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ERC000036.json
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ERC000036.json
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{"id": "ERC000036", "dataTypeId": "samples", "displayName": "ENA sewage checklist", "description": "Minimum information about sewage samples. A checklist for reporting of sewage surveillance samples associated with sequence data from metagenomic sequencing projects. This minimum metadata standard was developed by the COMPARE platform.", "spreadsheetTemplate": {"columnCaptures": {"alias": {"fieldName": "alias", "fieldType": "String", "required": true}, "title": {"fieldName": "title", "fieldType": "String", "required": true}, "description": {"fieldName": "description", "fieldType": "String", "required": false}, "release date": {"fieldName": "releaseDate", "required": true}, "taxon": {"fieldName": "taxon", "fieldType": "String", "required": true}, "taxon id": {"fieldName": "taxonId", "fieldType": "IntegerNumber", "required": true}, "name of the sampling site": {"required": false, "allowUnits": false, "allowTerms": false}, "nucleic acid extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "nucleic acid amplification": {"required": false, "allowUnits": false, "allowTerms": false}, "investigation type": {"required": true, "allowUnits": false, "allowTerms": false}, "collection date": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (country and/or sea)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (latitude)": {"required": false, "allowUnits": false, "allowTerms": false}, "geographic location (longitude)": {"required": false, "allowUnits": false, "allowTerms": false}, "geographic location (region and locality)": {"required": false, "allowUnits": false, "allowTerms": false}, "amount or size of sample collected": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage duration": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage location": {"required": false, "allowUnits": false, "allowTerms": false}, "sampling time point": {"required": false, "allowUnits": false, "allowTerms": false}, "sample transportation temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "sample transportation date": {"required": false, "allowUnits": false, "allowTerms": false}, "sample transportation time": {"required": false, "allowUnits": false, "allowTerms": false}, "receipt date": {"required": false, "allowUnits": false, "allowTerms": false}, "sewage type": {"required": true, "allowUnits": false, "allowTerms": false}, "temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "area of sampling site": {"required": false, "allowUnits": false, "allowTerms": false}, "size of the catchment area": {"required": false, "allowUnits": false, "allowTerms": false}, "population size of the catchment area": {"required": false, "allowUnits": false, "allowTerms": false}}, "defaultCapture": {"required": false, "allowUnits": false, "allowTerms": false}}, "version": 1, "new": true, "validationSchema": {"version": "1.0.0", "author": "ENA", "definitions": {"attribute": {"type": "array", "minItems": 1, "items": {"required": ["value"], "properties": {"value": {"minLength": 1, "type": "string"}, "terms": {"$ref": "#/definitions/terms"}, "units": {"minLength": 1, "type": "string"}}}}, "terms": {"type": "array", "items": {"required": ["url"], "type": "object", "properties": {"url": {"format": "uri", "type": "string"}}}}, "properties": {"attributes": {"required": [], "type": "object", "description": "Attributes for describing a sample.", "patternProperties": {"^.*$": {"$ref": "#/definitions/attribute"}}, "properties": {}}}}, "description": "Minimum information about sewage samples. A checklist for reporting of sewage surveillance samples associated with sequence data from metagenomic sequencing projects. This minimum metadata standard was developed by the COMPARE platform.", "properties": {"attributes": {"required": ["investigation type", "collection date", "geographic location (country and/or sea)", "sewage type"], "properties": {"sample transportation temperature": {"maxItems": 1, "description": "transportation temperature from sample site to storage", "items": {"required": ["units"]}}, "sample transportation date": {"description": "transportation/shipping date of the sample. Format:YYYY-MM-DD", "items": {"properties": {"value": {"pattern": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"}}}}, "investigation type": {"maxItems": 1, "description": "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardised by Genomic Standards Consortium", "items": {"properties": {"value": {"enum": ["bacteria_archaea", "eukaryote", "metagenome", "metagenome-assembled genome", "metatranscriptome", "mimarks-specimen", "mimarks-survey", "organelle", "plasmid", "single amplified genome", "uncultivated viral genomes", "virus"]}}}}, "sewage type": {"maxItems": 1, "description": "Type of sewage based on origin: wastewater treatment plant (municipal or industrial), open sewer line, river, stream, stagnant pool, or other.", "items": {}}, "size of the catchment area": {"maxItems": 1, "description": "Refers to the size of the area that is drained by the sampled sewage system in square km.", "items": {}}, "collection date": {"maxItems": 1, "description": "The date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.", "items": {"properties": {"value": {"pattern": "(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "geographic location (longitude)": {"maxItems": 1, "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "area of sampling site": {"description": "Please indicate if there are specific facilities in the area covered by the sewage sample. For example: farming, slaughterhouse(s), industry, hospital(s) or any other facility.", "items": {}}, "amount or size of sample collected": {"maxItems": 1, "description": "Amount or size of sample (volume, mass or area) that was collected", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "temperature": {"maxItems": 1, "description": "temperature of the sample at time of sampling", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample storage duration": {"maxItems": 1, "description": "duration for which sample was stored", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample storage temperature": {"maxItems": 1, "description": "temperature at which sample was stored, e.g. -80", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "name of the sampling site": {"maxItems": 1, "description": "Refers to the name of the site/station where data/sample collection is performed.", "items": {}}, "geographic location (latitude)": {"maxItems": 1, "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "sample transportation time": {"description": "transportation time from sample site to storage", "items": {}}, "receipt date": {"maxItems": 1, "description": "Date on which the sample was received. Format:YYYY-MM-DD. Please provide the highest precision possible. If the sample was received by the institution and not collected, the 'receipt date' must be provided instead. Either the 'collection date' or 'receipt date' must be provided. If available, provide both dates.", "items": {"properties": {"value": {"pattern": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"}}}}, "geographic location (country and/or sea)": {"maxItems": 1, "description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).", "items": {"properties": {"value": {"enum": ["Afghanistan", "Albania", "Algeria", "American Samoa", "Andorra", "Angola", "Anguilla", "Antarctica", "Antigua and Barbuda", "Arctic Ocean", "Argentina", "Armenia", "Aruba", "Ashmore and Cartier Islands", "Atlantic Ocean", "Australia", "Austria", "Azerbaijan", "Bahamas", "Bahrain", "Baker Island", "Baltic Sea", "Bangladesh", "Barbados", "Bassas da India", "Belarus", "Belgium", "Belize", "Benin", "Bermuda", "Bhutan", "Bolivia", "Borneo", "Bosnia and Herzegovina", "Botswana", "Bouvet Island", "Brazil", "British Virgin Islands", "Brunei", "Bulgaria", "Burkina Faso", "Burundi", "Cambodia", "Cameroon", "Canada", "Cape Verde", "Cayman Islands", "Central African Republic", "Chad", "Chile", "China", "Christmas Island", "Clipperton Island", "Cocos Islands", "Colombia", "Comoros", "Cook Islands", "Coral Sea Islands", "Costa Rica", "Cote d'Ivoire", "Croatia", "Cuba", "Curacao", "Cyprus", "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", "Dominica", "Dominican Republic", "East Timor", "Ecuador", "Egypt", "El Salvador", "Equatorial Guinea", "Eritrea", "Estonia", "Ethiopia", "Europa Island", "Falkland Islands (Islas Malvinas)", "Faroe Islands", "Fiji", "Finland", "France", "French Guiana", "French Polynesia", "French Southern and Antarctic Lands", "Gabon", "Gambia", "Gaza Strip", "Georgia", "Germany", "Ghana", "Gibraltar", "Glorioso Islands", "Greece", "Greenland", "Grenada", "Guadeloupe", "Guam", "Guatemala", "Guernsey", "Guinea", "Guinea-Bissau", "Guyana", "Haiti", "Heard Island and McDonald Islands", "Honduras", "Hong Kong", "Howland Island", "Hungary", "Iceland", "India", "Indian Ocean", "Indonesia", "Iran", "Iraq", "Ireland", "Isle of Man", "Israel", "Italy", "Jamaica", "Jan Mayen", "Japan", "Jarvis Island", "Jersey", "Johnston Atoll", "Jordan", "Juan de Nova Island", "Kazakhstan", "Kenya", "Kerguelen Archipelago", "Kingman Reef", "Kiribati", "Kosovo", "Kuwait", "Kyrgyzstan", "Laos", "Latvia", "Lebanon", "Lesotho", "Liberia", "Libya", "Liechtenstein", "Lithuania", "Luxembourg", "Macau", "Macedonia", "Madagascar", "Malawi", "Malaysia", "Maldives", "Mali", "Malta", "Marshall Islands", "Martinique", "Mauritania", "Mauritius", "Mayotte", "Mediterranean Sea", "Mexico", "Micronesia", "Midway Islands", "Moldova", "Monaco", "Mongolia", "Montenegro", "Montserrat", "Morocco", "Mozambique", "Myanmar", "Namibia", "Nauru", "Navassa Island", "Nepal", "Netherlands", "New Caledonia", "New Zealand", "Nicaragua", "Niger", "Nigeria", "Niue", "Norfolk Island", "North Korea", "North Sea", "Northern Mariana Islands", "Norway", "Oman", "Pacific Ocean", "Pakistan", "Palau", "Palmyra Atoll", "Panama", "Papua New Guinea", "Paracel Islands", "Paraguay", "Peru", "Philippines", "Pitcairn Islands", "Poland", "Portugal", "Puerto Rico", "Qatar", "Republic of the Congo", "Reunion", "Romania", "Ross Sea", "Russia", "Rwanda", "Saint Helena", "Saint Kitts and Nevis", "Saint Lucia", "Saint Pierre and Miquelon", "Saint Vincent and the Grenadines", "Samoa", "San Marino", "Sao Tome and Principe", "Saudi Arabia", "Senegal", "Serbia", "Seychelles", "Sierra Leone", "Singapore", "Sint Maarten", "Slovakia", "Slovenia", "Solomon Islands", "Somalia", "South Africa", "South Georgia and the South Sandwich Islands", "South Korea", "Southern Ocean", "Spain", "Spratly Islands", "Sri Lanka", "Sudan", "Suriname", "Svalbard", "Swaziland", "Sweden", "Switzerland", "Syria", "Taiwan", "Tajikistan", "Tanzania", "Tasman Sea", "Thailand", "Togo", "Tokelau", "Tonga", "Trinidad and Tobago", "Tromelin Island", "Tunisia", "Turkey", "Turkmenistan", "Turks and Caicos Islands", "Tuvalu", "USA", "Uganda", "Ukraine", "United Arab Emirates", "United Kingdom", "Uruguay", "Uzbekistan", "Vanuatu", "Venezuela", "Viet Nam", "Virgin Islands", "Wake Island", "Wallis and Futuna", "West Bank", "Western Sahara", "Yemen", "Zambia", "Zimbabwe", "not applicable", "not collected", "not provided", "restricted access"]}}}}, "geographic location (region and locality)": {"maxItems": 1, "description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.", "items": {}}, "nucleic acid amplification": {"description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}, "sampling time point": {"maxItems": 1, "description": "", "items": {}}, "population size of the catchment area": {"maxItems": 1, "description": "Refers to the number of people living in the area covered by the sewage system.", "items": {}}, "sample storage location": {"maxItems": 1, "description": "location at which sample was stored, usually name of a specific freezer/room", "items": {}}, "nucleic acid extraction": {"description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}}}}, "required": ["attributes"], "id": "ERC000036", "type": "object", "title": "ENA sewage checklist", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000036"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000036"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000036/spreadsheet.csv"}}}