by McMaster University CANCOGEN_MCMASTER_UNIVERSITY + sample collected by Mount Sinai Hospital " CANCOGEN_MOUNT_SINAI" - sample collected by National Microbiology Laboratory (NML) CANCOGEN_NML_IRV - sample collected by New Brunswick - Vitalité Health Network CANCOGEN_G_L_DUMONT - sample collected by Newfoundland and Labrador - Eastern Health CANCOGEN_STJOHNS_PHL - sample collected by Nova Scotia Health Authority CANCOGEN_QEII_HSC - sample collected by Nunuvut CANCOGEN_NUNAVUT_ - sample collected by Ontario Institute for Cancer Research (OICR) CANCOGEN_OICR - sample collected by Prince Edward Island - Health PEI CANCOGEN_QEH - sample collected by Public Health Ontario (PHO) CANCOGEN_ONTARIO_PHO - sample collected by Queen's University / Kingston Health Sciences Centre CANCOGEN_KINGSTON - sample collected by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) CANCOGEN_ROMANOW_PROV_LAB - sample collected by St. John's Rehab at Sunnybrook Hospital " + sample collected by National Microbiology Laboratory (NML) CANCOGEN_NML_IRV + sample collected by New Brunswick - Vitalité Health Network CANCOGEN_G_L_DUMONT + sample collected by Newfoundland and Labrador - Eastern Health CANCOGEN_STJOHNS_PHL + sample collected by Nova Scotia Health Authority CANCOGEN_QEII_HSC + sample collected by Nunuvut CANCOGEN_NUNAVUT_ + sample collected by Ontario Institute for Cancer Research (OICR) CANCOGEN_OICR + sample collected by Prince Edward Island - Health PEI CANCOGEN_QEH + sample collected by Public Health Ontario (PHO) CANCOGEN_ONTARIO_PHO + sample collected by Queen's University / Kingston Health Sciences Centre CANCOGEN_KINGSTON + sample collected by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) CANCOGEN_ROMANOW_PROV_LAB + sample collected by St. John's Rehab at Sunnybrook Hospital " CANCOGEN_SJRH" - sample collected by Sunnybrook Health Sciences Centre CANCOGEN_SUNNYBROOK - sample collected by Unity Health Toronto " + sample collected by Sunnybrook Health Sciences Centre CANCOGEN_SUNNYBROOK + sample collected by Unity Health Toronto " CANCOGEN_UNITY_HEALTH" - sample collected by William Osler Health System " + sample collected by William Osler Health System " CANCOGEN_WILLIAM_OSLER" - - -GAZ_00006882 geo_loc_name (country) Afghanistan -GAZ_00002953 geo_loc_name (country) Albania -GAZ_00000563 geo_loc_name (country) Algeria -GAZ_00003957 geo_loc_name (country) American Samoa -GAZ_00002948 geo_loc_name (country) Andorra -GAZ_00001095 geo_loc_name (country) Angola -GAZ_00009159 geo_loc_name (country) Anguilla -GAZ_00000462 geo_loc_name (country) Antarctica -GAZ_00006883 geo_loc_name (country) Antigua and Barbuda -GAZ_00002928 geo_loc_name (country) Argentina ARGENTINA -GAZ_00004094 geo_loc_name (country) Armenia -GAZ_00004025 geo_loc_name (country) Aruba -GAZ_00005901 geo_loc_name (country) Ashmore and Cartier Islands -GAZ_00000463 geo_loc_name (country) Australia AUSTRALIA -GAZ_00002942 geo_loc_name (country) Austria -GAZ_00004941 geo_loc_name (country) Azerbaijan -GAZ_00002733 geo_loc_name (country) Bahamas -GAZ_00005281 geo_loc_name (country) Bahrain -GAZ_00007117 geo_loc_name (country) Baker Island -GAZ_00003750 geo_loc_name (country) Bangladesh -GAZ_00001251 geo_loc_name (country) Barbados -GAZ_00005810 geo_loc_name (country) Bassas da India -GAZ_00006886 geo_loc_name (country) Belarus -GAZ_00002938 geo_loc_name (country) Belgium BELGIUM -GAZ_00002934 geo_loc_name (country) Belize -GAZ_00000904 geo_loc_name (country) Benin -GAZ_00001264 geo_loc_name (country) Bermuda -GAZ_00003920 geo_loc_name (country) Bhutan -GAZ_00002511 geo_loc_name (country) Bolivia -GAZ_00025355 geo_loc_name (country) Borneo -GAZ_00006887 geo_loc_name (country) Bosnia and Herzegovina -GAZ_00001097 geo_loc_name (country) Botswana -GAZ_00001453 geo_loc_name (country) Bouvet Island -GAZ_00002828 geo_loc_name (country) Brazil BRAZIL -GAZ_00003961 geo_loc_name (country) British Virgin Islands -GAZ_00003901 geo_loc_name (country) Brunei -GAZ_00002950 geo_loc_name (country) Bulgaria -GAZ_00000905 geo_loc_name (country) Burkina Faso -GAZ_00001090 geo_loc_name (country) Burundi -GAZ_00006888 geo_loc_name (country) Cambodia -GAZ_00001093 geo_loc_name (country) Cameroon -GAZ_00002560 geo_loc_name (country) Canada CA -GAZ_00001227 geo_loc_name (country) Cape Verde -GAZ_00003986 geo_loc_name (country) Cayman Islands -GAZ_00001089 geo_loc_name (country) Central African Republic -GAZ_00000586 geo_loc_name (country) Chad -GAZ_00002825 geo_loc_name (country) Chile CHILE -GAZ_00002845 geo_loc_name (country) China CHINA -GAZ_00005915 geo_loc_name (country) Christmas Island -GAZ_00005838 geo_loc_name (country) Clipperton Island -GAZ_00009721 geo_loc_name (country) Cocos Islands -GAZ_00002929 geo_loc_name (country) Colombia COLUMBIA -GAZ_00005820 geo_loc_name (country) Comoros -GAZ_00053798 geo_loc_name (country) Cook Islands -GAZ_00005917 geo_loc_name (country) Coral Sea Islands -GAZ_00002901 geo_loc_name (country) Costa Rica COSTA_RICA -GAZ_00000906 geo_loc_name (country) Cote d'Ivoire -GAZ_00002719 geo_loc_name (country) Croatia -GAZ_00003762 geo_loc_name (country) Cuba -GAZ_00004021 geo_loc_name (country) Curacao -GAZ_00004006 geo_loc_name (country) Cyprus -GAZ_00002954 geo_loc_name (country) Czech Republic -GAZ_00001086 geo_loc_name (country) Democratic Republic of the Congo -GAZ_00005852 geo_loc_name (country) Denmark DENMARK -GAZ_00000582 geo_loc_name (country) Djibouti -GAZ_00006890 geo_loc_name (country) Dominica -GAZ_00003952 geo_loc_name (country) Dominican Republic -GAZ_00002912 geo_loc_name (country) Ecuador ECUADOR -GAZ_00003934 geo_loc_name (country) Egypt -GAZ_00002935 geo_loc_name (country) El Salvador -GAZ_00001091 geo_loc_name (country) Equatorial Guinea -GAZ_00000581 geo_loc_name (country) Eritrea -GAZ_00002959 geo_loc_name (country) Estonia -GAZ_00001099 geo_loc_name (country) Eswatini -GAZ_00000567 geo_loc_name (country) Ethiopia -GAZ_00005811 geo_loc_name (country) Europa Island -GAZ_00001412 geo_loc_name (country) Falkland Islands (Islas Malvinas) -GAZ_00059206 geo_loc_name (country) Faroe Islands -GAZ_00006891 geo_loc_name (country) Fiji -GAZ_00002937 geo_loc_name (country) Finland -GAZ_00003940 geo_loc_name (country) France FRANCE -GAZ_00002516 geo_loc_name (country) French Guiana -GAZ_00002918 geo_loc_name (country) French Polynesia -GAZ_00003753 geo_loc_name (country) French Southern and Antarctic Lands -GAZ_00001092 geo_loc_name (country) Gabon -GAZ_00000907 geo_loc_name (country) Gambia -GAZ_00009571 geo_loc_name (country) Gaza Strip -GAZ_00004942 geo_loc_name (country) Georgia -GAZ_00002646 geo_loc_name (country) Germany GERMANY -GAZ_00000908 geo_loc_name (country) Ghana -GAZ_00003987 geo_loc_name (country) Gibraltar -GAZ_00005808 geo_loc_name (country) Glorioso Islands -GAZ_00002945 geo_loc_name (country) Greece -GAZ_00001507 geo_loc_name (country) Greenland -GAZ_02000573 geo_loc_name (country) Grenada -GAZ_00067142 geo_loc_name (country) Guadeloupe -GAZ_00003706 geo_loc_name (country) Guam -GAZ_00002936 geo_loc_name (country) Guatemala -GAZ_00001550 geo_loc_name (country) Guernsey -GAZ_00000909 geo_loc_name (country) Guinea -GAZ_00000910 geo_loc_name (country) Guinea-Bissau -GAZ_00002522 geo_loc_name (country) Guyana GUYANA -GAZ_00003953 geo_loc_name (country) Haiti -GAZ_00009718 geo_loc_name (country) Heard Island and McDonald Islands -GAZ_00002894 geo_loc_name (country) Honduras -GAZ_00003203 geo_loc_name (country) Hong Kong -GAZ_00007120 geo_loc_name (country) Howland Island -GAZ_00002952 geo_loc_name (country) Hungary -GAZ_00000843 geo_loc_name (country) Iceland -GAZ_00002839 geo_loc_name (country) India INDIA -GAZ_00003727 geo_loc_name (country) Indonesia -GAZ_00004474 geo_loc_name (country) Iran -GAZ_00004483 geo_loc_name (country) Iraq -GAZ_00002943 geo_loc_name (country) Ireland -GAZ_00052477 geo_loc_name (country) Isle of Man -GAZ_00002476 geo_loc_name (country) Israel -GAZ_00002650 geo_loc_name (country) Italy -GAZ_00003781 geo_loc_name (country) Jamaica JAMAICA -GAZ_00005853 geo_loc_name (country) Jan Mayen -GAZ_00002747 geo_loc_name (country) Japan -GAZ_00007118 geo_loc_name (country) Jarvis Island -GAZ_00001551 geo_loc_name (country) Jersey -GAZ_00007114 geo_loc_name (country) Johnston Atoll -GAZ_00002473 geo_loc_name (country) Jordan -GAZ_00005809 geo_loc_name (country) Juan de Nova Island -GAZ_00004999 geo_loc_name (country) Kazakhstan -GAZ_00001101 geo_loc_name (country) Kenya KENYA -GAZ_00005682 geo_loc_name (country) Kerguelen Archipelago -GAZ_00007116 geo_loc_name (country) Kingman Reef -GAZ_00006894 geo_loc_name (country) Kiribati -GAZ_00011337 geo_loc_name (country) Kosovo -GAZ_00005285 geo_loc_name (country) Kuwait -GAZ_00006893 geo_loc_name (country) Kyrgyzstan -GAZ_00006889 geo_loc_name (country) Laos -GAZ_00002958 geo_loc_name (country) Latvia -GAZ_00002478 geo_loc_name (country) Lebanon -GAZ_00001098 geo_loc_name (country) Lesotho -GAZ_00000911 geo_loc_name (country) Liberia -GAZ_00000566 geo_loc_name (country) Libya -GAZ_00003858 geo_loc_name (country) Liechtenstein -GAZ_00007144 geo_loc_name (country) Line Islands -GAZ_00002960 geo_loc_name (country) Lithuania -GAZ_00002947 geo_loc_name (country) Luxembourg -GAZ_00003202 geo_loc_name (country) Macau -GAZ_00001108 geo_loc_name (country) Madagascar -GAZ_00001105 geo_loc_name (country) Malawi -GAZ_00003902 geo_loc_name (country) Malaysia -GAZ_00006924 geo_loc_name (country) Maldives -GAZ_00000584 geo_loc_name (country) Mali -GAZ_00005459 geo_loc_name (country) Malta -GAZ_00007161 geo_loc_name (country) Marshall Islands -GAZ_00067143 geo_loc_name (country) Martinique -GAZ_00000583 geo_loc_name (country) Mauritania -GAZ_00003745 geo_loc_name (country) Mauritius -GAZ_00003943 geo_loc_name (country) Mayotte -GAZ_00002852 geo_loc_name (country) Mexico MEXICO -GAZ_00005862 geo_loc_name (country) Micronesia -GAZ_00007112 geo_loc_name (country) Midway Islands -GAZ_00003897 geo_loc_name (country) Moldova -GAZ_00003857 geo_loc_name (country) Monaco -GAZ_00008744 geo_loc_name (country) Mongolia -GAZ_00006898 geo_loc_name (country) Montenegro -GAZ_00003988 geo_loc_name (country) Montserrat -GAZ_00000565 geo_loc_name (country) Morocco -GAZ_00001100 geo_loc_name (country) Mozambique -GAZ_00006899 geo_loc_name (country) Myanmar -GAZ_00001096 geo_loc_name (country) Namibia -GAZ_00006900 geo_loc_name (country) Nauru -GAZ_00007119 geo_loc_name (country) Navassa Island -GAZ_00004399 geo_loc_name (country) Nepal -GAZ_00002946 geo_loc_name (country) Netherlands NETHERLANDS -GAZ_00005206 geo_loc_name (country) New Caledonia -GAZ_00000469 geo_loc_name (country) New Zealand -GAZ_00002978 geo_loc_name (country) Nicaragua -GAZ_00000585 geo_loc_name (country) Niger -GAZ_00000912 geo_loc_name (country) Nigeria NIGERIA -GAZ_00006902 geo_loc_name (country) Niue -GAZ_00005908 geo_loc_name (country) Norfolk Island -GAZ_00002801 geo_loc_name (country) North Korea -GAZ_00006895 geo_loc_name (country) North Macedonia -GAZ_00002284 geo_loc_name (country) North Sea -GAZ_00003958 geo_loc_name (country) Northern Mariana Islands -GAZ_00002699 geo_loc_name (country) Norway -GAZ_00005283 geo_loc_name (country) Oman -GAZ_00005246 geo_loc_name (country) Pakistan PAKISTAN -GAZ_00006905 geo_loc_name (country) Palau -GAZ_00002892 geo_loc_name (country) Panama -GAZ_00003922 geo_loc_name (country) Papua New Guinea -GAZ_00010832 geo_loc_name (country) Paracel Islands -GAZ_00002933 geo_loc_name (country) Paraguay -GAZ_00002932 geo_loc_name (country) Peru -GAZ_00004525 geo_loc_name (country) Philippines PHILIPPINE -GAZ_00005867 geo_loc_name (country) Pitcairn Islands -GAZ_00002939 geo_loc_name (country) Poland -GAZ_00004126 geo_loc_name (country) Portugal -GAZ_00006935 geo_loc_name (country) Puerto Rico -GAZ_00005286 geo_loc_name (country) Qatar -GAZ_00001088 geo_loc_name (country) Republic of the Congo -GAZ_00003945 geo_loc_name (country) Reunion -GAZ_00002951 geo_loc_name (country) Romania -GAZ_00023304 geo_loc_name (country) Ross Sea -GAZ_00002721 geo_loc_name (country) Russia -GAZ_00001087 geo_loc_name (country) Rwanda -GAZ_00000849 geo_loc_name (country) Saint Helena -GAZ_00006906 geo_loc_name (country) Saint Kitts and Nevis -GAZ_00006909 geo_loc_name (country) Saint Lucia -GAZ_00003942 geo_loc_name (country) Saint Pierre and Miquelon -GAZ_00005841 geo_loc_name (country) Saint Martin -GAZ_02000565 geo_loc_name (country) Saint Vincent and the Grenadines -GAZ_00006910 geo_loc_name (country) Samoa -GAZ_00003102 geo_loc_name (country) San Marino -GAZ_00006927 geo_loc_name (country) Sao Tome and Principe -GAZ_00005279 geo_loc_name (country) Saudi Arabia -GAZ_00000913 geo_loc_name (country) Senegal -GAZ_00002957 geo_loc_name (country) Serbia -GAZ_00006922 geo_loc_name (country) Seychelles -GAZ_00000914 geo_loc_name (country) Sierra Leone -GAZ_00003923 geo_loc_name (country) Singapore -GAZ_00012579 geo_loc_name (country) Sint Maarten -GAZ_00002956 geo_loc_name (country) Slovakia -GAZ_00002955 geo_loc_name (country) Slovenia -GAZ_00005275 geo_loc_name (country) Solomon Islands -GAZ_00001104 geo_loc_name (country) Somalia -GAZ_00001094 geo_loc_name (country) South Africa -GAZ_00003990 geo_loc_name (country) South Georgia and the South Sandwich Islands -GAZ_00002802 geo_loc_name (country) South Korea -GAZ_00233439 geo_loc_name (country) South Sudan -GAZ_00003936 geo_loc_name (country) Spain -GAZ_00010831 geo_loc_name (country) Spratly Islands -GAZ_00003924 geo_loc_name (country) Sri Lanka -GAZ_00002475 geo_loc_name (country) State of Palestine -GAZ_00000560 geo_loc_name (country) Sudan -GAZ_00002525 geo_loc_name (country) Suriname -GAZ_00005396 geo_loc_name (country) Svalbard -GAZ_00001099 geo_loc_name (country) Swaziland -GAZ_00002729 geo_loc_name (country) Sweden -GAZ_00002941 geo_loc_name (country) Switzerland -GAZ_00002474 geo_loc_name (country) Syria -GAZ_00005341 geo_loc_name (country) Taiwan -GAZ_00006912 geo_loc_name (country) Tajikistan -GAZ_00001103 geo_loc_name (country) Tanzania -GAZ_00003744 geo_loc_name (country) Thailand -GAZ_00006913 geo_loc_name (country) Timor-Leste -GAZ_00000915 geo_loc_name (country) Togo -GAZ_00260188 geo_loc_name (country) Tokelau -GAZ_00006916 geo_loc_name (country) Tonga -GAZ_00003767 geo_loc_name (country) Trinidad and Tobago -GAZ_00005812 geo_loc_name (country) Tromelin Island -GAZ_00000562 geo_loc_name (country) Tunisia -GAZ_00000558 geo_loc_name (country) Turkey -GAZ_00005018 geo_loc_name (country) Turkmenistan -GAZ_00003955 geo_loc_name (country) Turks and Caicos Islands -GAZ_00009715 geo_loc_name (country) Tuvalu -GAZ_00002459 geo_loc_name (country) United States of America US -GAZ_00001102 geo_loc_name (country) Uganda -GAZ_00002724 geo_loc_name (country) Ukraine -GAZ_00005282 geo_loc_name (country) United Arab Emirates -GAZ_00002637 geo_loc_name (country) United Kingdom UNITEDKING -GAZ_00002930 geo_loc_name (country) Uruguay URUGUAY -GAZ_00004979 geo_loc_name (country) Uzbekistan -GAZ_00006918 geo_loc_name (country) Vanuatu -GAZ_00002931 geo_loc_name (country) Venezuela -GAZ_00003756 geo_loc_name (country) Viet Nam -GAZ_00003959 geo_loc_name (country) Virgin Islands -GAZ_00007111 geo_loc_name (country) Wake Island -GAZ_00007191 geo_loc_name (country) Wallis and Futuna -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_00006882 geo_loc_name (country) Afghanistan +GAZ_00002953 geo_loc_name (country) Albania +GAZ_00000563 geo_loc_name (country) Algeria +GAZ_00003957 geo_loc_name (country) American Samoa +GAZ_00002948 geo_loc_name (country) Andorra +GAZ_00001095 geo_loc_name (country) Angola +GAZ_00009159 geo_loc_name (country) Anguilla +GAZ_00000462 geo_loc_name (country) Antarctica +GAZ_00006883 geo_loc_name (country) Antigua and Barbuda +GAZ_00002928 geo_loc_name (country) Argentina ARGENTINA +GAZ_00004094 geo_loc_name (country) Armenia +GAZ_00004025 geo_loc_name (country) Aruba +GAZ_00005901 geo_loc_name (country) Ashmore and Cartier Islands +GAZ_00000463 geo_loc_name (country) Australia AUSTRALIA +GAZ_00002942 geo_loc_name (country) Austria +GAZ_00004941 geo_loc_name (country) Azerbaijan +GAZ_00002733 geo_loc_name (country) Bahamas +GAZ_00005281 geo_loc_name (country) Bahrain +GAZ_00007117 geo_loc_name (country) Baker Island +GAZ_00003750 geo_loc_name (country) Bangladesh +GAZ_00001251 geo_loc_name (country) Barbados +GAZ_00005810 geo_loc_name (country) Bassas da India +GAZ_00006886 geo_loc_name (country) Belarus +GAZ_00002938 geo_loc_name (country) Belgium BELGIUM +GAZ_00002934 geo_loc_name (country) Belize +GAZ_00000904 geo_loc_name (country) Benin +GAZ_00001264 geo_loc_name (country) Bermuda +GAZ_00003920 geo_loc_name (country) Bhutan +GAZ_00002511 geo_loc_name (country) Bolivia +GAZ_00025355 geo_loc_name (country) Borneo +GAZ_00006887 geo_loc_name (country) Bosnia and Herzegovina +GAZ_00001097 geo_loc_name (country) Botswana +GAZ_00001453 geo_loc_name (country) Bouvet Island +GAZ_00002828 geo_loc_name (country) Brazil BRAZIL +GAZ_00003961 geo_loc_name (country) British Virgin Islands +GAZ_00003901 geo_loc_name (country) Brunei +GAZ_00002950 geo_loc_name (country) Bulgaria +GAZ_00000905 geo_loc_name (country) Burkina Faso +GAZ_00001090 geo_loc_name (country) Burundi +GAZ_00006888 geo_loc_name (country) Cambodia +GAZ_00001093 geo_loc_name (country) Cameroon +GAZ_00002560 geo_loc_name (country) Canada CA +GAZ_00001227 geo_loc_name (country) Cape Verde +GAZ_00003986 geo_loc_name (country) Cayman Islands +GAZ_00001089 geo_loc_name (country) Central African Republic +GAZ_00000586 geo_loc_name (country) Chad +GAZ_00002825 geo_loc_name (country) Chile CHILE +GAZ_00002845 geo_loc_name (country) China CHINA +GAZ_00005915 geo_loc_name (country) Christmas Island +GAZ_00005838 geo_loc_name (country) Clipperton Island +GAZ_00009721 geo_loc_name (country) Cocos Islands +GAZ_00002929 geo_loc_name (country) Colombia COLUMBIA +GAZ_00005820 geo_loc_name (country) Comoros +GAZ_00053798 geo_loc_name (country) Cook Islands +GAZ_00005917 geo_loc_name (country) Coral Sea Islands +GAZ_00002901 geo_loc_name (country) Costa Rica COSTA_RICA +GAZ_00000906 geo_loc_name (country) Cote d'Ivoire +GAZ_00002719 geo_loc_name (country) Croatia +GAZ_00003762 geo_loc_name (country) Cuba +GAZ:00012582 geo_loc_name (country) Curacao +GAZ_00004006 geo_loc_name (country) Cyprus +GAZ_00002954 geo_loc_name (country) Czech Republic +GAZ_00001086 geo_loc_name (country) Democratic Republic of the Congo +GAZ_00005852 geo_loc_name (country) Denmark DENMARK +GAZ_00000582 geo_loc_name (country) Djibouti +GAZ_00006890 geo_loc_name (country) Dominica +GAZ_00003952 geo_loc_name (country) Dominican Republic +GAZ_00002912 geo_loc_name (country) Ecuador ECUADOR +GAZ_00003934 geo_loc_name (country) Egypt +GAZ_00002935 geo_loc_name (country) El Salvador +GAZ_00001091 geo_loc_name (country) Equatorial Guinea +GAZ_00000581 geo_loc_name (country) Eritrea +GAZ_00002959 geo_loc_name (country) Estonia +GAZ_00001099 geo_loc_name (country) Eswatini +GAZ_00000567 geo_loc_name (country) Ethiopia +GAZ_00005811 geo_loc_name (country) Europa Island +GAZ_00001412 geo_loc_name (country) Falkland Islands (Islas Malvinas) +GAZ_00059206 geo_loc_name (country) Faroe Islands +GAZ_00006891 geo_loc_name (country) Fiji +GAZ_00002937 geo_loc_name (country) Finland +GAZ_00003940 geo_loc_name (country) France FRANCE +GAZ_00002516 geo_loc_name (country) French Guiana +GAZ_00002918 geo_loc_name (country) French Polynesia +GAZ_00003753 geo_loc_name (country) French Southern and Antarctic Lands +GAZ_00001092 geo_loc_name (country) Gabon +GAZ_00000907 geo_loc_name (country) Gambia +GAZ_00009571 geo_loc_name (country) Gaza Strip +GAZ_00004942 geo_loc_name (country) Georgia +GAZ_00002646 geo_loc_name (country) Germany GERMANY +GAZ_00000908 geo_loc_name (country) Ghana +GAZ_00003987 geo_loc_name (country) Gibraltar +GAZ_00005808 geo_loc_name (country) Glorioso Islands +GAZ_00002945 geo_loc_name (country) Greece +GAZ_00001507 geo_loc_name (country) Greenland +GAZ_02000573 geo_loc_name (country) Grenada +GAZ_00067142 geo_loc_name (country) Guadeloupe +GAZ_00003706 geo_loc_name (country) Guam +GAZ_00002936 geo_loc_name (country) Guatemala +GAZ_00001550 geo_loc_name (country) Guernsey +GAZ_00000909 geo_loc_name (country) Guinea +GAZ_00000910 geo_loc_name (country) Guinea-Bissau +GAZ_00002522 geo_loc_name (country) Guyana GUYANA +GAZ_00003953 geo_loc_name (country) Haiti +GAZ_00009718 geo_loc_name (country) Heard Island and McDonald Islands +GAZ_00002894 geo_loc_name (country) Honduras +GAZ_00003203 geo_loc_name (country) Hong Kong +GAZ_00007120 geo_loc_name (country) Howland Island +GAZ_00002952 geo_loc_name (country) Hungary +GAZ_00000843 geo_loc_name (country) Iceland +GAZ_00002839 geo_loc_name (country) India INDIA +GAZ_00003727 geo_loc_name (country) Indonesia +GAZ_00004474 geo_loc_name (country) Iran +GAZ_00004483 geo_loc_name (country) Iraq +GAZ_00002943 geo_loc_name (country) Ireland +GAZ_00052477 geo_loc_name (country) Isle of Man +GAZ_00002476 geo_loc_name (country) Israel +GAZ_00002650 geo_loc_name (country) Italy +GAZ_00003781 geo_loc_name (country) Jamaica JAMAICA +GAZ_00005853 geo_loc_name (country) Jan Mayen +GAZ_00002747 geo_loc_name (country) Japan +GAZ_00007118 geo_loc_name (country) Jarvis Island +GAZ_00001551 geo_loc_name (country) Jersey +GAZ_00007114 geo_loc_name (country) Johnston Atoll +GAZ_00002473 geo_loc_name (country) Jordan +GAZ_00005809 geo_loc_name (country) Juan de Nova Island +GAZ_00004999 geo_loc_name (country) Kazakhstan +GAZ_00001101 geo_loc_name (country) Kenya KENYA 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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 51efdcd7..13c9573c 100644 --- a/template/canada_covid19/reference.html +++ b/template/canada_covid19/reference.html @@ -1099,9 +1099,9 @@

    CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission bioinformatics protocol - 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 + A description of the overall bioinformatics strategy used. + Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. + https://github.com/phac-nml/ncov2019-artic-nf None