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PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json
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PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json
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{
"$schema": "http://json-schema.org/draft/2019-09/schema#",
"required": [
"sequence_submitted_by",
"sample_collected_by",
"sequencing_instrument",
"host_scientific_name",
"isolate",
"sample_collection_date",
"host_disease",
"consensus_sequence_software_name",
"geo_loc_name_state_province_territory",
"specimen_collector_sample_id",
"consensus_sequence_software_version",
"organism",
"geo_loc_name_country"
],
"type": "object",
"properties": {
"sample_collector_contact_email": {
"examples": ["[email protected]"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The email address of the contact responsible for follow-up regarding the sample.",
"format": "email"
},
"depth_of_coverage_value": {
"ontology": "GENEPIO:0001474",
"type": "number",
"description": "The average number of reads representing a given nucleotide in the reconstructed sequence.",
"examples": [400.0]
},
"exposure_details": {
"ontology": "GENEPIO:0001431",
"type": "string",
"description": "Additional host exposure information.",
"examples": ["Host role - Other: Bus Driver"]
},
"breadth_of_coverage_value": {
"ontology": "GENEPIO:0001472",
"type": "number",
"description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.",
"examples": [0.95]
},
"most_recent_travel_departure_date": {
"examples": ["16/03/2020"],
"ontology": "GENEPIO:0001414",
"type": "string",
"description": "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.",
"format": "date"
},
"sequencing_protocol": {
"ontology": "GENEPIO:0001454",
"type": "string",
"description": "The protocol used to generate the sequence.",
"examples": [
"Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."
]
},
"host_age_bin": {
"Enums": [
"0 - 9 [GENEPIO:0100049]",
"10 - 19 [GENEPIO:0100050]",
"20 - 29 [GENEPIO:0100051]",
"30 - 39 [GENEPIO:0100052]",
"40 - 49 [GENEPIO:0100053]",
"50 - 59 [GENEPIO:0100054]",
"60 - 69 [GENEPIO:0100055]",
"70 - 79 [GENEPIO:0100056]",
"80 - 89 [GENEPIO:0100057]",
"90 - 99 [GENEPIO:0100058]",
"100+ [GENEPIO:0100059]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001394",
"type": "string",
"description": "The age category of the host at the time of sampling.",
"examples": ["50 - 59 [GENEPIO:0100054]"]
},
"anatomical_material": {
"Enums": [
"Blood [UBERON:0000178]",
"Fluid [UBERON:0006314]",
"Fluid (Cerebrospinal (CSF)) [UBERON:0001359]",
"Fluid (Pericardial) [UBERON:0002409]",
"Fluid (Pleural) [UBERON:0001087]",
"Fluid (Vaginal) [UBERON:0036243]",
"Fluid (Amniotic) [UBERON:0000173]",
"Saliva [UBERON:0001836]",
"Tissue [UBERON:0000479]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001211",
"type": "string",
"description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.",
"examples": ["Blood [UBERON:0000178]"]
},
"sample_collection_date": {
"examples": ["19/03/2020"],
"ontology": "GENEPIO:0001174",
"type": "string",
"description": "The date on which the sample was collected. ",
"format": "date"
},
"diagnostic_pcr_ct_value_2": {
"ontology": "GENEPIO:0001512",
"type": "integer",
"description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"examples": [36]
},
"number_of_vaccine_doses_received": {
"ontology": "GENEPIO:0001406",
"type": "integer",
"description": "The number of doses of the vaccine recived by the host.",
"examples": [2]
},
"lab_host": {
"Enums": [
"293/ACE2 Cell Line [GENEPIO:0100041]",
"Caco2 Cell Line [BTO:0000195]",
"Calu3 Cell Line [BTO:0002750]",
"EFK3B Cell Line [GENEPIO:0100042]",
"HEK293T Cell Line [BTO:0002181]",
"HRCE Cell Line [GENEPIO:0100043]",
"Huh7 Cell Line [BTO:0001950]",
"LLCMk2 Cell Line [CLO:0007330]",
"MDBK Cell Line [BTO:0000836]",
"NHBE Cell Line [BTO:0002924]",
"PK-15 Cell Line [BTO:0001865]",
"RK-13 Cell Line [BTO:0002909]",
"U251 Cell Line [BTO:0002035]",
"Vero Cell Line [BTO:0001444]",
"Vero E6 Cell Line [BTO:0004755]",
"Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001255",
"type": "string",
"description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.",
"examples": ["Vero E6 Cell Line [BTO:0004755]"]
},
"anatomical_part": {
"Enums": [
"Anus [UBERON:0001245]",
"Duodenum [UBERON:0002114]",
"Eye [UBERON:0000970]",
"Intestine [UBERON:0000160]",
"Lower respiratory tract [UBERON:0001558]",
"Bronchus [UBERON:0002185]",
"Lung [UBERON:0002048]",
"Bronchiole [UBERON:0002186]",
"Alveolar sac [UBERON:0002169]",
"Pleural sac [UBERON:0009778]",
"Pleural cavity [UBERON:0002402]",
"Trachea [UBERON:0003126]",
"Rectum [UBERON:0001052]",
"Skin [UBERON:0001003]",
"Stomach [UBERON:0000945]",
"Upper respiratory tract [UBERON:0001557]",
"Anterior Nares [UBERON:2001427]",
"Esophagus [UBERON:0001043]",
"Ethmoid sinus [UBERON:0002453]",
"Nasal Cavity [UBERON:0001707]",
"Middle Nasal Turbinate [UBERON:0005921]",
"Inferior Nasal Turbinate [UBERON:0005922]",
"Nasopharynx (NP) [UBERON:0001728]",
"Oropharynx (OP) [UBERON:0001729]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001214",
"type": "string",
"description": "An anatomical part of an organism e.g. oropharynx. ",
"examples": ["Nasopharynx (NP) [UBERON:0001728]"]
},
"host_health_outcome": {
"Enums": [
"Deceased [NCIT:C28554]",
"Deteriorating [NCIT:C25254]",
"Recovered [NCIT:C49498]",
"Stable [NCIT:C30103]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001390",
"type": "string",
"description": "Disease outcome in the host.",
"examples": ["Recovered [NCIT:C49498]"]
},
"sequencing_date": {
"examples": ["22/06/2020"],
"ontology": "GENEPIO:0001447",
"type": "string",
"description": "The date the sample was sequenced.",
"format": "date"
},
"passage_number": {
"ontology": "GENEPIO:0001261",
"type": "integer",
"description": "Number of passages.",
"examples": [3]
},
"ns_per_100_kbp": {
"ontology": "GENEPIO:0001484",
"type": "integer",
"description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.",
"examples": [300]
},
"case_id": {
"ontology": "GENEPIO:0100281",
"type": "string",
"description": "The identifier used to specify an epidemiologically detected case of disease.",
"examples": ["ABCD1234"]
},
"biosample_accession": {
"pattern": "^SAM(D|N|E([AG]?))[0-9]+",
"ontology": "GENEPIO:0001139",
"type": "string",
"description": "The identifier assigned to a BioSample in INSDC archives.",
"examples": ["SAMN14180202"]
},
"last_dose_vacicnation_date": {
"examples": ["09/04/2021"],
"ontology": "GENEPIO:0001408",
"type": "string",
"description": "The date the host received their last dose of vaccine.",
"format": "date"
},
"bioinformatics_protocol": {
"ontology": "GENEPIO:0001489",
"type": "string",
"description": "The name and version number of the bioinformatics protocol used.",
"examples": [
"https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"
]
},
"prior_sars_cov_2_antiviral_treatment": {
"Enums": [
"Prior antiviral treatment [GENEPIO:0100037]",
"No prior antiviral treatment [GENEPIO:0100233]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001438",
"type": "string",
"description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.",
"examples": ["Prior antiviral treatment [GENEPIO:0100037]"]
},
"gene_name_2": {
"Enums": [
"E gene (orf4) [GENEPIO:0100151]",
"M gene (orf5) [GENEPIO:0100152]",
"N gene (orf9) [GENEPIO:0100153]",
"Spike gene (orf2) [GENEPIO:0100154]",
"orf1ab (rep) [GENEPIO:0100155]",
"orf1a (pp1a) [GENEPIO:0100156]",
"nsp11 [GENEPIO:0100157]",
"nsp1 [GENEPIO:0100158]",
"nsp2 [GENEPIO:0100159]",
"nsp3 [GENEPIO:0100160]",
"nsp4 [GENEPIO:0100161]",
"nsp5 [GENEPIO:0100162]",
"nsp6 [GENEPIO:0100163]",
"nsp7 [GENEPIO:0100164]",
"nsp8 [GENEPIO:0100165]",
"nsp9 [GENEPIO:0100166]",
"nsp10 [GENEPIO:0100167]",
"RdRp gene (nsp12) [GENEPIO:0100168]",
"hel gene (nsp13) [GENEPIO:0100169]",
"exoN gene (nsp14) [GENEPIO:0100170]",
"nsp15 [GENEPIO:0100171]",
"nsp16 [GENEPIO:0100172]",
"orf3a [GENEPIO:0100173]",
"orf3b [GENEPIO:0100174]",
"orf6 (ns6) [GENEPIO:0100175]",
"orf7a [GENEPIO:0100176]",
"orf7b (ns7b) [GENEPIO:0100177]",
"orf8 (ns8) [GENEPIO:0100178]",
"orf9b [GENEPIO:0100179]",
"orf9c [GENEPIO:0100180]",
"orf10 [GENEPIO:0100181]",
"orf14 [GENEPIO:0100182]",
"SARS-COV-2 5' UTR [GENEPIO:0100183]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001510",
"type": "string",
"description": "The name of the gene used in the diagnostic RT-PCR test.",
"examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"]
},
"body_product": {
"Enums": [
"Breast Milk [UBERON:0001913]",
"Feces [UBERON:0001988]",
"Mucus [UBERON:0000912]",
"Semen [UBERON:0006530]",
"Sputum [UBERON:0007311]",
"Sweat [UBERON:0001089]",
"Tear [UBERON:0001827]",
"Urine [UBERON:0001088]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001216",
"type": "string",
"description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.",
"examples": ["Feces [UBERON:0001988]"]
},
"host_age": {
"ontology": "GENEPIO:0001392",
"anyOf": [
{ "type": "integer" },
{ "pattern": "\\d+-\\d+", "type": "string" }
],
"description": "Age of host at the time of sampling.",
"examples": [79]
},
"host_ethnicity": {
"ontology": "GECKO:0000061",
"type": "string",
"description": "The self-identified ethnicity(ies) of the host.",
"examples": ["Indigenous, European"]
},
"collection_device": {
"Enums": [
"Air filter [ENVO:00003968]",
"Blood Collection Tube [OBI:0002859]",
"Bronchoscope [OBI:0002826]",
"Collection Container [OBI:0002088]",
"Collection Cup [GENEPIO:0100026]",
"Fibrobronchoscope Brush [OBI:0002825]",
"Filter [GENEPIO:0100103]",
"Fine Needle [OBI:0002827]",
"Microcapillary tube [OBI:0002858]",
"Micropipette [OBI:0001128]",
"Needle [OBI:0000436]",
"Serum Collection Tube [OBI:0002860]",
"Sputum Collection Tube [OBI:0002861]",
"Suction Catheter [OBI:0002831]",
"Swab [GENEPIO:0100027]",
"Urine Collection Tube [OBI:0002862]",
"Virus Transport Medium [OBI:0002866]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001234",
"type": "string",
"description": "The instrument or container used to collect the sample e.g. swab.",
"examples": ["Swab [GENEPIO:0100027]"]
},
"purpose_of_sequencing": {
"Enums": [
"Baseline surveillance (random sampling) [GENEPIO:0100005]",
"Targeted surveillance (non-random sampling) [GENEPIO:0100006]",
"Priority surveillance projects [GENEPIO:0100007]",
"Screening for Variants of Concern (VOC) [GENEPIO:0100008]",
"Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]",
"Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]",
"Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]",
"Re-infection surveillance [GENEPIO:0100010]",
"Vaccine escape surveillance [GENEPIO:0100011]",
"Travel-associated surveillance [GENEPIO:0100012]",
"Domestic travel surveillance [GENEPIO:0100013]",
"Interstate/ interprovincial travel surveillance [GENEPIO:0100275]",
"Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]",
"International travel surveillance [GENEPIO:0100014]",
"Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]",
"Surveillance of international border crossing by air travel [GENEPIO:0100016]",
"Surveillance of international border crossing by ground transport [GENEPIO:0100017]",
"Surveillance from international worker testing [GENEPIO:0100018]",
"Cluster/Outbreak investigation [GENEPIO:0100019]",
"Multi-jurisdictional outbreak investigation [GENEPIO:0100020]",
"Intra-jurisdictional outbreak investigation [GENEPIO:0100021]",
"Research [GENEPIO:0100022]",
"Viral passage experiment [GENEPIO:0100023]",
"Protocol testing [GENEPIO:0100024]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001445",
"type": "string",
"description": "The reason that the sample was sequenced.",
"examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"]
},
"raw_sequence_data_processing_method": {
"ontology": "GENEPIO:0001458",
"type": "string",
"description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.",
"examples": ["Porechop 0.2.3,Porechop 0.2.3"]
},
"sequence_submitter_contact_address": {
"ontology": "GENEPIO:0001167",
"type": "string",
"description": "The mailing address of the agency submitting the sequence.",
"examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"]
},
"depth_of_coverage_threshold": {
"ontology": "GENEPIO:0001475",
"type": "number",
"description": "The threshold used as a cut-off for the depth of coverage.",
"examples": [100.0]
},
"specimen_processing": {
"Enums": [
"Virus Passage [GENEPIO:0100039]",
"RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]",
"Specimens Pooled [OBI:0600016]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001253",
"type": "string",
"description": "Any processing applied to the sample during or after receiving the sample. ",
"examples": ["Virus Passage [GENEPIO:0100039]"]
},
"flow_cell_barcode": {
"ontology": "GENEPIO:0001451",
"type": "string",
"description": "The barcode of the flow cell used for sequencing.",
"examples": ["FAB06069"]
},
"r1_fastq_filename": {
"ontology": "GENEPIO:0001476",
"type": "string",
"description": "The user-specified filename of the r1 FASTQ file.",
"examples": ["ABC123_S1_L001_R1_001.fastq.gz"]
},
"destination_of_most_recent_travel_city": {
"ontology": "GENEPIO:0001411",
"type": "string",
"description": "The name of the city that was the destination of most recent travel.",
"examples": ["New York City"]
},
"r1_fastq_filepath": {
"ontology": "GENEPIO:0001478",
"type": "string",
"description": "The filepath of the r1 FASTQ file.",
"examples": [
"/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz"
]
},
"library_id": {
"ontology": "GENEPIO:0001448",
"type": "string",
"description": "The user-specified identifier for the library prepared for sequencing.",
"examples": ["XYZ_123345"]
},
"host_vaccination_status": {
"Enums": [
"Fully Vaccinated [GENEPIO:0100100]",
"Partially Vaccinated [GENEPIO:0100101]",
"Not Vaccinated [GENEPIO:0100102]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001404",
"type": "string",
"description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).",
"examples": ["Fully Vaccinated [GENEPIO:0100100]"]
},
"geo_loc_longitude": {
"ontology": "OBI:0001621",
"type": "string",
"description": "The longitude coordinates of the geographical location of sample collection.",
"examples": ["77.11 W"]
},
"genbank_ena_ddbj_accession": {
"pattern": "^([a-zA-Z]{2})\\d*.\\d{1}",
"ontology": "GENEPIO:0001145",
"type": "string",
"description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.",
"examples": ["MN908947.3"]
},
"bioproject_accession": {
"pattern": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*",
"ontology": "GENEPIO:0001136",
"type": "string",
"description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs. ",
"examples": ["PRJNA12345"]
},
"lineage_clade_analysis_software_name": {
"ontology": "GENEPIO:0001501",
"type": "string",
"description": "The name of the software used to determine the lineage/clade.",
"examples": ["Pangolin"]
},
"location_of_exposure_geo_loc_name_country": {
"Enums": [
"Afghanistan [GAZ:00006882]",
"Albania [GAZ:00002953]",
"Algeria [GAZ:00000563]",
"American Samoa [GAZ:00003957]",
"Andorra [GAZ:00002948]",
"Angola [GAZ:00001095]",
"Anguilla [GAZ:00009159]",
"Antarctica [GAZ:00000462]",
"Antigua and Barbuda [GAZ:00006883]",
"Argentina [GAZ:00002928]",
"Armenia [GAZ:00004094]",
"Aruba [GAZ:00004025]",
"Ashmore and Cartier Islands [GAZ:00005901]",
"Australia [GAZ:00000463]",
"Austria [GAZ:00002942]",
"Azerbaijan [GAZ:00004941]",
"Bahamas [GAZ:00002733]",
"Bahrain [GAZ:00005281]",
"Baker Island [GAZ:00007117]",
"Bangladesh [GAZ:00003750]",
"Barbados [GAZ:00001251]",
"Bassas da India [GAZ:00005810]",
"Belarus [GAZ:00006886]",
"Belgium [GAZ:00002938]",
"Belize [GAZ:00002934]",
"Benin [GAZ:00000904]",
"Bermuda [GAZ:00001264]",
"Bhutan [GAZ:00003920]",
"Bolivia [GAZ:00002511]",
"Borneo [GAZ:00025355]",
"Bosnia and Herzegovina [GAZ:00006887]",
"Botswana [GAZ:00001097]",
"Bouvet Island [GAZ:00001453]",
"Brazil [GAZ:00002828]",
"British Virgin Islands [GAZ:00003961]",
"Brunei [GAZ:00003901]",
"Bulgaria [GAZ:00002950]",
"Burkina Faso [GAZ:00000905]",
"Burundi [GAZ:00001090]",
"Cambodia [GAZ:00006888]",
"Cameroon [GAZ:00001093]",
"Canada [GAZ:00002560]",
"Cape Verde [GAZ:00001227]",
"Cayman Islands [GAZ:00003986]",
"Central African Republic [GAZ:00001089]",
"Chad [GAZ:00000586]",
"Chile [GAZ:00002825]",
"China [GAZ:00002845]",
"Christmas Island [GAZ:00005915]",
"Clipperton Island [GAZ:00005838]",
"Cocos Islands [GAZ:00009721]",
"Colombia [GAZ:00002929]",
"Comoros [GAZ:00005820]",
"Cook Islands [GAZ:00053798]",
"Coral Sea Islands [GAZ:00005917]",
"Costa Rica [GAZ:00002901]",
"Cote d'Ivoire [GAZ:00000906]",
"Croatia [GAZ:00002719]",
"Cuba [GAZ:00003762]",
"Curacao [GAZ:00012582]",
"Cyprus [GAZ:00004006]",
"Czech Republic [GAZ:00002954]",
"Democratic Republic of the Congo [GAZ:00001086]",
"Denmark [GAZ:00005852]",
"Djibouti [GAZ:00000582]",
"Dominica [GAZ:00006890]",
"Dominican Republic [GAZ:00003952]",
"Ecuador [GAZ:00002912]",
"Egypt [GAZ:00003934]",
"El Salvador [GAZ:00002935]",
"Equatorial Guinea [GAZ:00001091]",
"Eritrea [GAZ:00000581]",
"Estonia [GAZ:00002959]",
"Eswatini [GAZ:00001099]",
"Ethiopia [GAZ:00000567]",
"Europa Island [GAZ:00005811]",
"Falkland Islands (Islas Malvinas) [GAZ:00001412]",
"Faroe Islands [GAZ:00059206]",
"Fiji [GAZ:00006891]",
"Finland [GAZ:00002937]",
"France [GAZ:00003940]",
"French Guiana [GAZ:00002516]",
"French Polynesia [GAZ:00002918]",
"French Southern and Antarctic Lands [GAZ:00003753]",
"Gabon [GAZ:00001092]",
"Gambia [GAZ:00000907]",
"Gaza Strip [GAZ:00009571]",
"Georgia [GAZ:00004942]",
"Germany [GAZ:00002646]",
"Ghana [GAZ:00000908]",
"Gibraltar [GAZ:00003987]",
"Glorioso Islands [GAZ:00005808]",
"Greece [GAZ:00002945]",
"Greenland [GAZ:00001507]",
"Grenada [GAZ:02000573]",
"Guadeloupe [GAZ:00067142]",
"Guam [GAZ:00003706]",
"Guatemala [GAZ:00002936]",
"Guernsey [GAZ:00001550]",
"Guinea [GAZ:00000909]",
"Guinea-Bissau [GAZ:00000910]",
"Guyana [GAZ:00002522]",
"Haiti [GAZ:00003953]",
"Heard Island and McDonald Islands [GAZ:00009718]",
"Honduras [GAZ:00002894]",
"Hong Kong [GAZ:00003203]",
"Howland Island [GAZ:00007120]",
"Hungary [GAZ:00002952]",
"Iceland [GAZ:00000843]",
"India [GAZ:00002839]",
"Indonesia [GAZ:00003727]",
"Iran [GAZ:00004474]",
"Iraq [GAZ:00004483]",
"Ireland [GAZ:00002943]",
"Isle of Man [GAZ:00052477]",
"Israel [GAZ:00002476]",
"Italy [GAZ:00002650]",
"Jamaica [GAZ:00003781]",
"Jan Mayen [GAZ:00005853]",
"Japan [GAZ:00002747]",
"Jarvis Island [GAZ:00007118]",
"Jersey [GAZ:00001551]",
"Johnston Atoll [GAZ:00007114]",
"Jordan [GAZ:00002473]",
"Juan de Nova Island [GAZ:00005809]",
"Kazakhstan [GAZ:00004999]",
"Kenya [GAZ:00001101]",
"Kerguelen Archipelago [GAZ:00005682]",
"Kingman Reef [GAZ:00007116]",
"Kiribati [GAZ:00006894]",
"Kosovo [GAZ:00011337]",
"Kuwait [GAZ:00005285]",
"Kyrgyzstan [GAZ:00006893]",
"Laos [GAZ:00006889]",
"Latvia [GAZ:00002958]",
"Lebanon [GAZ:00002478]",
"Lesotho [GAZ:00001098]",
"Liberia [GAZ:00000911]",
"Libya [GAZ:00000566]",
"Liechtenstein [GAZ:00003858]",
"Line Islands [GAZ:00007144]",
"Lithuania [GAZ:00002960]",
"Luxembourg [GAZ:00002947]",
"Macau [GAZ:00003202]",
"Madagascar [GAZ:00001108]",
"Malawi [GAZ:00001105]",
"Malaysia [GAZ:00003902]",
"Maldives [GAZ:00006924]",
"Mali [GAZ:00000584]",
"Malta [GAZ:00004017]",
"Marshall Islands [GAZ:00007161]",
"Martinique [GAZ:00067143]",
"Mauritania [GAZ:00000583]",
"Mauritius [GAZ:00003745]",
"Mayotte [GAZ:00003943]",
"Mexico [GAZ:00002852]",
"Micronesia [GAZ:00005862]",
"Midway Islands [GAZ:00007112]",
"Moldova [GAZ:00003897]",
"Monaco [GAZ:00003857]",
"Mongolia [GAZ:00008744]",
"Montenegro [GAZ:00006898]",
"Montserrat [GAZ:00003988]",
"Morocco [GAZ:00000565]",
"Mozambique [GAZ:00001100]",
"Myanmar [GAZ:00006899]",
"Namibia [GAZ:00001096]",
"Nauru [GAZ:00006900]",
"Navassa Island [GAZ:00007119]",
"Nepal [GAZ:00004399]",
"Netherlands [GAZ:00002946]",
"New Caledonia [GAZ:00005206]",
"New Zealand [GAZ:00000469]",
"Nicaragua [GAZ:00002978]",
"Niger [GAZ:00000585]",
"Nigeria [GAZ:00000912]",
"Niue [GAZ:00006902]",
"Norfolk Island [GAZ:00005908]",
"North Korea [GAZ:00002801]",
"North Macedonia [GAZ:00006895]",
"North Sea [GAZ:00002284]",
"Northern Mariana Islands [GAZ:00003958]",
"Norway [GAZ:00002699]",
"Oman [GAZ:00005283]",
"Pakistan [GAZ:00005246]",
"Palau [GAZ:00006905]",
"Panama [GAZ:00002892]",
"Papua New Guinea [GAZ:00003922]",
"Paracel Islands [GAZ:00010832]",
"Paraguay [GAZ:00002933]",
"Peru [GAZ:00002932]",
"Philippines [GAZ:00004525]",
"Pitcairn Islands [GAZ:00005867]",
"Poland [GAZ:00002939]",
"Portugal [GAZ:00004126]",
"Puerto Rico [GAZ:00006935]",
"Qatar [GAZ:00005286]",
"Republic of the Congo [GAZ:00001088]",
"Reunion [GAZ:00003945]",
"Romania [GAZ:00002951]",
"Ross Sea [GAZ:00023304]",
"Russia [GAZ:00002721]",
"Rwanda [GAZ:00001087]",
"Saint Helena [GAZ:00000849]",
"Saint Kitts and Nevis [GAZ:00006906]",
"Saint Lucia [GAZ:00006909]",
"Saint Pierre and Miquelon [GAZ:00003942]",
"Saint Martin [GAZ:00005841]",
"Saint Vincent and the Grenadines [GAZ:02000565]",
"Samoa [GAZ:00006910]",
"San Marino [GAZ:00003102]",
"Sao Tome and Principe [GAZ:00006927]",
"Saudi Arabia [GAZ:00005279]",
"Senegal [GAZ:00000913]",
"Serbia [GAZ:00002957]",
"Seychelles [GAZ:00006922]",
"Sierra Leone [GAZ:00000914]",
"Singapore [GAZ:00003923]",
"Sint Maarten [GAZ:00012579]",
"Slovakia [GAZ:00002956]",
"Slovenia [GAZ:00002955]",
"Solomon Islands [GAZ:00005275]",
"Somalia [GAZ:00001104]",
"South Africa [GAZ:00001094]",
"South Georgia and the South Sandwich Islands [GAZ:00003990]",
"South Korea [GAZ:00002802]",
"South Sudan [GAZ:00233439]",
"Spain [GAZ:00003936]",
"Spratly Islands [GAZ:00010831]",
"Sri Lanka [GAZ:00003924]",
"State of Palestine [GAZ:00002475]",
"Sudan [GAZ:00000560]",
"Suriname [GAZ:00002525]",
"Svalbard [GAZ:00005396]",
"Swaziland [GAZ:00001099]",
"Sweden [GAZ:00002729]",
"Switzerland [GAZ:00002941]",
"Syria [GAZ:00002474]",
"Taiwan [GAZ:00005341]",
"Tajikistan [GAZ:00006912]",
"Tanzania [GAZ:00001103]",
"Thailand [GAZ:00003744]",
"Timor-Leste [GAZ:00006913]",
"Togo [GAZ:00000915]",
"Tokelau [GAZ:00260188]",
"Tonga [GAZ:00006916]",
"Trinidad and Tobago [GAZ:00003767]",
"Tromelin Island [GAZ:00005812]",
"Tunisia [GAZ:00000562]",
"Turkey [GAZ:00000558]",
"Turkmenistan [GAZ:00005018]",
"Turks and Caicos Islands [GAZ:00003955]",
"Tuvalu [GAZ:00009715]",
"USA [GAZ:00002459]",
"Uganda [GAZ:00001102]",
"Ukraine [GAZ:00002724]",
"United Arab Emirates [GAZ:00005282]",
"United Kingdom [GAZ:00002637]",
"Uruguay [GAZ:00002930]",
"Uzbekistan [GAZ:00004979]",
"Vanuatu [GAZ:00006918]",
"Venezuela [GAZ:00002931]",
"Viet Nam [GAZ:00003756]",
"Virgin Islands [GAZ:00003959]",
"Wake Island [GAZ:00007111]",
"Wallis and Futuna [GAZ:00007191]",
"West Bank [GAZ:00009572]",
"Western Sahara [GAZ:00000564]",
"Yemen [GAZ:00005284]",
"Zambia [GAZ:00001107]",
"Zimbabwe [GAZ:00001106]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001410",
"type": "string",
"description": "The country where the host was likely exposed to the causative agent of the illness.",
"examples": ["South Africa [GAZ:00001094]"]
},
"sample_plan_name": {
"ontology": "GENEPIO:0100285",
"type": "string",
"description": "The name of the sample plan implemented for sample collection.",
"examples": ["CanCOGeN Sampling Strategy 1.0"]
},
"prior_sars_cov_2_antiviral_treatment_date": {
"examples": ["28/01/2021"],
"ontology": "GENEPIO:0001440",
"type": "string",
"description": "The date treatment was first administered during the prior SARS-CoV-2 infection.",
"format": "date"
},
"library_preparation_kit": {
"ontology": "GENEPIO:0001450",
"type": "string",
"description": "The name of the DNA library preparation kit used to generate the library being sequenced.",
"examples": ["Nextera XT"]
},
"fast5_filename": {
"ontology": "GENEPIO:0001480",
"type": "string",
"description": "The user-specified filename of the FAST5 file.",
"examples": ["batch1a_sequences.fast5"]
},
"diagnostic_pcr_ct_value_1": {
"ontology": "GENEPIO:0001509",
"type": "integer",
"description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"examples": [21]
},
"collection_method": {
"Enums": [
"Amniocentesis [NCIT:C52009]",
"Aspiration [NCIT:C15631]",
"Suprapubic Aspiration [GENEPIO:0100028]",
"Tracheal Aspiration [GENEPIO:0100029]",
"Vacuum Aspiration [GENEPIO:0100030]",
"Biopsy [OBI:0002650]",
"Needle Biopsy [OBI:0002651]",
"Filtration [OBI:0302885]",
"Air Filtration [GENEPIO:0100031]",
"Lavage [OBI:0600044]",
"Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]",
"Gastric Lavage [GENEPIO:0100033]",
"Lumbar Puncture [NCIT:C15327]",
"Necropsy [MMO:0000344]",
"Phlebotomy [NCIT:C28221]",
"Rinsing [GENEPIO:0002116]",
"Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]",
"Scraping [GENEPIO:0100035]",
"Swabbing [GENEPIO:0002117]",
"Finger Prick [GENEPIO:0100036]",
"Washout Tear Collection [GENEPIO:0100038]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001241",
"type": "string",
"description": "The process used to collect the sample e.g. phlebotomy, necropsy.",
"examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"]
},
"geo_loc_name_county_region": {
"ontology": "GENEPIO:0100280",
"type": "string",
"description": "The county/region of origin of the sample.",
"examples": ["Derbyshire"]
},
"consensus_genome_length": {
"ontology": "GENEPIO:0001483",
"type": "integer",
"description": "Size of the assembled genome described as the number of base pairs.",
"examples": [38677]
},
"r2_fastq_filepath": {
"ontology": "GENEPIO:0001479",
"type": "string",
"description": "The filepath of the r2 FASTQ file.",
"examples": [
"/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz"
]
},
"destination_of_most_recent_travel_state_province_territory": {
"ontology": "GENEPIO:0001412",
"type": "string",
"description": "The name of the province that was the destination of most recent travel.",
"examples": ["California"]
},
"sample_received_date": {
"examples": ["20/03/2020"],
"ontology": "GENEPIO:0001179",
"type": "string",
"description": "The date on which the sample was received.",
"format": "date"
},
"host_common_name": {
"Enums": [
"Human [NCBITaxon:9606]",
"Bat [NCBITaxon:9397]",
"Cat [NCBITaxon:9685]",
"Chicken [NCBITaxon:9031]",
"Civet [NCBITaxon:9673]",
"Cow [NCBITaxon:9913]",
"Dog [NCBITaxon:9615]",
"Lion [NCBITaxon:9689]",
"Mink [NCBITaxon:452646]",
"Pangolin [NCBITaxon:9973]",
"Pig [NCBITaxon:9825]",
"Pigeon [NCBITaxon:8930]",
"Tiger [NCBITaxon:9694]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001386",
"type": "string",
"description": "The commonly used name of the host.",
"examples": ["Human [NCBITaxon:9606]"]
},
"geo_loc_name_state_province_territory": {
"ontology": "GENEPIO:0001185",
"type": "string",
"description": "The state/province/territory of origin of the sample.",
"examples": ["Western Cape"]
},
"lineage_clade_analysis_software_version": {
"ontology": "GENEPIO:0001502",
"type": "string",
"description": "The version of the software used to determine the lineage/clade.",
"examples": ["2.1.10"]
},
"host_subject_id": {
"ontology": "GENEPIO:0001398",
"type": "string",
"description": "A unique identifier by which each host can be referred to e.g. #131",
"examples": ["BCxy123"]
},
"sra_accession": {
"pattern": "^(SRR|ERR|DRR)[0-9]+",
"ontology": "GENEPIO:0001142",
"type": "string",
"description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.",
"examples": ["SRR11177792"]
},
"authors": {
"ontology": "GENEPIO:0001517",
"type": "string",
"description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.",
"examples": ["Tejinder Singh, Fei Hu, Johnny Blogs"]
},
"host_role": {
"Enums": [
"Attendee [GENEPIO:0100249]",
"Student [OMRSE:00000058]",
"Patient [OMRSE:00000030]",
"Inpatient [NCIT:C25182]",
"Outpatient [NCIT:C28293]",
"Passenger [GENEPIO:0100250]",
"Resident [GENEPIO:0100251]",
"Visitor [GENEPIO:0100252]",
"Volunteer [GENEPIO:0100253]",
"Work [GENEPIO:0100254]",
"Administrator [GENEPIO:0100255]",
"First Responder [GENEPIO:0100256]",
"Firefighter [GENEPIO:0100257]",
"Paramedic [GENEPIO:0100258]",
"Police Officer [GENEPIO:0100259]",
"Housekeeper [GENEPIO:0100260]",
"Kitchen Worker [GENEPIO:0100261]",
"Laboratory Worker [GENEPIO:0100262]",
"Nurse [OMRSE:00000014]",
"Personal Care Aid [GENEPIO:0100263]",
"Pharmacist [GENEPIO:0100264]",
"Physician [OMRSE:00000013]",
"Vet [GENEPIO:0100265]",
"Social role [OMRSE:00000001]",
"Acquaintance of case [GENEPIO:0100266]",
"Relative of case [GENEPIO:0100267]",
"Child of case [GENEPIO:0100268]",
"Parent of case [GENEPIO:0100269]",
"Father of case [GENEPIO:0100270]",
"Mother of case [GENEPIO:0100271]",
"Spouse of case [GENEPIO:0100272]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",