diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index 7f802b90..94499134 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -533,8 +533,8 @@ var DATA = [ "The Hospital for Sick Children (SickKids)": {}, "Laboratoire de sant\u00e9 publique du Qu\u00e9bec (LSPQ)": {}, "Manitoba Cadham Provincial Laboratory": {}, - "McMaster University": {}, "McGill University": {}, + "McMaster University": {}, "National Microbiology Laboratory (NML)": {}, "New Brunswick - Vitalit\u00e9 Health Network": {}, "Newfoundland and Labrador - Eastern Health": {}, @@ -542,10 +542,10 @@ var DATA = [ "Ontario Institute for Cancer Research (OICR)": {}, "Prince Edward Island - Health PEI": {}, "Public Health Ontario (PHO)": {}, + "Queen's University / Kingston Health Sciences Centre": {}, "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)": {}, "Sunnybrook Health Sciences Centre": {}, - "Thunder Bay Regional Health Sciences Centre": {}, - "Queen's University / Kingston Health Sciences Centre": {} + "Thunder Bay Regional Health Sciences Centre": {} } }, { @@ -1732,7 +1732,7 @@ var DATA = [ "ontology_id": "NCBITaxon:2709072" }, "RmYN02": { - "ontology_id": "NCBITaxon NTR" + "ontology_id": "GENEPIO:0100000" } } }, @@ -1832,16 +1832,16 @@ var DATA = [ }, "schema:ItemList": { "Cluster/Outbreak investigation": { - "ontology_id": "HSO:0000371" + "ontology_id": "GENEPIO:0100001" }, "Diagnostic testing": { - "ontology_id": "HSO or NCIT NTR?" + "ontology_id": "GENEPIO:0100002" }, "Research": { - "ontology_id": "NCIT:c15429" + "ontology_id": "GENEPIO:0100003" }, "Surveillance": { - "ontology_id": "HSO:0000268" + "ontology_id": "GENEPIO:0100004" } } }, @@ -2110,7 +2110,7 @@ var DATA = [ "ontology_id": "UBERON:0001245" }, "Buccal mucosa": { - "ontology_id": "UBERON:0006956 " + "ontology_id": "UBERON:0006956" }, "Duodenum": { "ontology_id": "UBERON:0002114" @@ -2118,7 +2118,39 @@ var DATA = [ "Eye": { "ontology_id": "UBERON:0000970" }, - "Intestine": {}, + "Intestine": { + "ontology_id": "UBERON:0000160" + }, + "Lower respiratory tract": { + "ontology_id": "UBERON:0001558", + "schema:ItemList": { + "Bronchus": { + "ontology_id": "UBERON:0002185" + }, + "Lung": { + "ontology_id": "UBERON:0002048", + "schema:ItemList": { + "Bronchiole": { + "ontology_id": "UBERON:0002186" + }, + "Alveolar sac": { + "ontology_id": "UBERON:0002169" + } + } + }, + "Pleural sac": { + "ontology_id": "UBERON:0009778", + "schema:ItemList": { + "Pleural cavity": { + "ontology_id": "UBERON:0002402" + } + } + }, + "Trachea": { + "ontology_id": "UBERON:0003126" + } + } + }, "Rectum": { "ontology_id": "UBERON:0001052" }, @@ -2141,10 +2173,10 @@ var DATA = [ "ontology_id": "UBERON:0002453" }, "Nasal Cavity": { - "ontology_id": "UBERON:0001707 ", + "ontology_id": "UBERON:0001707", "schema:ItemList": { "Middle Nasal Turbinate": { - "ontology_id": "UBERON:0005921 " + "ontology_id": "UBERON:0005921" }, "Inferior Nasal Turbinate": { "ontology_id": "UBERON:0005922" @@ -2158,36 +2190,6 @@ var DATA = [ "ontology_id": "UBERON:0001729" } } - }, - "Lower respiratory tract": { - "ontology_id": "UBERON:0001558", - "schema:ItemList": { - "Bronchus": { - "ontology_id": "UBERON:0002185 " - }, - "Lung": { - "ontology_id": "UBERON:0002048", - "schema:ItemList": { - "Bronchiole": { - "ontology_id": "UBERON:0002186" - }, - "Alveolar sac": { - "ontology_id": "UBERON:0002169" - } - } - }, - "Pleural sac": { - "ontology_id": "UBERON:0009778 ", - "schema:ItemList": { - "Pleural cavity": { - "ontology_id": "UBERON:0002402" - } - } - }, - "Trachea": { - "ontology_id": "UBERON:0003126" - } - } } } }, @@ -2241,14 +2243,14 @@ var DATA = [ ] }, "schema:ItemList": { + "Breast Milk": { + "ontology_id": "UBERON:0001913" + }, "Feces": { "ontology_id": "UBERON:0001988" }, - "Urine": { - "ontology_id": "UBERON:0001088" - }, - "Sweat": { - "ontology_id": "UBERON:0001089" + "Fluid (seminal)": { + "ontology_id": "UBERON:0006530" }, "Mucus": { "ontology_id": "UBERON:0000912", @@ -2258,14 +2260,14 @@ var DATA = [ } } }, + "Sweat": { + "ontology_id": "UBERON:0001089" + }, "Tear": { "ontology_id": "UBERON:0001827" }, - "Fluid (seminal)": { - "ontology_id": "UBERON:0006530" - }, - "Breast Milk": { - "ontology_id": "UBERON:0001913" + "Urine": { + "ontology_id": "UBERON:0001088" } } }, @@ -2362,7 +2364,7 @@ var DATA = [ "ontology_id": "ENVO:03501212" }, "Hospital gown": { - "ontology_id": "OBI:0002792" + "ontology_id": "OBI:0002796" }, "Light switch": { "ontology_id": "ENVO:03501213" @@ -2386,7 +2388,7 @@ var DATA = [ "ontology_id": "ENVO:01000404" }, "PPE gown": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100025" }, "Sewage": { "ontology_id": "ENVO:00002018" @@ -2492,7 +2494,7 @@ var DATA = [ "ontology_id": "ENVO:01000927" }, "Emergency room (ER)": { - "ontology_id": "ENVO:03501144" + "ontology_id": "ENVO:03501145" }, "Family practice clinic": { "ontology_id": "ENVO:03501186" @@ -2530,6 +2532,9 @@ var DATA = [ "Subway train": { "ontology_id": "ENVO:03501109" }, + "University campus": { + "ontology_id": "ENVO:00000467" + }, "Wet market": { "ontology_id": "ENVO:03501198" } @@ -2598,13 +2603,13 @@ var DATA = [ "ontology_id": "OBI:0002088" }, "Collection Cup": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100026" }, "Fibrobronchoscope Brush": { "ontology_id": "OBI:0002825" }, "Filter": { - "ontology_id": "ENVO NTR" + "ontology_id": "GENEPIO:0100103" }, "Fine Needle": { "ontology_id": "OBI:0002827" @@ -2628,7 +2633,7 @@ var DATA = [ "ontology_id": "OBI:0002831" }, "Swab": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100027" }, "Urine Collection Tube": { "ontology_id": "OBI:0002862" @@ -2689,19 +2694,19 @@ var DATA = [ }, "schema:ItemList": { "Amniocentesis": { - "ontology_id": "OBI NTR" + "ontology_id": "NCIT:C52009" }, "Aspiration": { - "ontology_id": "OBI NTR", + "ontology_id": "NCIT:C15631", "schema:ItemList": { "Suprapubic Aspiration": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100028" }, "Tracheal aspiration": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100029" }, "Vacuum Aspiration": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100030" } } }, @@ -2717,51 +2722,51 @@ var DATA = [ "ontology_id": "OBI:0302885", "schema:ItemList": { "Air filtration": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100031" } } }, "Lavage": { - "ontology_id": "OBI:0600044 ", + "ontology_id": "OBI:0600044", "schema:ItemList": { "Bronchoalveolar lavage (BAL)": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100032" }, "Gastric Lavage": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100033" } } }, "Lumbar Puncture": { - "ontology_id": "OBI NTR" + "ontology_id": "NCIT:C15327" }, "Necropsy": { - "ontology_id": "OBI NTR" + "ontology_id": "MMO:0000344" }, "Phlebotomy": { - "ontology_id": "OBI NTR" + "ontology_id": "NCIT:C28221" }, "Rinsing": { - "ontology_id": "OBI NTR", + "ontology_id": "GENEPIO:0002116", "schema:ItemList": { "Saline gargle (mouth rinse and gargle)": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100034" } } }, "Scraping": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100035" }, "Swabbing": { - "ontology_id": "OBI NTR", + "ontology_id": "GENEPIO:0002117", "schema:ItemList": { "Finger Prick": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100036" } } }, "Washout Tear Collection": { - "ontology_id": "OBI NTR" + "ontology_id": "GENEPIO:0100038" } } }, @@ -2819,16 +2824,30 @@ var DATA = [ }, "schema:ItemList": { "Virus passage": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100039" }, "RNA re-extraction (post RT-PCR)": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100040" }, "Specimens pooled": { "ontology_id": "OBI:0600016" } } }, + { + "fieldName": "specimen processing details", + "capitalize": "", + "ontology_id": "GENEPIO:0100311", + "datatype": "xs:token", + "source": "", + "dataStatus": null, + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", + "guidance": "Provide a free text description of any processing details applied to a sample.", + "examples": "25 swabs were pooled and further prepared as a single sample during library prep." + }, { "fieldName": "lab host", "capitalize": "", @@ -2867,22 +2886,22 @@ var DATA = [ }, "schema:ItemList": { "293/ACE2 cell line": { - "ontology_id": "BTO NTR" + "ontology_id": "GENEPIO:0100041" }, "Caco2 cell line": { - "ontology_id": "BTO:0000195 " + "ontology_id": "BTO:0000195" }, "Calu3 cell line": { "ontology_id": "BTO:0002750" }, "EFK3B cell line": { - "ontology_id": "BTO NTR" + "ontology_id": "GENEPIO:0100042" }, "HEK293T cell line": { "ontology_id": "BTO:0002181" }, "HRCE cell line": { - "ontology_id": "BTO NTR" + "ontology_id": "GENEPIO:0100043" }, "Huh7 cell line": { "ontology_id": "BTO:0001950" @@ -2891,7 +2910,7 @@ var DATA = [ "ontology_id": "CLO:0007330" }, "MDBK cell line": { - "ontology_id": "BTO:0000836 " + "ontology_id": "BTO:0000836" }, "NHBE cell line": { "ontology_id": "BTO:0002924" @@ -2906,13 +2925,13 @@ var DATA = [ "ontology_id": "BTO:0002035" }, "Vero cell line": { - "ontology_id": "BTO:0001444 " + "ontology_id": "BTO:0001444" }, "Vero E6 cell line": { "ontology_id": "BTO:0004755" }, "VeroE6/TMPRSS2 cell line": { - "ontology_id": "BTO NTR" + "ontology_id": "GENEPIO:0100044" } } }, @@ -3019,7 +3038,7 @@ var DATA = [ "ontology_id": "OBI:0002627" }, "mRNA (messenger RNA)": { - "ontology_id": "OBI REQUEST" + "ontology_id": "GENEPIO:0100104" }, "mRNA (cDNA)": { "ontology_id": "OBI:0002754" @@ -3089,7 +3108,7 @@ var DATA = [ } }, "Dog": { - "ontology_id": "NCBITaxon:9615 " + "ontology_id": "NCBITaxon:9615" }, "Lion": { "ontology_id": "NCBITaxon:9689" @@ -3174,7 +3193,7 @@ var DATA = [ "ontology_id": "NCBITaxon:9913" }, "Canis lupus familiaris": { - "ontology_id": "NCBITaxon:9615 " + "ontology_id": "NCBITaxon:9615" }, "Chiroptera": { "ontology_id": "NCBITaxon:9397" @@ -3204,7 +3223,7 @@ var DATA = [ "ontology_id": "NCBITaxon:9694" }, "Rhinolophidae": { - "ontology_id": "NCBITaxon:58055 " + "ontology_id": "NCBITaxon:58055" }, "Rhinolophus affinis": { "ontology_id": "NCBITaxon:59477" @@ -3268,8 +3287,12 @@ var DATA = [ "Healthy": { "ontology_id": "NCIT:C115935" }, - "Recovered": {}, - "Symptomatic": {} + "Recovered": { + "ontology_id": "NCIT:C49498" + }, + "Symptomatic": { + "ontology_id": "NCIT:C25269" + } } }, { @@ -3305,18 +3328,30 @@ var DATA = [ }, "schema:ItemList": { "Hospitalized": { + "ontology_id": "NCIT:C25179", "schema:ItemList": { - "Hospitalized (Non-ICU)": {}, - "Hospitalized (ICU)": {} + "Hospitalized (Non-ICU)": { + "ontology_id": "GENEPIO:0100045" + }, + "Hospitalized (ICU)": { + "ontology_id": "GENEPIO:0100046" + } } }, - "Mechanical Ventilation": {}, + "Mechanical Ventilation": { + "ontology_id": "NCIT:C70909" + }, "Medically Isolated": { + "ontology_id": "GENEPIO:0100047", "schema:ItemList": { - "Medically Isolated (Negative Pressure)": {} + "Medically Isolated (Negative Pressure)": { + "ontology_id": "GENEPIO:0100048" + } } }, - "Self-quarantining": {} + "Self-quarantining": { + "ontology_id": "NCIT:C173768" + } } }, { @@ -3351,10 +3386,18 @@ var DATA = [ ] }, "schema:ItemList": { - "Deceased": {}, - "Deteriorating": {}, - "Recovered": {}, - "Stable": {} + "Deceased": { + "ontology_id": "NCIT:C28554" + }, + "Deteriorating": { + "ontology_id": "NCIT:C25254" + }, + "Recovered": { + "ontology_id": "NCIT:C49498" + }, + "Stable": { + "ontology_id": "NCIT:C30103" + } } }, { @@ -3534,34 +3577,34 @@ var DATA = [ }, "schema:ItemList": { "0 - 9": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100049" }, "10 - 19": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100050" }, "20 - 29": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100051" }, "30 - 39": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100052" }, "40 - 49": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100053" }, "50 - 59": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100054" }, "60 - 69": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100055" }, "70 - 79": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100056" }, "80 - 89": { - "ontology_id": "GENEPIO NTR" + "ontology_id": "GENEPIO:0100057" }, "90 - 99": { - "ontology_id": "GENEPIO NTR", + "ontology_id": "GENEPIO:0100058", "exportField": { "VirusSeq_Portal": [ { @@ -3571,7 +3614,7 @@ var DATA = [ } }, "100+": { - "ontology_id": "GENEPIO NTR", + "ontology_id": "GENEPIO:0100059", "exportField": { "VirusSeq_Portal": [ { @@ -3644,8 +3687,9 @@ var DATA = [ "Transgender (assigned female at birth)": { "ontology_id": "GSSO:004005" }, - "Undeclared": {}, - "Unknown": {} + "Undeclared": { + "ontology_id": "NCIT:C110959" + } } }, { @@ -3795,7 +3839,7 @@ var DATA = [ }, "schema:ItemList": { "Abnormal lung auscultation": { - "ontology_id": "HP REQUEST" + "ontology_id": "HP:0030829" }, "Abnormality of taste sensation": { "ontology_id": "HP:0000223", @@ -3807,7 +3851,7 @@ var DATA = [ "ontology_id": "HP:0031249" }, "Hypogeusia (reduced sense of taste)": { - "ontology_id": "HP:0000224 " + "ontology_id": "HP:0000224" } } }, @@ -3850,10 +3894,10 @@ var DATA = [ } }, "Inability to arouse (inability to stay awake)": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100061" }, "Irritability": { - "ontology_id": "HP:0000737 " + "ontology_id": "HP:0000737" }, "Loss of speech": { "ontology_id": "HP:0002371" @@ -3875,7 +3919,7 @@ var DATA = [ } }, "Chills (sudden cold sensation)": { - "ontology_id": "HP:0025143 ", + "ontology_id": "HP:0025143", "exportField": { "CNPHI": [ { @@ -3921,20 +3965,20 @@ var DATA = [ "ontology_id": "HP:0032556" }, "Cyanotic face (bluish face)": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100062" } } }, "Central Cyanosis": { - "ontology_id": "HP REQUEST", + "ontology_id": "GENEPIO:0100063", "schema:ItemList": { "Cyanotic lips (bluish lips)": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100064" } } }, "Peripheral Cyanosis": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100065" } } }, @@ -3978,10 +4022,10 @@ var DATA = [ } }, "Fever": { - "ontology_id": "HP:0001945 ", + "ontology_id": "HP:0001945", "schema:ItemList": { "Fever (>=38\u00b0C)": { - "ontology_id": "HP REQUEST", + "ontology_id": "GENEPIO:0100066", "exportField": { "CNPHI": [ { @@ -3996,7 +4040,7 @@ var DATA = [ "ontology_id": "HP:0000206" }, "Ground Glass Opacities (GGO)": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100067" }, "Headache": { "ontology_id": "HP:0002315" @@ -4014,7 +4058,7 @@ var DATA = [ "ontology_id": "HP:0012418", "schema:ItemList": { "Silent hypoxemia": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100068" } } }, @@ -4025,7 +4069,7 @@ var DATA = [ "ontology_id": "NCIT:C121416" }, "Low appetite": { - "ontology_id": "HP:0004396 " + "ontology_id": "HP:0004396" }, "Malaise (general discomfort/unease)": { "ontology_id": "HP:0033834" @@ -4046,7 +4090,7 @@ var DATA = [ "ontology_id": "HP:0000421" }, "Otitis": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100069" }, "Pain": { "ontology_id": "HP:0012531", @@ -4074,7 +4118,7 @@ var DATA = [ "ontology_id": "HP:0025439" }, "Pharyngeal exudate": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100070" }, "Pleural effusion": { "ontology_id": "HP:0002202" @@ -4086,10 +4130,10 @@ var DATA = [ "ontology_id": "HP:0033696", "schema:ItemList": { "Pseudo-chilblains on fingers (covid fingers)": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100072" }, "Pseudo-chilblains on toes (covid toes)": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100073" } } }, @@ -4227,7 +4271,7 @@ var DATA = [ "ontology_id": "HP:0001638" }, "Cardiac injury": { - "ontology_id": "NCIT:C45430" + "ontology_id": "GENEPIO:0100074" }, "Hypertension (high blood pressure)": { "ontology_id": "HP:0000822" @@ -4241,10 +4285,10 @@ var DATA = [ "ontology_id": "HP:0011410" }, "Chronic cough": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100075" }, "Chronic gastrointestinal disease": { - "ontology_id": "HP REQUEST" + "ontology_id": "GENEPIO:0100076" }, "Chronic lung disease": { "ontology_id": "HP:0006528" @@ -4426,7 +4470,9 @@ var DATA = [ } } }, - "Postpartum (\u22646 weeks)": {}, + "Postpartum (\u22646 weeks)": { + "ontology_id": "GENEPIO:0100077" + }, "Pregnancy": { "ontology_id": "NCIT:C25742" }, @@ -4443,15 +4489,18 @@ var DATA = [ "ontology_id": "MONDO:0002046" }, "Drug abuse": { + "ontology_id": "GENEPIO:0100078", "schema:ItemList": { - "Injection drug abuse": {} + "Injection drug abuse": { + "ontology_id": "GENEPIO:0100079" + } } }, "Smoking": { "ontology_id": "NBO:0015005" }, "Vaping": { - "ontology_id": "NBO NTR" + "ontology_id": "NCIT:C173621" } } }, @@ -4464,11 +4513,15 @@ var DATA = [ "Hematopoietic stem cell transplant (bone marrow transplant)": { "ontology_id": "NCIT:C131759" }, - "Cardiac transplant": {}, + "Cardiac transplant": { + "ontology_id": "GENEPIO:0100080" + }, "Kidney transplant": { "ontology_id": "NCIT:C157332" }, - "Liver transplant": {} + "Liver transplant": { + "ontology_id": "GENEPIO:0100081" + } } } } @@ -4503,6 +4556,17 @@ var DATA = [ "Abnormal blood oxygen level": { "ontology_id": "HP:0500165" }, + "Acute kidney injury": { + "ontology_id": "HP:0001919" + }, + "Acute lung injury": { + "ontology_id": "MONDO:0015796", + "schema:ItemList": { + "Ventilation induced lung injury (VILI)": { + "ontology_id": "GENEPIO:0100092" + } + } + }, "Acute respiratory failure": { "ontology_id": "MONDO:0001208" }, @@ -4516,30 +4580,14 @@ var DATA = [ "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)": { - "ontology_id": "NCIT:C171551" - }, - "Neurogenic pulmonary edema (NPE)": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100084" } } } } }, "Cardiac injury": { - "ontology_id": "NCIT:C45430" + "ontology_id": "GENEPIO:0100074" }, "Cardiac arrest": { "ontology_id": "HP:0001695" @@ -4585,7 +4633,7 @@ var DATA = [ "ontology_id": "HP:0011097" }, "COVID-19 associated coagulopathy (CAC)": { - "ontology_id": "HP NTR" + "ontology_id": "NCIT:C171562" }, "Cystic fibrosis": { "ontology_id": "MONDO:0009061" @@ -4600,7 +4648,7 @@ var DATA = [ "ontology_id": "HP:0001298" }, "Fulminant myocarditis": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100088" }, "Guillain-Barr\u00e9 syndrome": { "ontology_id": "MONDO:0016218" @@ -4614,37 +4662,26 @@ var DATA = [ } }, "Kawasaki disease": { - "ontology_id": "HP NTR", + "ontology_id": "MONDO:0012727", "schema:ItemList": { "Complete Kawasaki disease": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100089" }, "Incomplete Kawasaki disease": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100090" } } }, - "Acute kidney injury": { - "ontology_id": "HP:0001919" - }, - "Long COVID-19": { - "ontology_id": "MONDO:0100233" - }, "Liver dysfunction": { "ontology_id": "HP:0001410", "schema:ItemList": { "Acute liver injury": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100091" } } }, - "Acute lung injury": { - "ontology_id": "MONDO:0015796", - "schema:ItemList": { - "Ventilation induced lung injury (VILI)": { - "ontology_id": "HP NTR" - } - } + "Long COVID-19": { + "ontology_id": "MONDO:0100233" }, "Meningitis": { "ontology_id": "HP:0001287" @@ -4658,8 +4695,11 @@ var DATA = [ "Multisystem inflammatory syndrome in children (MIS-C)": { "ontology_id": "MONDO:0100163" }, + "Multisystem inflammatory syndrome in adults (MIS-A)": { + "ontology_id": "MONDO:0100319" + }, "Muscle injury": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100093" }, "Myalgic encephalomyelitis (ME)": { "ontology_id": "MONDO:0005404" @@ -4676,13 +4716,29 @@ var DATA = [ } }, "Myocardial injury": { - "ontology_id": "HP NTR" + "ontology_id": "HP:0001700" }, "Neonatal complications": { "ontology_id": "NCIT:C168498" }, + "Noncardiogenic pulmonary edema": { + "ontology_id": "GENEPIO:0100085", + "schema:ItemList": { + "Acute respiratory distress syndrome (ARDS)": { + "ontology_id": "HP:0033677", + "schema:ItemList": { + "COVID-19 associated ARDS (CARDS)": { + "ontology_id": "NCIT:C171551" + }, + "Neurogenic pulmonary edema (NPE)": { + "ontology_id": "GENEPIO:0100086" + } + } + } + } + }, "Organ failure": { - "ontology_id": "HP NTR", + "ontology_id": "GENEPIO:0100094", "schema:ItemList": { "Heart failure": { "ontology_id": "HP:0001635" @@ -4724,10 +4780,10 @@ var DATA = [ "ontology_id": "IDO:0000567", "schema:ItemList": { "Secondary staph infection": { - "ontology_id": "IDO NTR" + "ontology_id": "GENEPIO:0100095" }, "Secondary strep infection": { - "ontology_id": "IDO NTR" + "ontology_id": "GENEPIO:0100096" } } }, @@ -4754,16 +4810,16 @@ var DATA = [ "ontology_id": "HP:0031273", "schema:ItemList": { "Hyperinflammatory shock": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100097" }, "Refractory cardiogenic shock": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100098" }, "Refractory cardiogenic plus vasoplegic shock": { - "ontology_id": "HP NTR" + "ontology_id": "GENEPIO:0100099" }, "Septic shock": { - "ontology_id": "HP NTR" + "ontology_id": "NCIT:C35018" } } }, @@ -4804,9 +4860,15 @@ var DATA = [ ] }, "schema:ItemList": { - "Fully Vaccinated": {}, - "Partially Vaccinated": {}, - "Not Vaccinated": {} + "Fully Vaccinated": { + "ontology_id": "GENEPIO:0100100" + }, + "Partially Vaccinated": { + "ontology_id": "GENEPIO:0100101" + }, + "Not Vaccinated": { + "ontology_id": "GENEPIO:0100102" + } } }, { @@ -5262,6 +5324,79 @@ var DATA = [ ] } }, + { + "fieldName": "travel point of entry type", + "capitalize": "", + "ontology_id": "", + "datatype": "select", + "source": "", + "dataStatus": [ + "Not Applicable", + "Missing", + "Not Collected", + "Not Provided", + "Restricted Access" + ], + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "recommended", + "description": "The type of entry point a traveler arrives through.", + "guidance": "Select the point of entry type.", + "examples": "Air", + "exportField": { + "NML_LIMS": [ + { + "field": "PH_POINT_OF_ENTRY" + } + ] + }, + "schema:ItemList": { + "Air": { + "ontology_id": "GENEPIO:0100408" + }, + "Land": { + "ontology_id": "GENEPIO:0100409" + } + } + }, + { + "fieldName": "border testing test day type", + "capitalize": "", + "ontology_id": "", + "datatype": "select", + "source": "", + "dataStatus": [ + "Not Applicable", + "Missing", + "Not Collected", + "Not Provided", + "Restricted Access" + ], + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "recommended", + "description": "The day a traveller was tested on or after arrival at their point of entry. ", + "guidance": "Select the test day.", + "examples": "day 1", + "exportField": { + "NML_LIMS": [ + { + "field": "PH_DAY" + } + ] + }, + "schema:ItemList": { + "day 1": { + "ontology_id": "GENEPIO:0100410" + }, + "day 8": { + "ontology_id": "GENEPIO:0100411" + }, + "day 10": { + "ontology_id": "GENEPIO:0100412" + } + } + }, { "fieldName": "travel history", "capitalize": "", @@ -5321,35 +5456,35 @@ var DATA = [ }, "schema:ItemList": { "Mass Gathering": { - "ontology_id": "PCO NTR", + "ontology_id": "GENEPIO:0100237", "schema:ItemList": { "Agricultural Event": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100240" }, "Convention": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100238" }, "Convocation": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100239" }, "Recreational Event": { - "ontology_id": "PCO NTR", + "ontology_id": "GENEPIO:0100417", "schema:ItemList": { "Concert": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100418" }, "Sporting Event": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100419" } } } } }, "Religious Gathering": { - "ontology_id": "PCO NTR", + "ontology_id": "GENEPIO:0100241", "schema:ItemList": { "Mass": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100242" } } }, @@ -5363,15 +5498,15 @@ var DATA = [ "ontology_id": "PCO:0000034" }, "Family Gathering": { - "ontology_id": "PCO NTR", + "ontology_id": "GENEPIO:0100243", "schema:ItemList": { "Family Reunion": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100244" } } }, "Funeral": { - "ontology_id": "PCO NTR" + "ontology_id": "GENEPIO:0100245" }, "Party": { "ontology_id": "PCO:0000035" @@ -5384,9 +5519,7 @@ var DATA = [ } } }, - "Other exposure event": { - "ontology_id": "NCIT:C168623" - } + "Other exposure event": {} } }, { @@ -5417,19 +5550,19 @@ var DATA = [ }, "schema:ItemList": { "Contact with infected individual": { - "ontology_id": "NCIT NTR?", + "ontology_id": "GENEPIO:0100357", "schema:ItemList": { "Direct contact (direct human-to-human contact)": { - "ontology_id": "NCIT NTR?" + "ontology_id": "TRANS:0000001" }, "Indirect contact": { - "ontology_id": "NCIT NTR?", + "ontology_id": "GENEPIO:0100246", "schema:ItemList": { "Close contact (face-to-face, no direct contact)": { - "ontology_id": "NCIT NTR?" + "ontology_id": "GENEPIO:0100247" }, "Casual contact": { - "ontology_id": "NCIT:C102606" + "ontology_id": "GENEPIO:0100248" } } } @@ -5459,7 +5592,7 @@ var DATA = [ }, "schema:ItemList": { "Attendee": { - "ontology_id": "OMRSE NTR", + "ontology_id": "GENEPIO:0100249", "schema:ItemList": { "Student": { "ontology_id": "OMRSE:00000058" @@ -5470,96 +5603,90 @@ var DATA = [ "ontology_id": "OMRSE:00000030", "schema:ItemList": { "Inpatient": { - "ontology_id": "OMRSE NTR" + "ontology_id": "NCIT:C25182" }, "Outpatient": { - "ontology_id": "OMRSE NTR" + "ontology_id": "NCIT:C28293" } } }, "Passenger": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100250" }, "Resident": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100251" }, "Visitor": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100252" }, "Volunteer": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100253" }, "Work": { - "ontology_id": "OMRSE NTR", + "ontology_id": "GENEPIO:0100254", "schema:ItemList": { "Administrator": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100255" }, + "Child Care/Education Worker": {}, + "Essential Worker": {}, "First Responder": { - "ontology_id": "OMRSE NTR", + "ontology_id": "GENEPIO:0100256", "schema:ItemList": { "Firefighter": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100257" }, "Paramedic": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100258" }, "Police Officer": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100259" } } }, - "Child Care/Education Worker": { - "ontology_id": "OMRSE NTR" - }, - "Essential Worker": { - "ontology_id": "OMRSE NTR" - }, "Healthcare Worker": { - "ontology_id": "OMRSE NTR", + "ontology_id": "GENEPIO:0100334", "schema:ItemList": { + "Community Healthcare Worker": { + "ontology_id": "GENEPIO:0100420" + }, + "Laboratory Worker": { + "ontology_id": "GENEPIO:0100262" + }, "Nurse": { "ontology_id": "OMRSE:00000014" }, "Personal Care Aid": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100263" }, "Pharmacist": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100264" }, "Physician": { - "ontology_id": "OMRSE:00000050" + "ontology_id": "OMRSE:00000013" } } }, "Housekeeper": { - "ontology_id": "OMRSE NTR" - }, - "International worker": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100260" }, + "International worker": {}, "Kitchen Worker": { - "ontology_id": "OMRSE NTR" - }, - "Laboratory Worker": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100261" }, "Rotational Worker": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100354" }, "Seasonal Worker": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100355" }, "Transport Worker": { - "ontology_id": "OMRSE NTR", "schema:ItemList": { - "Transport Truck Driver": { - "ontology_id": "OMRSE NTR" - } + "Transport Truck Driver": {} } }, "Veterinarian": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100265" } } }, @@ -5567,33 +5694,31 @@ var DATA = [ "ontology_id": "OMRSE:00000001", "schema:ItemList": { "Acquaintance of case": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100266" }, "Relative of case": { - "ontology_id": "OMRSE NTR", + "ontology_id": "GENEPIO:0100267", "schema:ItemList": { "Child of case": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100268" }, "Parent of case": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100269" }, "Father of case": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100270" }, "Mother of case": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100271" } } }, "Spouse of case": { - "ontology_id": "OMRSE NTR" + "ontology_id": "GENEPIO:0100272" } } }, - "Other Host Role": { - "ontology_id": "OMRSE NTR" - } + "Other Host Role": {} } }, { @@ -5621,92 +5746,95 @@ var DATA = [ "ontology_id": "ECTO:3000005", "schema:ItemList": { "Contact with Known COVID-19 Case": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100184" }, "Contact with Patient": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100185" }, "Contact with Probable COVID-19 Case": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100186" }, "Contact with Person with Acute Respiratory Illness": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100187" }, "Contact with Person with Fever and/or Cough": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100188" }, "Contact with Person who Recently Travelled": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100189" } } }, "Occupational, Residency or Patronage Exposure": { - "ontology_id": "ECTO NTR?", + "ontology_id": "GENEPIO:0100190", "schema:ItemList": { "Abbatoir": { "ontology_id": "ECTO:1000033" }, "Animal Rescue": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100191" }, "Childcare": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100192", "schema:ItemList": { "Daycare": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100193" } } }, "Nursery": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100194" }, "Community Service Centre": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100195" }, "Correctional Facility": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100196" }, "Dormitory": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100197" }, "Farm": { "ontology_id": "ECTO:1000034" }, "First Nations Reserve": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100198" }, "Funeral Home": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100199" }, "Group Home": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100200" }, "Healthcare Setting": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100201", "schema:ItemList": { "Ambulance": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100202" }, "Acute Care Facility": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100203" }, "Clinic": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100204" + }, + "Community Healthcare (At-Home) Setting": { + "ontology_id": "GENEPIO:0100415" }, "Community Health Centre": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100205" }, "Hospital": { "ontology_id": "ECTO:1000035", "schema:ItemList": { "Emergency Department": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100206" }, "ICU": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100207" }, "Ward": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100208" } } }, @@ -5714,27 +5842,27 @@ var DATA = [ "ontology_id": "ECTO:1000036" }, "Long-Term Care Facility": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100209" }, "Pharmacy": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100210" }, "Physician's Office": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100211" } } }, "Household": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100212" }, "Insecure Housing (Homeless)": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100213" }, "Occupational Exposure": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100214", "schema:ItemList": { "Worksite": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100215" }, "Office": { "ontology_id": "ECTO:1000037" @@ -5742,19 +5870,19 @@ var DATA = [ } }, "Outdoors": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100216", "schema:ItemList": { "Camp/camping": { "ontology_id": "ECTO:5000009" }, "Hiking Trail": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100217" }, "Hunting Ground": { "ontology_id": "ECTO:6000030" }, "Ski Resort": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100218" } } }, @@ -5762,16 +5890,16 @@ var DATA = [ "ontology_id": "ECTO:5000008" }, "Place of Worship": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100220", "schema:ItemList": { "Church": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100221" }, "Mosque": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100222" }, "Temple": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100223" } } }, @@ -5782,46 +5910,46 @@ var DATA = [ "ontology_id": "ECTO:1000041" }, "School": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100224" }, "Temporary Residence": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100225", "schema:ItemList": { "Homeless Shelter": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100226" }, "Hotel": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100227" } } }, "Veterinary Care Clinic": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100228" } } }, "Travel Exposure": { - "ontology_id": "ECTO NTR", + "ontology_id": "GENEPIO:0100229", "schema:ItemList": { "Travelled on a Cruise Ship": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100230" }, "Travelled on a Plane": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100231" }, "Travelled on Ground Transport": { - "ontology_id": "ECTO NTR" + "ontology_id": "GENEPIO:0100232" }, "Travelled outside Province/Territory": { - "ontology_id": "GENEPIO:0001119" + "ontology_id": "GENEPIO:0001118" }, "Travelled outside Canada": { - "ontology_id": "GENEPIO:0001118" + "ontology_id": "GENEPIO:0001119" } } }, "Other Exposure Setting": { - "ontology_id": "GENEPIO NTR?" + "ontology_id": "GENEPIO:0100235" } } }, @@ -5878,8 +6006,12 @@ var DATA = [ ] }, "schema:ItemList": { - "Prior antiviral treatment": {}, - "No prior antiviral treatment": {} + "Prior infection": { + "ontology_id": "GENEPIO:0100037" + }, + "No prior infection": { + "ontology_id": "GENEPIO:0100233" + } } }, { @@ -5951,8 +6083,12 @@ var DATA = [ ] }, "schema:ItemList": { - "Prior antivrial treatment": {}, - "No prior antivrial treatment": {}, + "Prior antiviral treatment": { + "ontology_id": "GENEPIO:0100037" + }, + "No prior antiviral treatment": { + "ontology_id": "GENEPIO:0100233" + }, "Unknown": {} } }, @@ -6046,37 +6182,65 @@ var DATA = [ }, "schema:ItemList": { "Baseline surveillance (random sampling)": { - "ontology_id": "See comment" + "ontology_id": "GENEPIO:0100005" }, "Targeted surveillance (non-random sampling)": { + "ontology_id": "GENEPIO:0100006", "schema:ItemList": { "Priority surveillance project": { + "ontology_id": "GENEPIO:0100007", "schema:ItemList": { "Screening for Variants of Concern (VoC)": { + "ontology_id": "GENEPIO:0100008", "schema:ItemList": { "Sample has epidemiological link to Variant of Concern (VoC)": { + "ontology_id": "GENEPIO:0100273", "schema:ItemList": { - "Sample has epidemiological link to Omicron Variant": {} + "Sample has epidemiological link to Omicron Variant": { + "ontology_id": "GENEPIO:0100274" + } } } } }, - "Longitudinal surveillance (repeat sampling of individuals)": {}, - "Re-infection surveillance": {}, - "Vaccine escape surveillance": {}, + "Longitudinal surveillance (repeat sampling of individuals)": { + "ontology_id": "GENEPIO:0100009" + }, + "Re-infection surveillance": { + "ontology_id": "GENEPIO:0100010" + }, + "Vaccine escape surveillance": { + "ontology_id": "GENEPIO:0100011" + }, "Travel-associated surveillance": { + "ontology_id": "GENEPIO:0100012", "schema:ItemList": { "Domestic travel surveillance": { + "ontology_id": "GENEPIO:0100013", "schema:ItemList": { - "Interstate/ interprovincial travel surveillance": {}, - "Intra-state/ intra-provincial travel surveillance": {} + "Interstate/ interprovincial travel surveillance": { + "ontology_id": "GENEPIO:0100275" + }, + "Intra-state/ intra-provincial travel surveillance": { + "ontology_id": "GENEPIO:0100276" + } } }, - "International travel surveillance": {}, - "Surveillance of international border crossing by air travel or ground transport": {}, - "Surveillance of international border crossing by air travel": {}, - "Surveillance of international border crossing by ground transport": {}, - "Surveillance from international worker testing": {} + "International travel surveillance": { + "ontology_id": "GENEPIO:0100014" + }, + "Surveillance of international border crossing by air travel or ground transport": { + "ontology_id": "GENEPIO:0100015" + }, + "Surveillance of international border crossing by air travel": { + "ontology_id": "GENEPIO:0100016" + }, + "Surveillance of international border crossing by ground transport": { + "ontology_id": "GENEPIO:0100017" + }, + "Surveillance from international worker testing": { + "ontology_id": "GENEPIO:0100018" + } } } } @@ -6084,20 +6248,30 @@ var DATA = [ } }, "Cluster/Outbreak investigation": { - "ontology_id": "HSO:0000371", + "ontology_id": "GENEPIO:0100019", "schema:ItemList": { - "Multi-jurisdictional outbreak investigation": {}, - "Intra-jurisdictional outbreak investigation": {} + "Multi-jurisdictional outbreak investigation": { + "ontology_id": "GENEPIO:0100020" + }, + "Intra-jurisdictional outbreak investigation": { + "ontology_id": "GENEPIO:0100021" + } } }, "Research": { - "ontology_id": "NCIT:c15429", + "ontology_id": "GENEPIO:0100022", "schema:ItemList": { - "Viral passage experiment": {}, - "Protocol testing experiment": {} + "Viral passage experiment": { + "ontology_id": "GENEPIO:0100023" + }, + "Protocol testing experiment": { + "ontology_id": "GENEPIO:0100024" + } } }, - "Retrospective sequencing": {} + "Retrospective sequencing": { + "ontology_id": "GENEPIO:0100356" + } } }, { @@ -6291,160 +6465,160 @@ var DATA = [ }, "schema:ItemList": { "Illumina": { - "ontology_id": "OBI:0000759", + "ontology_id": "GENEPIO:0100105", "schema:ItemList": { "Illumina Genome Analyzer": { - "ontology_id": "OBI:0002128", + "ontology_id": "GENEPIO:0100106", "schema:ItemList": { "Illumina Genome Analyzer II": { - "ontology_id": "OBI:0000703" + "ontology_id": "GENEPIO:0100107" }, "Illumina Genome Analyzer IIx": { - "ontology_id": "OBI:0002000" + "ontology_id": "GENEPIO:0100108" } } }, "Illumina HiScanSQ": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100109" }, "Illumina HiSeq": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100110" }, "Illumina HiSeq X": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100111", "schema:ItemList": { "Illumina HiSeq X Five": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100112" }, "Illumina HiSeq X Ten": { - "ontology_id": "OBI:0002129" + "ontology_id": "GENEPIO:0100113" } } }, "Illumina HiSeq 1000": { - "ontology_id": "OBI:0002022" + "ontology_id": "GENEPIO:0100114" }, "Illumina HiSeq 1500": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100115" }, "Illumina HiSeq 2000": { - "ontology_id": "OBI:0002001" + "ontology_id": "GENEPIO:0100116" }, "Illumina HiSeq 2500": { - "ontology_id": "OBI:0002002" + "ontology_id": "GENEPIO:0100117" }, "Illumina HiSeq 3000": { - "ontology_id": "OBI:0002048" + "ontology_id": "GENEPIO:0100118" }, "Illumina HiSeq 4000": { - "ontology_id": "OBI:0002049" + "ontology_id": "GENEPIO:0100119" }, "Illumina iSeq": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100120", "schema:ItemList": { "Illumina iSeq 100": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100121" } } }, "Illumina NovaSeq": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100122", "schema:ItemList": { "Illumina NovaSeq 6000": { - "ontology_id": "OBI:0002630" + "ontology_id": "GENEPIO:0100123" } } }, "Illumina MiniSeq": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100124" }, "Illumina MiSeq": { - "ontology_id": "OBI:0002003" + "ontology_id": "GENEPIO:0100125" }, "Illumina NextSeq": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100126" }, "Illumina NextSeq 500": { - "ontology_id": "OBI:0002021" + "ontology_id": "GENEPIO:0100127" }, "Illumina NextSeq 550": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100128" }, "Illumina NextSeq 2000": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100129" } } }, "Pacific Biosciences": { - "ontology_id": "OBI:0001856", + "ontology_id": "GENEPIO:0100130", "schema:ItemList": { "PacBio RS": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100131" }, "PacBio RS II": { - "ontology_id": "OBI:0002012" + "ontology_id": "GENEPIO:0100132" }, "PacBio Sequel": { - "ontology_id": "OBI:0002632" + "ontology_id": "GENEPIO:0100133" }, "PacBio Sequel II": { - "ontology_id": "OBI:0002633" + "ontology_id": "GENEPIO:0100134" } } }, "Ion Torrent": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100135", "schema:ItemList": { "Ion Torrent PGM": { - "ontology_id": "GENEPIO:0001935" + "ontology_id": "GENEPIO:0100136" }, "Ion Torrent Proton": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100137" }, "Ion Torrent S5 XL": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100138" }, "Ion Torrent S5": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100139" } } }, "Oxford Nanopore": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100140", "schema:ItemList": { "Oxford Nanopore GridION": { - "ontology_id": "OBI:0002751" + "ontology_id": "GENEPIO:0100141" }, "Oxford Nanopore MinION": { - "ontology_id": "OBI:0002750" + "ontology_id": "GENEPIO:0100142" }, "Oxford Nanopore PromethION": { - "ontology_id": "OBI:0002752" + "ontology_id": "GENEPIO:0100143" } } }, "BGI Genomics": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100144", "schema:ItemList": { "BGI Genomics BGISEQ-500": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100145" } } }, "MGI": { - "ontology_id": "OBI NTR?", + "ontology_id": "GENEPIO:0100146", "schema:ItemList": { "MGI DNBSEQ-T7": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100147" }, "MGI DNBSEQ-G400": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100148" }, "MGI DNBSEQ-G400 FAST": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100149" }, "MGI DNBSEQ-G50": { - "ontology_id": "OBI NTR?" + "ontology_id": "GENEPIO:0100150" } } } @@ -7146,12 +7320,14 @@ var DATA = [ }, "schema:ItemList": { "Variant of Concern (VOC)": { - "ontology_id": "GENEPIO" + "ontology_id": "GENEPIO:0100082" }, "Variant of Interest (VOI)": { - "ontology_id": "GENEPIO" + "ontology_id": "GENEPIO:0100083" }, - "Variant Under Monitoring (VUM)": {} + "Variant Under Monitoring (VUM)": { + "ontology_id": "GENEPIO:0100279" + } } }, { @@ -7258,7 +7434,7 @@ var DATA = [ }, "schema:ItemList": { "E gene (orf4)": { - "ontology_id": "PR:P0DTC4", + "ontology_id": "GENEPIO:0100151", "exportField": { "CNPHI": [ { @@ -7273,7 +7449,7 @@ var DATA = [ } }, "M gene (orf5)": { - "ontology_id": "PR:P0DTC5", + "ontology_id": "GENEPIO:0100152", "exportField": { "BIOSAMPLE": [ { @@ -7283,7 +7459,7 @@ var DATA = [ } }, "N gene (orf9)": { - "ontology_id": "PR:P0DTC9", + "ontology_id": "GENEPIO:0100153", "exportField": { "BIOSAMPLE": [ { @@ -7293,7 +7469,7 @@ var DATA = [ } }, "Spike gene (orf2)": { - "ontology_id": "PR:P0DTC2", + "ontology_id": "GENEPIO:0100154", "exportField": { "BIOSAMPLE": [ { @@ -7303,7 +7479,7 @@ var DATA = [ } }, "orf1ab (rep)": { - "ontology_id": "PR:000050281", + "ontology_id": "GENEPIO:0100155", "exportField": { "BIOSAMPLE": [ { @@ -7313,7 +7489,7 @@ var DATA = [ }, "schema:ItemList": { "orf1a (pp1a)": { - "ontology_id": "PR:P0DTC1-1", + "ontology_id": "GENEPIO:0100156", "exportField": { "BIOSAMPLE": [ { @@ -7323,7 +7499,7 @@ var DATA = [ }, "schema:ItemList": { "nsp11": { - "ontology_id": "PR:000050280", + "ontology_id": "GENEPIO:0100157", "exportField": { "BIOSAMPLE": [ { @@ -7335,7 +7511,7 @@ var DATA = [ } }, "nsp1": { - "ontology_id": "PR:000050270", + "ontology_id": "GENEPIO:0100158", "exportField": { "BIOSAMPLE": [ { @@ -7345,7 +7521,7 @@ var DATA = [ } }, "nsp2": { - "ontology_id": "PR:000050271", + "ontology_id": "GENEPIO:0100159", "exportField": { "BIOSAMPLE": [ { @@ -7355,7 +7531,7 @@ var DATA = [ } }, "nsp3": { - "ontology_id": "PR:000050272", + "ontology_id": "GENEPIO:0100160", "exportField": { "BIOSAMPLE": [ { @@ -7365,7 +7541,7 @@ var DATA = [ } }, "nsp4": { - "ontology_id": "PR:000050273", + "ontology_id": "GENEPIO:0100161", "exportField": { "BIOSAMPLE": [ { @@ -7375,7 +7551,7 @@ var DATA = [ } }, "nsp5": { - "ontology_id": "PR:000050274", + "ontology_id": "GENEPIO:0100162", "exportField": { "BIOSAMPLE": [ { @@ -7385,7 +7561,7 @@ var DATA = [ } }, "nsp6": { - "ontology_id": "PR:000050275", + "ontology_id": "GENEPIO:0100163", "exportField": { "BIOSAMPLE": [ { @@ -7395,7 +7571,7 @@ var DATA = [ } }, "nsp7": { - "ontology_id": "PR:000050276", + "ontology_id": "GENEPIO:0100164", "exportField": { "BIOSAMPLE": [ { @@ -7405,7 +7581,7 @@ var DATA = [ } }, "nsp8": { - "ontology_id": "PR:000050277", + "ontology_id": "GENEPIO:0100165", "exportField": { "BIOSAMPLE": [ { @@ -7415,7 +7591,7 @@ var DATA = [ } }, "nsp9": { - "ontology_id": "PR:000050278", + "ontology_id": "GENEPIO:0100166", "exportField": { "BIOSAMPLE": [ { @@ -7425,7 +7601,7 @@ var DATA = [ } }, "nsp10": { - "ontology_id": "PR:000050279", + "ontology_id": "GENEPIO:0100167", "exportField": { "BIOSAMPLE": [ { @@ -7435,7 +7611,7 @@ var DATA = [ } }, "RdRp gene (nsp12)": { - "ontology_id": "PR:000050284", + "ontology_id": "GENEPIO:0100168", "exportField": { "BIOSAMPLE": [ { @@ -7445,7 +7621,7 @@ var DATA = [ } }, "hel gene (nsp13)": { - "ontology_id": "PR:000050285", + "ontology_id": "GENEPIO:0100169", "exportField": { "BIOSAMPLE": [ { @@ -7455,7 +7631,7 @@ var DATA = [ } }, "exoN gene (nsp14)": { - "ontology_id": "PR:000050286", + "ontology_id": "GENEPIO:0100170", "exportField": { "BIOSAMPLE": [ { @@ -7465,7 +7641,7 @@ var DATA = [ } }, "nsp15": { - "ontology_id": "PR:000050287", + "ontology_id": "GENEPIO:0100171", "exportField": { "BIOSAMPLE": [ { @@ -7475,7 +7651,7 @@ var DATA = [ } }, "nsp16": { - "ontology_id": "PR:000050288", + "ontology_id": "GENEPIO:0100172", "exportField": { "BIOSAMPLE": [ { @@ -7487,7 +7663,7 @@ var DATA = [ } }, "orf3a": { - "ontology_id": "PR:P0DTC3", + "ontology_id": "GENEPIO:0100173", "exportField": { "BIOSAMPLE": [ { @@ -7497,7 +7673,7 @@ var DATA = [ } }, "orf3b": { - "ontology_id": "PR NTR", + "ontology_id": "GENEPIO:0100174", "exportField": { "BIOSAMPLE": [ { @@ -7507,7 +7683,7 @@ var DATA = [ } }, "orf6 (ns6)": { - "ontology_id": "PR:P0DTC6", + "ontology_id": "GENEPIO:0100175", "exportField": { "BIOSAMPLE": [ { @@ -7517,7 +7693,7 @@ var DATA = [ } }, "orf7a": { - "ontology_id": "PR:P0DTC7", + "ontology_id": "GENEPIO:0100176", "exportField": { "BIOSAMPLE": [ { @@ -7527,7 +7703,7 @@ var DATA = [ } }, "orf7b (ns7b)": { - "ontology_id": "PR:P0DTD8", + "ontology_id": "GENEPIO:0100177", "exportField": { "BIOSAMPLE": [ { @@ -7537,7 +7713,7 @@ var DATA = [ } }, "orf8 (ns8)": { - "ontology_id": "PR:P0DTC8", + "ontology_id": "GENEPIO:0100178", "exportField": { "BIOSAMPLE": [ { @@ -7547,7 +7723,7 @@ var DATA = [ } }, "orf9b": { - "ontology_id": "PR:P0DTD2", + "ontology_id": "GENEPIO:0100179", "exportField": { "BIOSAMPLE": [ { @@ -7557,7 +7733,7 @@ var DATA = [ } }, "orf9c": { - "ontology_id": "PR NTR?", + "ontology_id": "GENEPIO:0100180", "exportField": { "BIOSAMPLE": [ { @@ -7567,7 +7743,7 @@ var DATA = [ } }, "orf10": { - "ontology_id": "PR:A0A663DJA2", + "ontology_id": "GENEPIO:0100181", "exportField": { "BIOSAMPLE": [ { @@ -7577,7 +7753,7 @@ var DATA = [ } }, "orf14": { - "ontology_id": "PR NTR?", + "ontology_id": "GENEPIO:0100182", "exportField": { "BIOSAMPLE": [ { @@ -7586,7 +7762,9 @@ var DATA = [ ] } }, - "SARS-COV-2 5' UTR": {} + "SARS-COV-2 5' UTR": { + "ontology_id": "GENEPIO:0100183" + } } }, { diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index a68ff457..b3e8abb2 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -41,6 +41,7 @@ GENEPIO:0001234 Sample collection and processing collection device select Not 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@sfu.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:0100311 Sample collection and processing specimen processing details xs:token Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. 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 @@ -59,7 +60,7 @@ GENEPIO:0001395 Host Information host gender select Not Applicable; Missing; N 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. Canada 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:0001399 FLU:0000976 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 @@ -82,6 +83,8 @@ GENEPIO:0001412 Host exposure information destination of most recent travel (st 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 + Host exposure information travel point of entry type select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The type of entry point a traveler arrives through. Select the point of entry type. Air PH_POINT_OF_ENTRY + Host exposure information border testing test day type select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The day a traveller was tested on or after arrival at their point of entry. Select the test day. day 1 PH_DAY 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 PH_TRAVEL 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 @@ -151,6 +154,8 @@ GENEPIO:0001512 Pathogen diagnostic testing diagnostic pcr Ct value 2 xs:decima 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 @@ -159,12 +164,6 @@ GENEPIO:0001518 Contributor acknowledgement DataHarmonizer provenance provenanc umbrella bioproject accession PRJNA623807 - - - - - - GAZ:00002566 geo_loc_name (state/province/territory) Alberta GAZ:00002562 geo_loc_name (state/province/territory) British Columbia GAZ:00002571 geo_loc_name (state/province/territory) Manitoba @@ -179,25 +178,28 @@ GAZ:00002569 geo_loc_name (state/province/territory) Quebec GAZ:00002564 geo_loc_name (state/province/territory) Saskatchewan GAZ:00002576 geo_loc_name (state/province/territory) Yukon + UO:0000035 host age unit month UO:0000036 host age unit year + UO:0000036 sample collection date precision year UO:0000035 sample collection date precision month UO:0000033 sample collection date precision 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) +GENEPIO:0100104 biomaterial extracted mRNA (messenger RNA) OBI:0002754 biomaterial extracted mRNA (cDNA) -HP REQUEST signs and symptoms Abnormal lung auscultation +HP:0030829 signs and symptoms Abnormal lung auscultation HP:0000223 signs and symptoms Abnormality of taste sensation HP:0041051 Abnormality of taste sensation Ageusia (complete loss of taste) HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) -HP:0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) +HP:0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) HP:0004408 signs and symptoms Abnormality of the sense of smell HP:0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) HP:0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) @@ -207,14 +209,14 @@ HP:0100543 Altered mental status Cognitive impairment HP:0001259 Altered mental status Coma HP:0001289 Altered mental status Confusion HP:0031258 Confusion Delirium (sudden severe confusion) -HP REQUEST Altered mental status Inability to arouse (inability to stay awake) -HP:0000737 Altered mental status Irritability +GENEPIO:0100061 Altered mental status Inability to arouse (inability to stay awake) +HP:0000737 Altered mental status Irritability HP:0002371 Altered mental status Loss of speech HP:0011675 signs and symptoms Arrhythmia HP:0025406 signs and symptoms Asthenia (generalized weakness) HP:0031352 signs and symptoms Chest tightness or pressure HP:0025145 Chest tightness or pressure Rigors (fever shakes) -HP:0025143 signs and symptoms Chills (sudden cold sensation) Chills +HP:0025143 signs and symptoms Chills (sudden cold sensation) Chills HP:0030953 signs and symptoms Conjunctival injection HP:0000509 signs and symptoms Conjunctivitis (pink eye) Conjunctivitis MP:0001867 signs and symptoms Coryza (rhinitis) @@ -224,36 +226,36 @@ HP:0031245 Cough Productive cough (wet cough) HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis HP:0032556 Acrocyanosis Circumoral cyanosis (bluish around mouth) -HP REQUEST Acrocyanosis Cyanotic face (bluish face) -HP REQUEST Cyanosis (blueish skin discolouration) Central Cyanosis -HP REQUEST Central Cyanosis Cyanotic lips (bluish lips) -HP REQUEST Cyanosis (blueish skin discolouration) Peripheral Cyanosis +GENEPIO:0100062 Acrocyanosis Cyanotic face (bluish face) +GENEPIO:0100063 Cyanosis (blueish skin discolouration) Central Cyanosis +GENEPIO:0100064 Central Cyanosis Cyanotic lips (bluish lips) +GENEPIO:0100065 Cyanosis (blueish skin discolouration) Peripheral Cyanosis HP:0002094 signs and symptoms Dyspnea (breathing difficulty) HP:0002014 signs and symptoms Diarrhea (watery stool) Diarrhea, watery MP:0031127 signs and symptoms Dry gangrene HP:0002383 signs and symptoms Encephalitis (brain inflammation) Encephalitis HP:0001298 signs and symptoms Encephalopathy HP:0012378 signs and symptoms Fatigue (tiredness) Fatigue -HP:0001945 signs and symptoms Fever -HP REQUEST Fever Fever (>=38°C) Fever +HP:0001945 signs and symptoms Fever +GENEPIO:0100066 Fever Fever (>=38°C) Fever HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) -HP REQUEST signs and symptoms Ground Glass Opacities (GGO) +GENEPIO:0100067 signs and symptoms Ground Glass Opacities (GGO) HP:0002315 signs and symptoms Headache HP:0002105 signs and symptoms Hemoptysis (coughing up blood) HP:0012417 signs and symptoms Hypocapnia HP:0002615 signs and symptoms Hypotension (low blood pressure) HP:0012418 signs and symptoms Hypoxemia (low blood oxygen) -HP REQUEST Hypoxemia (low blood oxygen) Silent hypoxemia +GENEPIO:0100068 Hypoxemia (low blood oxygen) Silent hypoxemia HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) NCIT:C121416 signs and symptoms Loss of Fine Movements -HP:0004396 signs and symptoms Low appetite +HP:0004396 signs and symptoms Low appetite HP:0033834 signs and symptoms Malaise (general discomfort/unease) HP:0031179 signs and symptoms Meningismus/nuchal rigidity HP:0001324 signs and symptoms Muscle weakness HP:0001742 signs and symptoms Nasal obstruction (stuffy nose) HP:0002018 signs and symptoms Nausea HP:0000421 signs and symptoms Nose bleed -HP REQUEST signs and symptoms Otitis +GENEPIO:0100069 signs and symptoms Otitis HP:0012531 signs and symptoms Pain HP:0002027 Pain Abdominal pain HP:0002829 Pain Arthralgia (painful joints) @@ -261,12 +263,12 @@ HP:0100749 Pain Chest pain HP:0033771 Chest pain Pleuritic chest pain HP:0003326 Pain Myalgia (muscle pain) HP:0025439 signs and symptoms Pharyngitis (sore throat) -HP REQUEST signs and symptoms Pharyngeal exudate +GENEPIO:0100070 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) -HP REQUEST Pseudo-chilblains Pseudo-chilblains on toes (covid toes) +GENEPIO:0100072 Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) +GENEPIO:0100073 Pseudo-chilblains Pseudo-chilblains on toes (covid toes) HP:0000988 signs and symptoms Rash HP:0031417 signs and symptoms Rhinorrhea (runny nose) HP:0001250 signs and symptoms Seizure @@ -281,15 +283,17 @@ HP:0002789 signs and symptoms Tachypnea (accelerated respiratory rate) HP:0002321 signs and symptoms Vertigo (dizziness) HP:0002013 signs and symptoms Vomiting (throwing up) - host vaccination status Fully Vaccinated - host vaccination status Partially Vaccinated - host vaccination status Not Vaccinated + +GENEPIO:0100100 host vaccination status Fully Vaccinated +GENEPIO:0100101 host vaccination status Partially Vaccinated +GENEPIO:0100102 host vaccination status Not Vaccinated - prior SARS-CoV-2 antiviral treatment Prior antivrial treatment - prior SARS-CoV-2 antiviral treatment No prior antivrial treatment +GENEPIO:0100037 prior SARS-CoV-2 antiviral treatment Prior antiviral treatment +GENEPIO:0100233 prior SARS-CoV-2 antiviral treatment No prior antiviral treatment prior SARS-CoV-2 antiviral treatment Unknown + OBI:0002600 NML submitted specimen type Swab OBI:0000880 NML submitted specimen type RNA OBI:0002754 NML submitted specimen type mRNA (cDNA) @@ -326,12 +330,12 @@ 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 +GENEPIO:0100074 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 +GENEPIO:0100075 pre-existing conditions and risk factors Chronic cough +GENEPIO:0100076 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) @@ -382,42 +386,43 @@ 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) +GENEPIO:0100077 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 +GENEPIO:0100078 Substance use Drug abuse +GENEPIO:0100079 Drug abuse Injection drug abuse NBO:0015005 Substance use Smoking -NBO NTR Substance use Vaping +NCIT:C173621 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 Hematopoietic stem cell transplant (bone marrow transplant) - Transplant Cardiac transplant +GENEPIO:0100080 Transplant Cardiac transplant NCIT:C157332 Transplant Kidney transplant - Transplant Liver transplant +GENEPIO:0100081 Transplant Liver transplant + + +GENEPIO:0100082 variant designation Variant of Concern (VOC) +GENEPIO:0100083 variant designation Variant of Interest (VOI) +GENEPIO:0100279 variant designation Variant Under Monitoring (VUM) -GENEPIO variant designation Variant of Concern (VOC) -GENEPIO variant designation Variant of Interest (VOI) - variant designation Variant Under Monitoring (VUM) CIDO:0000019 variant evidence RT-qPCR CIDO:0000027 variant evidence Sequencing HP:0500165 complications Abnormal blood oxygen level +HP:0001919 complications Acute kidney injury +MONDO:0015796 complications Acute lung injury +GENEPIO:0100092 Acute lung injury Ventilation induced lung injury (VILI) 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) -NCIT:C171551 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 +GENEPIO:0100084 Tachycardia Tachyarrhythmia +GENEPIO:0100074 complications Cardiac injury HP:0001695 complications Cardiac arrest HP:0030149 complications Cardiogenic shock HP:0001977 complications Blood clot @@ -431,36 +436,38 @@ MONDO:0003346 Stroke (complication) Central Nervous System Vasculitis HP:0002140 Stroke (complication) Acute ischemic stroke HP:0001259 complications Coma HP:0011097 complications Convulsions -HP NTR complications COVID-19 associated coagulopathy (CAC) +NCIT:C171562 complications COVID-19 associated coagulopathy (CAC) MONDO:0009061 complications Cystic fibrosis MONDO:0600008 complications Cytokine release syndrome MPATH:108 complications Disseminated intravascular coagulation (DIC) HP:0001298 complications Encephalopathy -HP NTR complications Fulminant myocarditis +GENEPIO:0100088 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 Complete Kawasaki disease -HP NTR Kawasaki disease Incomplete Kawasaki disease -HP:0001919 complications Acute kidney injury -MONDO:0100233 complications Long COVID-19 +MONDO:0012727 complications Kawasaki disease +GENEPIO:0100089 Kawasaki disease Complete Kawasaki disease +GENEPIO:0100090 Kawasaki disease Incomplete Kawasaki disease HP:0001410 complications Liver dysfunction -HP NTR Liver dysfunction Acute liver injury -MONDO:0015796 complications Acute lung injury -HP NTR Acute lung injury Ventilation induced lung injury (VILI) +GENEPIO:0100091 Liver dysfunction Acute liver injury +MONDO:0100233 complications Long COVID-19 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:0100319 complications Multisystem inflammatory syndrome in adults (MIS-A) +GENEPIO:0100093 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 +HP:0001700 complications Myocardial injury NCIT:C168498 complications Neonatal complications -HP NTR complications Organ failure +GENEPIO:0100085 complications Noncardiogenic pulmonary edema +HP:0033677 Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) +NCIT:C171551 Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) +GENEPIO:0100086 Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) +GENEPIO:0100094 complications Organ failure HP:0001635 Organ failure Heart failure MONDO:0100192 Organ failure Liver failure HP:0003470 complications Paralysis @@ -472,18 +479,18 @@ NCIT:C171550 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 +GENEPIO:0100095 Secondary infection Secondary staph infection +GENEPIO:0100096 Secondary infection Secondary strep infection HP:0001250 complications Seizure (complication) HP:0020219 Seizure (complication) Motor seizure HP:0100806 complications Sepsis/Septicemia IDO:0000636 Sepsis/Septicemia Sepsis NCIT:C3364 Sepsis/Septicemia 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 +GENEPIO:0100097 Shock Hyperinflammatory shock +GENEPIO:0100098 Shock Refractory cardiogenic shock +GENEPIO:0100099 Shock Refractory cardiogenic plus vasoplegic shock +NCIT:C35018 Shock Septic shock HP:0002633 complications Vasculitis @@ -505,12 +512,19 @@ UBERON:0000173 Fluid Fluid (amniotic) UBERON:0000479 anatomical material Tissue - UBERON:0001245 anatomical part Anus -UBERON:0006956 anatomical part Buccal mucosa +UBERON:0006956 anatomical part Buccal mucosa UBERON:0002114 anatomical part Duodenum UBERON:0000970 anatomical part Eye - anatomical part Intestine +UBERON:0000160 anatomical part Intestine +UBERON:0001558 anatomical part Lower respiratory tract +UBERON:0002185 Lower respiratory tract Bronchus +UBERON:0002048 Lower respiratory tract Lung +UBERON:0002186 Lung Bronchiole +UBERON:0002169 Lung Alveolar sac +UBERON:0009778 Lower respiratory tract Pleural sac +UBERON:0002402 Pleural sac Pleural cavity +UBERON:0003126 Lower respiratory tract Trachea UBERON:0001052 anatomical part Rectum UBERON:0001003 anatomical part Skin UBERON:0000945 anatomical part Stomach @@ -518,34 +532,25 @@ UBERON:0001557 anatomical part Upper respiratory tract UBERON:2001427 Upper respiratory tract Anterior Nares UBERON:0001043 Upper respiratory tract Esophagus UBERON:0002453 Upper respiratory tract Ethmoid sinus -UBERON:0001707 Upper respiratory tract Nasal Cavity -UBERON:0005921 Nasal Cavity Middle Nasal Turbinate +UBERON:0001707 Upper respiratory tract Nasal Cavity +UBERON:0005921 Nasal Cavity Middle Nasal Turbinate UBERON:0005922 Nasal Cavity Inferior Nasal Turbinate UBERON:0001728 Upper respiratory tract Nasopharynx (NP) UBERON:0001729 Upper respiratory tract Oropharynx (OP) -UBERON:0001558 anatomical part Lower respiratory tract -UBERON:0002185 Lower respiratory tract Bronchus -UBERON:0002048 Lower respiratory tract Lung -UBERON:0002186 Lung Bronchiole -UBERON:0002169 Lung Alveolar sac -UBERON:0009778 Lower respiratory tract Pleural sac -UBERON:0002402 Pleural sac Pleural cavity -UBERON:0003126 Lower respiratory tract Trachea - - +UBERON:0001913 body product Breast Milk UBERON:0001988 body product Feces -UBERON:0001088 body product Urine -UBERON:0001089 body product Sweat +UBERON:0006530 body product Fluid (seminal) UBERON:0000912 body product Mucus UBERON:0007311 Mucus Sputum +UBERON:0001089 body product Sweat UBERON:0001827 body product Tear -UBERON:0006530 body product Fluid (seminal) -UBERON:0001913 body product Breast Milk +UBERON:0001088 body product Urine - prior SARS-CoV-2 infection Prior antiviral treatment - prior SARS-CoV-2 infection No prior antiviral treatment + +GENEPIO:0100037 prior SARS-CoV-2 infection Prior infection +GENEPIO:0100233 prior SARS-CoV-2 infection No prior infection ENVO:03501208 environmental material Air vent @@ -562,7 +567,7 @@ FOODON:00002403 environmental material Food FOODON:03490100 environmental material Food packaging ENVO:01000481 environmental material Glass ENVO:03501212 environmental material Handrail -OBI:0002792 environmental material Hospital gown +OBI:0002796 environmental material Hospital gown ENVO:03501213 environmental material Light switch ENVO:03501214 environmental material Locker OBI:0002790 environmental material N95 mask @@ -570,7 +575,7 @@ ENVO:03501215 environmental material Nurse call button ENVO:03501256 environmental material Paper ENVO:01000060 environmental material Particulate matter ENVO:01000404 environmental material Plastic -OBI NTR? environmental material PPE gown +GENEPIO:0100025 environmental material PPE gown ENVO:00002018 environmental material Sewage ENVO:01000990 environmental material Sink ENVO:00001998 environmental material Soil @@ -582,6 +587,7 @@ ENVO:00002001 environmental material Wastewater ENVO:03501219 environmental material Window ENVO:00002040 environmental material Wood + ENVO:03501135 environmental site Acute care facility ENVO:00003040 environmental site Animal house ENVO:01000422 environmental site Bathroom @@ -589,7 +595,7 @@ ENVO:03501136 environmental site Clinical assessment centre ENVO:03501127 environmental site Conference venue ENVO:03501121 environmental site Corridor ENVO:01000927 environmental site Daycare -ENVO:03501144 environmental site Emergency room (ER) +ENVO:03501145 environmental site Emergency room (ER) ENVO:03501186 environmental site Family practice clinic ENVO:03501196 environmental site Group home ENVO:03501133 environmental site Homeless shelter @@ -602,39 +608,40 @@ ENVO:01000536 environmental site Production Facility ENVO:03501130 environmental site School ENVO:00003043 environmental site Sewage Plant ENVO:03501109 environmental site Subway train +ENVO:00000467 environmental site University campus ENVO:03501198 environmental site Wet market -OBI NTR collection method Amniocentesis -OBI NTR collection method Aspiration -OBI NTR Aspiration Suprapubic Aspiration -OBI NTR Aspiration Tracheal aspiration -OBI NTR Aspiration Vacuum Aspiration +NCIT:C52009 collection method Amniocentesis +NCIT:C15631 collection method Aspiration +GENEPIO:0100028 Aspiration Suprapubic Aspiration +GENEPIO:0100029 Aspiration Tracheal aspiration +GENEPIO:0100030 Aspiration Vacuum Aspiration OBI:0002650 collection method Biopsy OBI:0002651 Biopsy Needle Biopsy OBI:0302885 collection method Filtration -OBI NTR Filtration Air filtration -OBI:0600044 collection method Lavage -OBI NTR Lavage Bronchoalveolar lavage (BAL) -OBI NTR Lavage Gastric Lavage -OBI NTR collection method Lumbar Puncture -OBI NTR collection method Necropsy -OBI NTR collection method Phlebotomy -OBI NTR collection method Rinsing -OBI NTR Rinsing Saline gargle (mouth rinse and gargle) -OBI NTR collection method Scraping -OBI NTR collection method Swabbing -OBI NTR Swabbing Finger Prick -OBI NTR collection method Washout Tear Collection +GENEPIO:0100031 Filtration Air filtration +OBI:0600044 collection method Lavage +GENEPIO:0100032 Lavage Bronchoalveolar lavage (BAL) +GENEPIO:0100033 Lavage Gastric Lavage +NCIT:C15327 collection method Lumbar Puncture +MMO:0000344 collection method Necropsy +NCIT:C28221 collection method Phlebotomy +GENEPIO:0002116 collection method Rinsing +GENEPIO:0100034 Rinsing Saline gargle (mouth rinse and gargle) +GENEPIO:0100035 collection method Scraping +GENEPIO:0002117 collection method Swabbing +GENEPIO:0100036 Swabbing Finger Prick +GENEPIO:0100038 collection method Washout Tear Collection ENVO:00003968 collection device Air filter OBI:0002859 collection device Blood Collection Tube OBI:0002826 collection device Bronchoscope OBI:0002088 collection device Collection Container -OBI NTR? collection device Collection Cup +GENEPIO:0100026 collection device Collection Cup OBI:0002825 collection device Fibrobronchoscope Brush -ENVO NTR collection device Filter +GENEPIO:0100103 collection device Filter OBI:0002827 collection device Fine Needle OBI:0002858 collection device Microcapillary tube OBI:0001128 collection device Micropipette @@ -642,14 +649,14 @@ OBI:0000436 collection device Needle OBI:0002860 collection device Serum Collection Tube OBI:0002861 collection device Sputum Collection Tube OBI:0002831 collection device Suction Catheter -OBI NTR? collection device Swab +GENEPIO:0100027 collection device Swab OBI:0002862 collection device Urine Collection Tube OBI:0002866 collection device Virus Transport Medium NCBITaxon:9606 host (scientific name) Homo sapiens Human NCBITaxon:9913 host (scientific name) Bos taurus -NCBITaxon:9615 host (scientific name) Canis lupus familiaris +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 @@ -659,7 +666,7 @@ 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: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 @@ -671,7 +678,7 @@ NCBITaxon:9685 host (common name) Cat NCBITaxon:9031 host (common name) Chicken NCBITaxon:9673 host (common name) Civets NCBITaxon:9913 host (common name) Cow bovine -NCBITaxon:9615 host (common name) Dog +NCBITaxon:9615 host (common name) Dog NCBITaxon:9689 host (common name) Lion NCBITaxon:452646 host (common name) Mink NCBITaxon:9973 host (common name) Pangolin @@ -683,325 +690,341 @@ NCBITaxon:9694 host (common name) Tiger NCIT:C3833 host health state Asymptomatic NCIT:C28554 host health state Deceased NCIT:C115935 host health state Healthy - host health state Recovered - host health state Symptomatic +NCIT:C49498 host health state Recovered +NCIT:C25269 host health state Symptomatic - host health status details Hospitalized - Hospitalized Hospitalized (Non-ICU) - Hospitalized Hospitalized (ICU) - host health status details Mechanical Ventilation - host health status details Medically Isolated - Medically Isolated Medically Isolated (Negative Pressure) - host health status details Self-quarantining +NCIT:C25179 host health status details Hospitalized +GENEPIO:0100045 Hospitalized Hospitalized (Non-ICU) +GENEPIO:0100046 Hospitalized Hospitalized (ICU) +NCIT:C70909 host health status details Mechanical Ventilation +GENEPIO:0100047 host health status details Medically Isolated +GENEPIO:0100048 Medically Isolated Medically Isolated (Negative Pressure) +NCIT:C173768 host health status details Self-quarantining + + +NCIT:C28554 host health outcome Deceased +NCIT:C25254 host health outcome Deteriorating +NCIT:C49498 host health outcome Recovered +NCIT:C30103 host health outcome Stable - 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) - Screening for Variants of Concern (VoC) Sample has epidemiological link to Variant of Concern (VoC) - Sample has epidemiological link to Variant of Concern (VoC) Sample has epidemiological link to Omicron Variant - 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 - Domestic travel surveillance Interstate/ interprovincial travel surveillance - Domestic travel surveillance Intra-state/ intra-provincial travel surveillance - Travel-associated surveillance International travel surveillance - Travel-associated surveillance Surveillance of international border crossing by air travel or ground transport - 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 - purpose of sequencing Retrospective sequencing - - -OBI NTR? specimen processing Virus passage -OBI NTR? specimen processing RNA re-extraction (post RT-PCR) +GENEPIO:0100000 organism RmYN02 + + +GENEPIO:0100001 purpose of sampling Cluster/Outbreak investigation +GENEPIO:0100002 purpose of sampling Diagnostic testing +GENEPIO:0100003 purpose of sampling Research +GENEPIO:0100004 purpose of sampling Surveillance + + +GENEPIO:0100005 purpose of sequencing Baseline surveillance (random sampling) +GENEPIO:0100006 purpose of sequencing Targeted surveillance (non-random sampling) +GENEPIO:0100007 Targeted surveillance (non-random sampling) Priority surveillance project +GENEPIO:0100008 Priority surveillance project Screening for Variants of Concern (VoC) +GENEPIO:0100273 Screening for Variants of Concern (VoC) Sample has epidemiological link to Variant of Concern (VoC) +GENEPIO:0100274 Sample has epidemiological link to Variant of Concern (VoC) Sample has epidemiological link to Omicron Variant +GENEPIO:0100009 Priority surveillance project Longitudinal surveillance (repeat sampling of individuals) +GENEPIO:0100010 Priority surveillance project Re-infection surveillance +GENEPIO:0100011 Priority surveillance project Vaccine escape surveillance +GENEPIO:0100012 Priority surveillance project Travel-associated surveillance +GENEPIO:0100013 Travel-associated surveillance Domestic travel surveillance +GENEPIO:0100275 Domestic travel surveillance Interstate/ interprovincial travel surveillance +GENEPIO:0100276 Domestic travel surveillance Intra-state/ intra-provincial travel surveillance +GENEPIO:0100014 Travel-associated surveillance International travel surveillance +GENEPIO:0100015 Travel-associated surveillance Surveillance of international border crossing by air travel or ground transport +GENEPIO:0100016 Travel-associated surveillance Surveillance of international border crossing by air travel +GENEPIO:0100017 Travel-associated surveillance Surveillance of international border crossing by ground transport +GENEPIO:0100018 Travel-associated surveillance Surveillance from international worker testing +GENEPIO:0100019 purpose of sequencing Cluster/Outbreak investigation +GENEPIO:0100020 Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation +GENEPIO:0100021 Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation +GENEPIO:0100022 purpose of sequencing Research +GENEPIO:0100023 Research Viral passage experiment +GENEPIO:0100024 Research Protocol testing experiment +GENEPIO:0100356 purpose of sequencing Retrospective sequencing + + +GENEPIO:0100039 specimen processing Virus passage +GENEPIO:0100040 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 + +GENEPIO:0100041 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 +GENEPIO:0100042 lab host EFK3B cell line BTO:0002181 lab host HEK293T cell line -BTO NTR lab host HRCE cell line +GENEPIO:0100043 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: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:0001444 lab host Vero cell line BTO:0004755 lab host Vero E6 cell line -BTO NTR lab host VeroE6/TMPRSS2 cell line +GENEPIO:0100044 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+ + +GENEPIO:0100049 host age bin 0 - 9 +GENEPIO:0100050 host age bin 10 - 19 +GENEPIO:0100051 host age bin 20 - 29 +GENEPIO:0100052 host age bin 30 - 39 +GENEPIO:0100053 host age bin 40 - 49 +GENEPIO:0100054 host age bin 50 - 59 +GENEPIO:0100055 host age bin 60 - 69 +GENEPIO:0100056 host age bin 70 - 79 +GENEPIO:0100057 host age bin 80 - 89 +GENEPIO:0100058 host age bin 90 - 99 90+ +GENEPIO:0100059 host age bin 100+ 90+ + NCIT:C46110 host gender Female NCIT:C46109 host gender Male GSSO:000132 host gender Non-binary gender GSSO:004004 host gender Transgender (assigned male at birth) GSSO:004005 host gender Transgender (assigned female at birth) - host gender Undeclared - host gender Unknown - -PCO NTR exposure event Mass Gathering -PCO NTR Mass Gathering Agricultural Event -PCO NTR Mass Gathering 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 -PCO NTR Religious Gathering Mass +NCIT:C110959 host gender Undeclared + + +GENEPIO:0100237 exposure event Mass Gathering +GENEPIO:0100240 Mass Gathering Agricultural Event +GENEPIO:0100238 Mass Gathering Convention +GENEPIO:0100239 Mass Gathering Convocation +GENEPIO:0100417 Mass Gathering Recreational Event +GENEPIO:0100418 Recreational Event Concert +GENEPIO:0100419 Recreational Event Sporting Event +GENEPIO:0100241 exposure event Religious Gathering +GENEPIO:0100242 Religious Gathering Mass PCO:0000033 exposure event Social Gathering 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 +GENEPIO:0100243 Social Gathering Family Gathering +GENEPIO:0100244 Family Gathering Family Reunion +GENEPIO:0100245 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 + 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 +GENEPIO:0100357 exposure contact level Contact with infected individual +TRANS:0000001 Contact with infected individual Direct contact (direct human-to-human contact) +GENEPIO:0100246 Contact with infected individual Indirect contact +GENEPIO:0100247 Indirect contact Close contact (face-to-face, no direct contact) +GENEPIO:0100248 Indirect contact Casual contact -OMRSE NTR host role Attendee +GENEPIO:0100249 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 +NCIT:C25182 Patient Inpatient +NCIT:C28293 Patient Outpatient +GENEPIO:0100250 host role Passenger +GENEPIO:0100251 host role Resident +GENEPIO:0100252 host role Visitor +GENEPIO:0100253 host role Volunteer +GENEPIO:0100254 host role Work +GENEPIO:0100255 Work Administrator + Work Child Care/Education Worker + Work Essential Worker +GENEPIO:0100256 Work First Responder +GENEPIO:0100257 First Responder Firefighter +GENEPIO:0100258 First Responder Paramedic +GENEPIO:0100259 First Responder Police Officer +GENEPIO:0100334 Work Healthcare Worker +GENEPIO:0100420 Healthcare Worker Community Healthcare Worker +GENEPIO:0100262 Healthcare Worker Laboratory 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 +GENEPIO:0100263 Healthcare Worker Personal Care Aid +GENEPIO:0100264 Healthcare Worker Pharmacist +OMRSE:00000013 Healthcare Worker Physician +GENEPIO:0100260 Work Housekeeper + Work International worker +GENEPIO:0100261 Work Kitchen Worker +GENEPIO:0100354 Work Rotational Worker +GENEPIO:0100355 Work Seasonal Worker + Work Transport Worker + Transport Worker Transport Truck Driver +GENEPIO:0100265 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 +GENEPIO:0100266 Social role Acquaintance of case +GENEPIO:0100267 Social role Relative of case +GENEPIO:0100268 Relative of case Child of case +GENEPIO:0100269 Relative of case Parent of case +GENEPIO:0100270 Relative of case Father of case +GENEPIO:0100271 Relative of case Mother of case +GENEPIO:0100272 Social role Spouse of case + 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 +GENEPIO:0100184 Human Exposure Contact with Known COVID-19 Case +GENEPIO:0100185 Human Exposure Contact with Patient +GENEPIO:0100186 Human Exposure Contact with Probable COVID-19 Case +GENEPIO:0100187 Human Exposure Contact with Person with Acute Respiratory Illness +GENEPIO:0100188 Human Exposure Contact with Person with Fever and/or Cough +GENEPIO:0100189 Human Exposure Contact with Person who Recently Travelled +GENEPIO:0100190 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 Nursery -ECTO NTR Occupational, Residency or Patronage Exposure Community Service Centre -ECTO NTR Occupational, Residency or Patronage Exposure Correctional Facility -ECTO NTR Occupational, Residency or Patronage Exposure Dormitory +GENEPIO:0100191 Occupational, Residency or Patronage Exposure Animal Rescue +GENEPIO:0100192 Occupational, Residency or Patronage Exposure Childcare +GENEPIO:0100193 Childcare Daycare +GENEPIO:0100194 Occupational, Residency or Patronage Exposure Nursery +GENEPIO:0100195 Occupational, Residency or Patronage Exposure Community Service Centre +GENEPIO:0100196 Occupational, Residency or Patronage Exposure Correctional Facility +GENEPIO:0100197 Occupational, Residency or Patronage Exposure Dormitory ECTO:1000034 Occupational, Residency or Patronage Exposure Farm -ECTO NTR Occupational, Residency or Patronage Exposure First Nations Reserve -ECTO NTR Occupational, Residency or Patronage Exposure Funeral Home -ECTO NTR Occupational, Residency or Patronage Exposure Group Home -ECTO NTR Occupational, Residency or Patronage Exposure Healthcare Setting -ECTO NTR Healthcare Setting Ambulance -ECTO NTR Healthcare Setting Acute Care Facility -ECTO NTR Healthcare Setting Clinic -ECTO NTR Healthcare Setting Community Health Centre +GENEPIO:0100198 Occupational, Residency or Patronage Exposure First Nations Reserve +GENEPIO:0100199 Occupational, Residency or Patronage Exposure Funeral Home +GENEPIO:0100200 Occupational, Residency or Patronage Exposure Group Home +GENEPIO:0100201 Occupational, Residency or Patronage Exposure Healthcare Setting +GENEPIO:0100202 Healthcare Setting Ambulance +GENEPIO:0100203 Healthcare Setting Acute Care Facility +GENEPIO:0100204 Healthcare Setting Clinic +GENEPIO:0100415 Healthcare Setting Community Healthcare (At-Home) Setting +GENEPIO:0100205 Healthcare Setting Community Health Centre ECTO:1000035 Healthcare Setting Hospital -ECTO NTR Hospital Emergency Department -ECTO NTR Hospital ICU -ECTO NTR Hospital Ward +GENEPIO:0100206 Hospital Emergency Department +GENEPIO:0100207 Hospital ICU +GENEPIO:0100208 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 Household -ECTO NTR Occupational, Residency or Patronage Exposure Insecure Housing (Homeless) -ECTO NTR Occupational, Residency or Patronage Exposure Occupational Exposure -ECTO NTR Occupational Exposure Worksite +GENEPIO:0100209 Healthcare Setting Long-Term Care Facility +GENEPIO:0100210 Healthcare Setting Pharmacy +GENEPIO:0100211 Healthcare Setting Physician's Office +GENEPIO:0100212 Occupational, Residency or Patronage Exposure Household +GENEPIO:0100213 Occupational, Residency or Patronage Exposure Insecure Housing (Homeless) +GENEPIO:0100214 Occupational, Residency or Patronage Exposure Occupational Exposure +GENEPIO:0100215 Occupational Exposure Worksite ECTO:1000037 Occupational Exposure Office -ECTO NTR Occupational, Residency or Patronage Exposure Outdoors +GENEPIO:0100216 Occupational, Residency or Patronage Exposure Outdoors ECTO:5000009 Outdoors Camp/camping -ECTO NTR Outdoors Hiking Trail +GENEPIO:0100217 Outdoors Hiking Trail ECTO:6000030 Outdoors Hunting Ground -ECTO NTR Outdoors Ski Resort +GENEPIO:0100218 Outdoors Ski Resort ECTO:5000008 Occupational, Residency or Patronage Exposure Petting zoo -ECTO NTR Occupational, Residency or Patronage Exposure Place of Worship -ECTO NTR Place of Worship Church -ECTO NTR Place of Worship Mosque -ECTO NTR Place of Worship Temple +GENEPIO:0100220 Occupational, Residency or Patronage Exposure Place of Worship +GENEPIO:0100221 Place of Worship Church +GENEPIO:0100222 Place of Worship Mosque +GENEPIO:0100223 Place of Worship Temple ECTO:1000040 Occupational, Residency or Patronage Exposure Restaurant ECTO:1000041 Occupational, Residency or Patronage Exposure Retail Store -ECTO NTR Occupational, Residency or Patronage Exposure School -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 (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 +GENEPIO:0100224 Occupational, Residency or Patronage Exposure School +GENEPIO:0100225 Occupational, Residency or Patronage Exposure Temporary Residence +GENEPIO:0100226 Temporary Residence Homeless Shelter +GENEPIO:0100227 Temporary Residence Hotel +GENEPIO:0100228 Occupational, Residency or Patronage Exposure Veterinary Care Clinic +GENEPIO:0100229 exposure setting Travel Exposure +GENEPIO:0100230 Travel Exposure Travelled on a Cruise Ship +GENEPIO:0100231 Travel Exposure Travelled on a Plane +GENEPIO:0100232 Travel Exposure Travelled on Ground Transport +GENEPIO:0001118 Travel Exposure Travelled outside Province/Territory +GENEPIO:0001119 Travel Exposure Travelled outside Canada +GENEPIO:0100235 exposure setting Other Exposure Setting + + +GENEPIO:0100408 travel point of entry type Air +GENEPIO:0100409 travel point of entry type Land + + +GENEPIO:0100410 border testing test day type day 1 +GENEPIO:0100411 border testing test day type day 8 +GENEPIO:0100412 border testing test day type day 10 + + +GENEPIO:0100105 sequencing instrument Illumina +GENEPIO:0100106 Illumina Illumina Genome Analyzer +GENEPIO:0100107 Illumina Genome Analyzer Illumina Genome Analyzer II +GENEPIO:0100108 Illumina Genome Analyzer Illumina Genome Analyzer IIx +GENEPIO:0100109 Illumina Illumina HiScanSQ +GENEPIO:0100110 Illumina Illumina HiSeq +GENEPIO:0100111 Illumina Illumina HiSeq X +GENEPIO:0100112 Illumina HiSeq X Illumina HiSeq X Five +GENEPIO:0100113 Illumina HiSeq X Illumina HiSeq X Ten +GENEPIO:0100114 Illumina Illumina HiSeq 1000 +GENEPIO:0100115 Illumina Illumina HiSeq 1500 +GENEPIO:0100116 Illumina Illumina HiSeq 2000 +GENEPIO:0100117 Illumina Illumina HiSeq 2500 +GENEPIO:0100118 Illumina Illumina HiSeq 3000 +GENEPIO:0100119 Illumina Illumina HiSeq 4000 +GENEPIO:0100120 Illumina Illumina iSeq +GENEPIO:0100121 Illumina iSeq Illumina iSeq 100 +GENEPIO:0100122 Illumina Illumina NovaSeq +GENEPIO:0100123 Illumina NovaSeq Illumina NovaSeq 6000 +GENEPIO:0100124 Illumina Illumina MiniSeq +GENEPIO:0100125 Illumina Illumina MiSeq +GENEPIO:0100126 Illumina Illumina NextSeq +GENEPIO:0100127 Illumina Illumina NextSeq 500 +GENEPIO:0100128 Illumina Illumina NextSeq 550 +GENEPIO:0100129 Illumina Illumina NextSeq 2000 +GENEPIO:0100130 sequencing instrument Pacific Biosciences +GENEPIO:0100131 Pacific Biosciences PacBio RS +GENEPIO:0100132 Pacific Biosciences PacBio RS II +GENEPIO:0100133 Pacific Biosciences PacBio Sequel +GENEPIO:0100134 Pacific Biosciences PacBio Sequel II +GENEPIO:0100135 sequencing instrument Ion Torrent +GENEPIO:0100136 Ion Torrent Ion Torrent PGM +GENEPIO:0100137 Ion Torrent Ion Torrent Proton +GENEPIO:0100138 Ion Torrent Ion Torrent S5 XL +GENEPIO:0100139 Ion Torrent Ion Torrent S5 +GENEPIO:0100140 sequencing instrument Oxford Nanopore +GENEPIO:0100141 Oxford Nanopore Oxford Nanopore GridION +GENEPIO:0100142 Oxford Nanopore Oxford Nanopore MinION +GENEPIO:0100143 Oxford Nanopore Oxford Nanopore PromethION +GENEPIO:0100144 sequencing instrument BGI Genomics +GENEPIO:0100145 BGI Genomics BGI Genomics BGISEQ-500 +GENEPIO:0100146 sequencing instrument MGI +GENEPIO:0100147 MGI MGI DNBSEQ-T7 +GENEPIO:0100148 MGI MGI DNBSEQ-G400 +GENEPIO:0100149 MGI MGI DNBSEQ-G400 FAST +GENEPIO:0100150 MGI MGI DNBSEQ-G50 + + +GENEPIO:0100151 gene name 1 E gene (orf4) E gene E (orf4) +GENEPIO:0100152 gene name 1 M gene (orf5) M (orf5) +GENEPIO:0100153 gene name 1 N gene (orf9) N (orf9) +GENEPIO:0100154 gene name 1 Spike gene (orf2) S (orf2) +GENEPIO:0100155 gene name 1 orf1ab (rep) orf1ab (rep) +GENEPIO:0100156 orf1ab (rep) orf1a (pp1a) orf1a (pp1a) +GENEPIO:0100157 orf1a (pp1a) nsp11 nsp11 +GENEPIO:0100158 orf1ab (rep) nsp1 nsp1 +GENEPIO:0100159 orf1ab (rep) nsp2 nsp2 +GENEPIO:0100160 orf1ab (rep) nsp3 nsp3 +GENEPIO:0100161 orf1ab (rep) nsp4 nsp4 +GENEPIO:0100162 orf1ab (rep) nsp5 nsp5 +GENEPIO:0100163 orf1ab (rep) nsp6 nsp6 +GENEPIO:0100164 orf1ab (rep) nsp7 nsp7 +GENEPIO:0100165 orf1ab (rep) nsp8 nsp8 +GENEPIO:0100166 orf1ab (rep) nsp9 nsp9 +GENEPIO:0100167 orf1ab (rep) nsp10 nsp10 +GENEPIO:0100168 orf1ab (rep) RdRp gene (nsp12) nsp12 (RdRp) +GENEPIO:0100169 orf1ab (rep) hel gene (nsp13) nsp13 (Hel) +GENEPIO:0100170 orf1ab (rep) exoN gene (nsp14) nsp14 (ExoN) +GENEPIO:0100171 orf1ab (rep) nsp15 nsp15 +GENEPIO:0100172 orf1ab (rep) nsp16 nsp16 +GENEPIO:0100173 gene name 1 orf3a orf3a +GENEPIO:0100174 gene name 1 orf3b orf3b +GENEPIO:0100175 gene name 1 orf6 (ns6) orf6 (ns6) +GENEPIO:0100176 gene name 1 orf7a orf7a +GENEPIO:0100177 gene name 1 orf7b (ns7b) orf7b (ns7b) +GENEPIO:0100178 gene name 1 orf8 (ns8) orf8 (ns8) +GENEPIO:0100179 gene name 1 orf9b orf9b +GENEPIO:0100180 gene name 1 orf9c orf9c +GENEPIO:0100181 gene name 1 orf10 orf10 +GENEPIO:0100182 gene name 1 orf14 orf14 +GENEPIO:0100183 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) + 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) @@ -1011,8 +1034,8 @@ PR NTR? gene name 1 orf14 orf14 sequence submitted by The Hospital for Sick Children (SickKids) 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 McMaster University sequence submitted by National Microbiology Laboratory (NML) sequence submitted by New Brunswick - Vitalité Health Network sequence submitted by Newfoundland and Labrador - Eastern Health @@ -1020,15 +1043,15 @@ PR NTR? gene name 1 orf14 orf14 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 Queen's University / Kingston Health Sciences Centre 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) - Alberta Precision Labs (APL) Alberta ProvLab South (APLS) + Alberta Precision Labs (APL) Alberta ProvLab North (APLN) + Alberta Precision Labs (APL) Alberta ProvLab South (APLS) sample collected by BCCDC Public Health Laboratory sample collected by Dynacare sample collected by Dynacare (Manitoba) @@ -1327,6 +1350,4 @@ GAZ:00009572 geo_loc_name (country) West Bank GAZ:00000564 geo_loc_name (country) Western Sahara GAZ:00005284 geo_loc_name (country) Yemen GAZ:00001107 geo_loc_name (country) Zambia -GAZ:00001106 geo_loc_name (country) Zimbabwe - - \ No newline at end of file +GAZ:00001106 geo_loc_name (country) Zimbabwe \ No newline at end of file diff --git a/template/canada_covid19/export.js b/template/canada_covid19/export.js index 5d658167..df94e698 100644 --- a/template/canada_covid19/export.js +++ b/template/canada_covid19/export.js @@ -417,6 +417,8 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => { ['VE_SYMP_AVAIL', []], // Calculated field (not in import) ['PH_EXPOSURE_COUNTRY', []], ['PH_TRAVEL', []], + ['PH_POINT_OF_ENTRY', []], + ['PH_DAY', []], ['PH_EXPOSURE', []], ['PH_EXPOSURE_DETAILS', []], ['PH_HOST_ROLE', []], diff --git a/template/canada_covid19/reference.html b/template/canada_covid19/reference.html index eefb9821..5d521262 100644 --- a/template/canada_covid19/reference.html +++ b/template/canada_covid19/reference.html @@ -389,6 +389,15 @@

    CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission + + specimen processing details + Detailed information regarding the processing applied to a sample during or after receiving the sample. + Provide a free text description of any processing details applied to a sample. + 25 swabs were pooled and further prepared as a single sample during library prep. + None + + + lab host Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. @@ -743,6 +752,24 @@

    CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission + + travel point of entry type + The type of entry point a traveler arrives through. + Select the point of entry type. + Air + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] + + + + + border testing test day type + The day a traveller was tested on or after arrival at their point of entry. + Select the test day. + day 1 + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] + + + travel history Travel history in last six months.