ERC000028.json

{"id": "ERC000028", "dataTypeId": "samples", "displayName": "ENA prokaryotic pathogen minimal sample checklist", "description": "Minimum information required for a prokaryotic pathogen sample", "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}, "isolation_source": {"required": true, "allowUnits": false, "allowTerms": false}, "lat_lon": {"required": false, "allowUnits": false, "allowTerms": false}, "collected_by": {"required": false, "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 (region and locality)": {"required": false, "allowUnits": false, "allowTerms": false}, "identified_by": {"required": false, "allowUnits": false, "allowTerms": false}, "environmental_sample": {"required": false, "allowUnits": false, "allowTerms": false}, "mating_type": {"required": false, "allowUnits": false, "allowTerms": false}, "host health state": {"required": true, "allowUnits": false, "allowTerms": false}, "lab_host": {"required": false, "allowUnits": false, "allowTerms": false}, "host scientific name": {"required": true, "allowUnits": false, "allowTerms": false}, "bio_material": {"required": false, "allowUnits": false, "allowTerms": false}, "culture_collection": {"required": false, "allowUnits": false, "allowTerms": false}, "specimen_voucher": {"required": false, "allowUnits": false, "allowTerms": false}, "isolate": {"required": true, "allowUnits": false, "allowTerms": false}, "sub_species": {"required": false, "allowUnits": false, "allowTerms": false}, "sub_strain": {"required": false, "allowUnits": false, "allowTerms": false}, "serovar": {"required": false, "allowUnits": false, "allowTerms": false}, "strain": {"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": {"$ref": "#/definitions/terms"}, "units": {"minLength": 1, "type": "string"}}}}, "terms": {"type": "array", "items": {"required": ["url"], "type": "object", "properties": {"url": {"format": "uri", "type": "string"}}}}, "properties": {"attributes": {"required": [], "type": "object", "description": "Attributes for describing a sample.", "patternProperties": {"^.*$": {"$ref": "#/definitions/attribute"}}, "properties": {}}}}, "description": "Minimum information required for a prokaryotic pathogen sample", "properties": {"attributes": {"required": ["isolation_source", "collection date", "geographic location (country and/or sea)", "host health state", "host scientific name", "isolate"], "properties": {"identified_by": {"description": "name of the expert who identified the specimen taxonomically", "items": {}}, "environmental_sample": {"description": "identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism", "items": {"properties": {"value": {"enum": ["No", "Yes"]}}}}, "specimen_voucher": {"description": "identifier for the specimen from which the sample was obtained", "items": {}}, "collection date": {"description": "The date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.", "items": {"properties": {"value": {"pattern": "(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "isolate": {"description": "individual isolate from which the sample was obtained", "items": {}}, "host health state": {"description": "Health status of the host at the time of sample collection.", "items": {"properties": {"value": {"enum": ["diseased", "healthy", "not applicable", "not collected", "not provided", "restricted access"]}}}}, "serovar": {"description": "serological variety of a species (usually a prokaryote) characterized by its antigenic properties", "items": {}}, "sub_strain": {"description": "name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained", "items": {}}, "isolation_source": {"description": "describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived", "items": {}}, "collected_by": {"description": "name of persons or institute who collected the specimen", "items": {}}, "lab_host": {"description": "scientific name of the laboratory host used to propagate the source organism from which the sample was obtained", "items": {}}, "sub_species": {"description": "name of sub-species of organism from which sample was obtained", "items": {}}, "geographic location (region and locality)": {"description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.", "items": {}}, "geographic location (country and/or sea)": {"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"]}}}}, "strain": {"description": "Name of the strain from which the sample was obtained.", "items": {}}, "bio_material": {"description": "identifier for the biological material from which the sample was obtained, with optional institution code and collection code for the place where it is currently stored.", "items": {}}, "host scientific name": {"description": "Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.", "items": {}}, "lat_lon": {"description": "geographical coordinates of the location where the specimen was collected", "items": {}}, "mating_type": {"description": "mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes", "items": {}}, "culture_collection": {"description": "institution code and identifier for the culture from which the sample was obtained, with optional collection code.", "items": {}}}}}, "required": ["attributes"], "id": "ERC000028", "type": "object", "title": "ENA prokaryotic pathogen minimal sample checklist", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000028"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000028"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000028/spreadsheet.csv"}}}