ERC000041.json

{"id": "ERC000041", "dataTypeId": "samples", "displayName": "ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist", "description": "Minimum information to standardise metadata related to samples used in GMI PT (Global Microbial Identifier Proficiency Test). A checklist for reporting metadata of GMI PT samples associated with molecular data. This minimum metadata standard was developed by the COMPARE platform and can be used for submission of sample metadata derived from Campylobacter coli, Campylobacter jejuni, Listeria monocytogenes, Klebsiella pneumoniae, Salmonella enterica, Escherichia coli and Staphylococcus aureus.", "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}, "nucleic acid extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "library construction method": {"required": false, "allowUnits": false, "allowTerms": false}, "protocol": {"required": false, "allowUnits": false, "allowTerms": false}, "instrument for DNA concentration measurement": {"required": false, "allowUnits": false, "allowTerms": false}, "read quality filter": {"required": false, "allowUnits": false, "allowTerms": false}, "DNA concentration": {"required": false, "allowUnits": false, "allowTerms": false}, "collection_date": {"required": false, "allowUnits": false, "allowTerms": false}, "isolation_source": {"required": false, "allowUnits": false, "allowTerms": false}, "geographic location (country and/or sea)": {"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}, "links to additional analysis": {"required": false, "allowUnits": false, "allowTerms": false}, "isolate": {"required": true, "allowUnits": false, "allowTerms": false}, "sub_species": {"required": false, "allowUnits": false, "allowTerms": false}, "Further Details": {"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": {"$ref": "#/definitions/terms"}, "units": {"minLength": 1, "type": "string"}}}}, "terms": {"type": "array", "items": {"required": ["url"], "type": "object", "properties": {"url": {"format": "uri", "type": "string"}}}}, "properties": {"attributes": {"required": [], "type": "object", "description": "Attributes for describing a sample.", "patternProperties": {"^.*$": {"$ref": "#/definitions/attribute"}}, "properties": {}}}}, "description": "Minimum information to standardise metadata related to samples used in GMI PT (Global Microbial Identifier Proficiency Test). A checklist for reporting metadata of GMI PT samples associated with molecular data. This minimum metadata standard was developed by the COMPARE platform and can be used for submission of sample metadata derived from Campylobacter coli, Campylobacter jejuni, Listeria monocytogenes, Klebsiella pneumoniae, Salmonella enterica, Escherichia coli and Staphylococcus aureus.", "properties": {"attributes": {"required": ["isolate"], "properties": {"protocol": {"maxItems": 1, "description": "The laboratory method used to reveal the presence of the sample sequenced in the experiment.", "items": {}}, "Further Details": {"description": "Reference details related to a sample in form of an URI.", "items": {}}, "sample transportation temperature": {"maxItems": 1, "description": "transportation temperature from sample site to storage", "items": {"required": ["units"]}}, "sample transportation date": {"maxItems": 1, "description": "transportation/shipping date of the sample. Format:YYYY-MM-DD", "items": {"properties": {"value": {"pattern": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"}}}}, "collection_date": {"maxItems": 1, "description": "date that the specimen was collected", "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})?)?)?)?)?$"}}}}, "DNA concentration": {"maxItems": 1, "description": "DNA concentration used for sequencing in ng/\u00c2\u00b5l", "items": {"required": ["units"]}}, "isolate": {"maxItems": 1, "description": "individual isolate from which the sample was obtained", "items": {}}, "library construction method": {"maxItems": 1, "description": "Library construction method used for clone libraries", "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]+)?"}}}}, "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]+)?"}}}}, "isolation_source": {"maxItems": 1, "description": "describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived", "items": {}}, "sample transportation time": {"maxItems": 1, "description": "transportation time from sample site to storage", "items": {}}, "links to additional analysis": {"description": "link to additional analysis results performed on the sample", "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})?)?$"}}}}, "read quality filter": {"description": "Programme used to filter reads quality before conducting the analysis", "items": {}}, "sub_species": {"maxItems": 1, "description": "name of sub-species of organism from which sample was obtained", "items": {}}, "instrument for DNA concentration measurement": {"maxItems": 1, "description": "Name/type of instrument used to measure the DNA concentration (ng/\u00c2\u00b5l) prior to library preparation", "items": {}}, "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": {}}, "sampling time point": {"maxItems": 1, "description": "", "items": {}}, "sample storage location": {"maxItems": 1, "description": "location at which sample was stored, usually name of a specific freezer/room", "items": {}}, "nucleic acid extraction": {"maxItems": 1, "description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}}}}, "required": ["attributes"], "id": "ERC000041", "type": "object", "title": "ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000041"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000041"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000041/spreadsheet.csv"}}}