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relecov_schema.json
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relecov_schema.json
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{
"schema": "https://json-schema.org/draft/2020-12/schema",
"id": "https://github.com/BU-ISCIII/relecov-tools/blob/develop/relecov_tools/schema/relecov_schema.json",
"title": "RELECOV schema",
"description":"Json schema that specifies the structure, content, and validation rules for RELECOV metadata",
"version": "2.1.0",
"required": [
"collecting_lab_sample_id",
"sequencing_sample_id",
"collecting_institution",
"submitting_institution",
"sample_collection_date",
"geo_loc_country",
"geo_loc_state",
"organism",
"isolate_sample_id",
"host_scientific_name",
"sequencing_instrument_model",
"sequencing_instrument_platform",
"library_source",
"library_layout",
"enrichment_panel",
"enrichment_panel_version"
],
"type": "object",
"properties": {
"public_health_sample_id_sivies": {
"examples": [
"2022CEU03926"
],
"ontology": "0",
"type": "string",
"description": "",
"classification": "Sample collection and processing",
"label": "Public Health sample id (SIVIES)",
"fill_mode": "sample",
"minLenght": "1"
},
"collecting_lab_sample_id": {
"examples": [
"prov_rona_99"
],
"ontology": "GENEPIO:0001123",
"type": "string",
"description": "The name given for the sample by the collecting institution.",
"classification": "Database Identifiers",
"label": "Sample ID given by originating laboratory",
"fill_mode": "sample",
"minLenght": "1"
},
"collecting_institution": {
"examples": [
"Public Health Agency of Canada"
],
"ontology": "GENEPIO:0001153",
"type": "string",
"description": "The name of the agency/institution that collected the sample.",
"classification": "Sample collection and processing",
"label": "Originating Laboratory",
"fill_mode": "sample",
"minLenght": "1"
},
"collecting_institution_email": {
"examples": [
],
"ontology": "OBI:0001890",
"type": "string",
"description": "The email address of the contact responsible for follow-up regarding the sample.",
"classification": "Sample collection and processing",
"label": "Originating Laboratory Email",
"fill_mode": "batch"
},
"collecting_institution_address": {
"examples": [
"655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada"
],
"ontology": "GENEPIO:0001158",
"type": "string",
"description": "The mailing address of the agency submitting the sample.",
"classification": "Sample collection and processing",
"label": "Originating Laboratory Address",
"fill_mode": "batch"
},
"microbiology_lab_sample_id": {
"examples": [
""
],
"ontology": "0",
"type": "string",
"description": "",
"classification": "Sample collection and processing",
"label": "Sample ID given in the microbiology lab",
"fill_mode": "sample",
"minLenght": "1"
},
"isolate_sample_id": {
"examples": [
""
],
"ontology": "GENEPIO:0001644",
"type": "string",
"description": "",
"classification": "Database Identifiers",
"label": "Sample ID given if multiple rna-extraction or passages",
"fill_mode": "sample",
"minLenght": "1"
},
"sequencing_sample_id": {
"examples": [
""
],
"ontology": "GENEPIO:0000079",
"type": "string",
"description": "If the information is unknown or can not be shared, leave blank.",
"classification": "Database Identifiers",
"label": "Sample ID given for sequencing",
"fill_mode": "sample",
"minLenght": "1"
},
"sequencing_institution": {
"ontology": "GENEPIO:0100416",
"type": "string",
"description": "The name of the agency that generated the sequence",
"classification": "Sequencing",
"label": "Sequencing Institution",
"fill_mode": "sample",
"minLenght": "1"
},
"submitting_lab_sample_id": {
"examples": [
""
],
"ontology": "GENEPIO:0001148",
"type": "string",
"description": "Sample ID given by the submitting laboratory",
"classification": "Sequencing",
"label": "Sample ID given by the submitting laboratory",
"fill_mode": "sample",
"minLenght": "1"
},
"submitting_institution": {
"examples": [
"Centers for Disease Control and Prevention"
],
"ontology": "GENEPIO:0001159",
"type": "string",
"description": "The name of the agency that submitted the sequence to public databases.",
"classification": "Sample collection and processing",
"label": "Submitting Institution",
"fill_mode": "sample",
"minLenght": "1"
},
"submitting_institution_email": {
"examples": [
],
"ontology": "GENEPIO:0001165",
"type": "string",
"description": "The email address of the contact responsible for follow-up regarding the sequence.",
"classification": "Sample collection and processing",
"label": "Submitting Institution Email",
"fill_mode": "batch"
},
"submitting_institution_address": {
"examples": [
"123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"
],
"ontology": "GENEPIO:0001167",
"type": "string",
"description": "The mailing address of the agency submitting the sequence.",
"classification": "Sample collection and processing",
"label": "Submitting Institution Address",
"fill_mode": "batch"
},
"sample_collection_date": {
"examples": [
"3/19/2020"
],
"ontology": "GENEPIO:0001174",
"type": "string",
"description": "The date on which the sample was collected.",
"format": "date",
"classification": "Sample collection and processing",
"label": "Sample Collection Date",
"fill_mode": "sample",
"minLenght": "1"
},
"sample_received_date": {
"examples": [
"3/21/2020"
],
"ontology": "NCIT:C93644",
"type": "string",
"description": "The date on which the sample was received.",
"format": "date",
"classification": "Sample collection and processing",
"label": "Sample Received Date",
"fill_mode": "sample"
},
"sample_storage_conditions": {
"examples": [
"24 degrees celsius"
],
"ontology": "NCIT:C115535",
"type": "string",
"description": "The name and version of a particular protocol used for sampling.",
"classification": "Sample collection and processing",
"label": "Biological Sample Storage Condition",
"fill_mode": "batch"
},
"geo_loc_country": {
"enum": [
"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 [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]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001181",
"type": "string",
"description": "The country of origin of the sample.",
"examples": [
"South Africa [GAZ:00001094]"
],
"classification": "Sample collection and processing",
"label": "Country",
"fill_mode": "batch",
"minLenght": "1"
},
"geo_loc_state": {
"examples": [
"Western Cape"
],
"ontology": "GENEPIO:0001185",
"type": "string",
"description": "The state/province/territory of origin of the sample.",
"classification": "Sample collection and processing",
"label": "Autonomic Community",
"fill_mode": "batch",
"minLenght": "1"
},
"geo_loc_region": {
"examples": [
"Derbyshire"
],
"ontology": "NCIT:C87189",
"type": "string",
"description": "The county/region of origin of the sample.",
"classification": "Sample collection and processing",
"label": "Province",
"fill_mode": "batch"
},
"geo_loc_city": {
"examples": [
"Vancouver"
],
"ontology": "GENEPIO:0001189",
"type": "string",
"description": "The city of origin of the sample.",
"classification": "Sample collection and processing",
"label": "City",
"fill_mode": "batch"
},
"geo_loc_latitude": {
"examples": [
"38.98 N"
],
"ontology": "OBI:0001620",
"type": "string",
"description": "The latitude coordinates of the geographical location of sample collection.",
"classification": "Sample collection and processing",
"label": "Geo Loc Latitude",
"fill_mode": "batch"
},
"study_type": {
"examples": [
""
],
"enum": [
"Whole Genome Sequencing [NCIT:C101294]",
"Metagenomics [NCIT:C153191]",
"Transcriptome Analysis [GENEPIO:0001111]",
"Resequencing [NCIT:C41254]",
"Epigenetics [OMIT:0027036] ",
"Synthetic Genomics [NCIT:C84343]",
"Forensic or Paleo-genomics [topic:3943]",
"Gene Regulation Study [topic:0204]",
"Cancer Genomics [NCIT:C18247]",
"Population Genomics [topic:3796]",
"RNASeq [OBI:0001177]",
"Exome Sequencing [OBI:0002118]",
"Pooled Clone Sequencing [OBI:2100402]",
"Transcriptome Sequencing [NCIT:C124261]",
"Other [NCIT:C17649]"
],
"ontology": "GENEPIO:0000156",
"type": "string",
"description": "",
"classification": "Submission ENA",
"label": "Study type",
"fill_mode": "batch"
},
"geo_loc_longitude": {
"examples": [
"77.11 W"
],
"ontology": "OBI:0001621",
"type": "string",
"description": "The longitude coordinates of the geographical location of sample collection.",
"classification": "Sample collection and processing",
"label": "Geo Loc Longitude",
"fill_mode": "batch"
},
"purpose_sampling": {
"enum": [
"Cluster/Outbreak Investigation [GENEPIO:0100001]",
"Diagnostic Testing [GENEPIO:0100002]",
"Research [GENEPIO:0100003]",
"Protocol Testing [GENEPIO:0100024]",
"Surveillance [GENEPIO:0100004]",
"Other [NCIT:C124261]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001198",
"type": "string",
"description": "The reason that the sample was collected.",
"examples": [
"Diagnostic Testing [GENEPIO:0100002]"
],
"classification": "Sample collection and processing",
"label": "Purpose of sampling",
"fill_mode": "batch"
},
"anatomical_material": {
"enum": [
"Blood [UBERON:0000178]",
"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]",
"Placenta [UBERON:0001987]",
"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]"
],
"classification": "Sample collection and processing",
"label": "Anatomical Material",
"fill_mode": "batch"
},
"specimen_source": {
"enum": [
"Lower respiratory tract Aspiration",
"Bronchus Aspiration",
"Lung Aspiration",
"Bronchiole Aspiration",
"Alveolar sac Aspiration",
"Pleural sac Aspiration",
"Pleural cavity Aspiration",
"Trachea Aspiration",
"Upper respiratory tract Aspiration",
"Anterior Nares Aspiration",
"Esophagus Aspiration",
"Ethmoid sinus Aspiration",
"Nasal Cavity Aspiration",
"Middle Nasal Turbinate Aspiration",
"Pharynx Aspiration",
"Nasopharynx Aspiration",
"Oropharynx Aspiration",
"Lower respiratory tract Vacuum Aspiration",
"Bronchus Vacuum Aspiration",
"Lung Vacuum Aspiration",
"Bronchiole Vacuum Aspiration",
"Alveolar sac Vacuum Aspiration",
"Pleural sac Vacuum Aspiration",
"Pleural cavity Vacuum Aspiration",
"Trachea Vacuum Aspiration",
"Upper respiratory tract Vacuum Aspiration",
"Anterior Nares Vacuum Aspiration",
"Esophagus Vacuum Aspiration",
"Ethmoid sinus Vacuum Aspiration",
"Nasal Cavity Vacuum Aspiration",
"Middle Nasal Turbinate Vacuum Aspiration",
"Nasopharynx Vacuum Aspiration",
"Oropharynx Vacuum Aspiration",
"Lower respiratory tract Biopsy",
"Bronchus Biopsy",
"Lung biopsy",
"Bronchiole Biopsy",
"Alveolar sac Biopsy",
"Pleural sac Biopsy",
"Pleural cavity Biopsy",
"Trachea Biopsy",
"Rectum Biopsy",
"Skin Biopsy",
"Stomach Biopsy",
"Upper respiratory tract Biopsy",
"Anterior Nares Biopsy",
"Esophagus Biopsy",
"Ethmoid sinus Biopsy",
"Nasal Cavity Biopsy",
"Middle Nasal Turbinate Biopsy",
"Anus Biopsy",
"Duodenum Biopsy",
"Nasopharynx Biopsy",
"Oropharynx Biopsy",
"Lower respiratory tract Needle Biopsy",
"Bronchus Needle Biopsy",
"Lung Needle Biopsy",
"Bronchiole Needle Biopsy",
"Alveolar sac Needle Biopsy",
"Pleural sac Needle Biopsy",
"Pleural cavity Needle Biopsy",
"Trachea Needle Biopsy",
"Rectum Needle Biopsy",
"Skin Needle Biopsy",
"Stomach Needle Biopsy",
"Upper respiratory tract Needle Biopsy",
"Anterior Nares Needle Biopsy",
"Esophagus Needle Biopsy",
"Ethmoid sinus Needle Biopsy",
"Nasal Cavity Needle Biopsy",
"Middle Nasal Turbinate Needle Biopsy",
"Anus Needle Biopsy",
"Duodenum Needle Biopsy",
"Nasopharynx Needle Biopsy",
"Oropharynx Needle Biopsy",
"Lower respiratory tract Lavage ",
"Pleural sac Lavage ",
"Pleural cavity Lavage ",
"Trachea Lavage ",
"Upper respiratory tract Lavage ",
"Anterior Nares Lavage ",
"Esophagus Lavage ",
"Ethmoid sinus Lavage ",
"Nasal Cavity Lavage ",
"Middle Nasal Turbinate Lavage ",
"Nasopharynx Lavage ",
"Oropharynx Lavage ",
"Bronchoalveolar Lavage",
"Gastric Lavage",
"Lower respiratory tract Necropsy",
"Bronchus Necropsy",
"Lung Necropsy",
"Bronchiole Necropsy",
"Alveolar sac Necropsy",
"Pleural sac Necropsy",
"Pleural cavity Necropsy",
"Trachea Necropsy",
"Rectum Necropsy",
"Skin Necropsy",
"Stomach Necropsy",
"Upper respiratory tract Necropsy",
"Anterior Nares Necropsy",
"Esophagus Necropsy",
"Ethmoid sinus Necropsy",
"Nasal Cavity Necropsy",
"Middle Nasal Turbinate Necropsy",
"Anus Necropsy",
"Duodenum Necropsy",
"Nasopharynx (NP) Necropsy",
"Oropharynx (OP) Necropsy",
"Lower respiratory tract Rinsing",
"Bronchus Rinsing",
"Lung Rinsing",
"Bronchiole Rinsing",
"Alveolar sac Rinsing",
"Pleural sac Rinsing",
"Pleural cavity Rinsing",
"Trachea Rinsing",
"Upper respiratory tract Rinsing",
"Anterior Nares Rinsing",
"Esophagus Rinsing",
"Ethmoid sinus Rinsing",
"Nasal Cavity Rinsing",
"Middle Nasal Turbinate Rinsing",
"Nasopharynx Rinsing",
"Oropharynx Rinsing",
"Bronchiole Scraping",
"Alveolar sac Scraping",
"Pleural sac Scraping",
"Pleural cavity Scraping",
"Trachea Scraping",
"Upper respiratory tract Scraping",
"Anterior Nares Scraping",
"Esophagus Scraping",
"Ethmoid sinus Scraping",
"Nasal Cavity Scraping",
"Middle Nasal Turbinate Scraping",
"Nasopharynx Scraping",
"Oropharynx Scraping",
"Nasopharynx swab",
"Oropharynx Swab",
"Pharynx Swab",
"Lower respiratory tract Wash",
"Bronchus Wash",
"Lung Wash",
"Bronchiole Wash",
"Alveolar sac Wash",
"Pleural sac Wash",
"Pleural cavity Wash",
"Trachea Wash",
"Upper respiratory tract Wash",
"Anterior Nares Wash",
"Esophagus Wash",
"Ethmoid sinus Wash",
"Nasal Cavity Wash",
"Middle Nasal Turbinate Wash",
"Nasopharynx Wash",
"Oropharynx Wash",
"Feces",
"Mucus",
"Sputum",
"Sweat",
"Tear",
"Urine",
"Blood",
"Fluid (Cerebrospinal (CSF))",
"Saliva",
"Tissue",
"Placenta",
"Scraping",
"Not Applicable",
"Not Collected",
"Not Provided",
"Missing",
"Restricted Access",
"Not Provided [GENEPIO:0001668]"
],
"ontology": "GENEPIO:0001211",
"type": "string",
"description": "Source of the specimen, merge of anatomical_part, anatomical_material, body_product and collection method.",
"examples": [
""
],
"classification": "Sample collection and processing",
"label": "Specimen source",
"fill_mode": "batch"
},
"anatomical_part": {
"enum": [
"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:0001762]",
"Anus [UBERON:0001245]",
"Duodenum [UBERON:0002114]",
"Pharynx [UBERON:0006562]",
"Nasopharynx [UBERON:0001728]",
"Oropharynx [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": "",
"examples": [
""
],
"classification": "Sample collection and processing",
"label": "Anatomical Part",
"fill_mode": "batch"
},
"collection_device": {
"enum": [
"Air filter [ENVO:00003968]",
"Blood Collection Tube [NCIT:C113122]",
"Bronchoscope [NCIT:C17611]",
"Collection Container [NCIT:C43446]",
"Collection Cup [GENEPIO:0100026]",
"Filter [NCIT:C45801]",
"Needle [NCIT:C69013]",
"Serum Collection Tube [NCIT:C113675]",
"Sputum Collection Tube [GENEPIO:0002115]",
"Suction Catheter [58253008]",
"Swab [GENEPIO:0100027]",
"Other [NCIT:C17649]",
"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": "",
"examples": [
""
],
"classification": "Sample collection and processing",
"label": "Collection Device",
"fill_mode": "batch"
},
"collection_method": {
"enum": [
"Amniocentesis [NCIT:C52009]",
"Suprapublic Aspiration [GENEPIO:0100028]",
"Tracheal Aspiration [GENEPIO:0100029]",
"Vacuum Aspiration [GENEPIO:0100030]",
"Needle Biopsy [OBI:0002654]",
"Filtration [NCIT:C16583]",
"Lavage [NCIT:C38068]",
"Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]",
"Gastric Lavage [GENEPIO:0100033]",
"Lumbar Puncture [NCIT:C15327]",
"Necropsy [NCIT:C166270]",
"Phlebotomy [NCIT:C28221]",
"Rinsing [GENEPIO:0002116]",
"Scraping [GENEPIO:0100035]",
"Swab [NCIT:C17627]",
"Finger Pick [GENEPIO:0100036]",
"Wash [NCIT:C65077]",
"Washout Tear Collection [GENEPIO:0100038]",
"Inferior Nasal Turbinate [NCIT:C32794]",
"Aspiration [NCIT:C15631]",
"Biopsy [NCIT:C15189]",
"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": "",
"examples": [
""
],
"classification": "Sample collection and processing",
"label": "Collection Method",
"fill_mode": "batch"
},
"body_product": {
"enum": [
"Breast Milk [UBERON:0001913]",
"Feces [UBERON:0001988]",
"Mucus [UBERON:0000912]",
"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": "",
"examples": [
""
],
"classification": "Sample collection and processing",
"label": "Body Product",
"fill_mode": "batch"
},
"environmental_material": {
"enum": [
"Air vent [ENVO:03501208]",
"Banknote [ENVO:00003896]",
"Bed rail [ENVO:03501209]",
"Building Floor [ENVO:01000486]",
"Cloth [ENVO:02000058]",
"Control Panel [ENVO:03501210]",
"Door [ENVO:03501220]",
"Door Handle [ENVO:03501211]",
"Face Mask [OBI:0002787]",
"Face Shield [OBI:0002791]",
"Food [FOODON:00002403]",
"Food Packaging [FOODON:03490100]",
"Glass [ENVO:01000481]",
"Handrail [ENVO:03501212]",
"Hospital Gown [OBI:0002796]",
"Light Switch [ENVO:03501213]",
"Locker [ENVO:03501214]",
"N95 Mask [OBI:0002790]",
"Nurse Call Button [ENVO:03501215]",
"Paper [ENVO:03501256]",
"Particulate matter [ENVO:01000060]",
"Plastic [ENVO:01000404]",
"PPE Gown [GENEPIO:0100025]",
"Sewage [ENVO:00002018]",
"Sink [ENVO:01000990]",
"Soil [ENVO:00001998]",
"Stainless Steel [ENVO:03501216]",
"Tissue Paper [ENVO:03501217]",
"Toilet Bowl [ENVO:03501218]",
"Water [ENVO:00002006]",
"Wastewater [ENVO:00002001]",
"Window [ENVO:03501219]",
"Wood [ENVO:00002040]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Other [NCIT:C17649]",