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ERC000029.json
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ERC000029.json
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{"id": "ERC000029", "dataTypeId": "samples", "displayName": "ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1", "description": "Minimum Data for Matching (MDM). A checklist for reporting metadata of pathogen samples for the Global Microbial Identifier (GMI) reporting system. More about GMI can be found here http://www.g-m-i.org/", "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}, "subject exposure": {"required": false, "allowUnits": false, "allowTerms": false}, "subject exposure duration": {"required": false, "allowUnits": false, "allowTerms": false}, "travel-relation": {"required": false, "allowUnits": false, "allowTerms": false}, "clinical setting": {"required": false, "allowUnits": false, "allowTerms": false}, "country of travel": {"required": false, "allowUnits": false, "allowTerms": false}, "collected_by": {"required": true, "allowUnits": false, "allowTerms": false}, "collection date": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (altitude)": {"required": false, "allowUnits": false, "allowTerms": false}, "geographic location (country and/or sea)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (latitude)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (longitude)": {"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}, "geographic location (depth)": {"required": false, "allowUnits": false, "allowTerms": false}, "amount or size of sample collected": {"required": false, "allowUnits": false, "allowTerms": false}, "environmental_sample": {"required": true, "allowUnits": false, "allowTerms": false}, "mating_type": {"required": false, "allowUnits": false, "allowTerms": false}, "genotype": {"required": false, "allowUnits": false, "allowTerms": false}, "pathotype": {"required": false, "allowUnits": false, "allowTerms": false}, "host disease status": {"required": false, "allowUnits": false, "allowTerms": false}, "host disease outcome": {"required": false, "allowUnits": false, "allowTerms": false}, "host subject id": {"required": false, "allowUnits": false, "allowTerms": false}, "host age": {"required": false, "allowUnits": false, "allowTerms": false}, "host taxid": {"required": false, "allowUnits": false, "allowTerms": false}, "host life stage": {"required": false, "allowUnits": false, "allowTerms": false}, "host health state": {"required": true, "allowUnits": false, "allowTerms": false}, "host sex": {"required": false, "allowUnits": false, "allowTerms": false}, "lab_host": {"required": false, "allowUnits": false, "allowTerms": false}, "host scientific name": {"required": true, "allowUnits": false, "allowTerms": false}, "passage_history": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage conditions": {"required": false, "allowUnits": false, "allowTerms": false}, "Is the sequenced pathogen host associated?": {"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}, "sub_group": {"required": false, "allowUnits": false, "allowTerms": false}, "sub_type": {"required": false, "allowUnits": false, "allowTerms": false}, "serovar": {"required": false, "allowUnits": false, "allowTerms": false}, "strain": {"required": false, "allowUnits": false, "allowTerms": false}, "host disease stage": {"required": false, "allowUnits": false, "allowTerms": false}, "isolation source host-associated": {"required": false, "allowUnits": false, "allowTerms": false}, "host description": {"required": false, "allowUnits": false, "allowTerms": false}, "isolation source non-host-associated": {"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 Data for Matching (MDM). A checklist for reporting metadata of pathogen samples for the Global Microbial Identifier (GMI) reporting system. More about GMI can be found here http://www.g-m-i.org/", "properties": {"attributes": {"required": ["collected_by", "collection date", "geographic location (country and/or sea)", "geographic location (latitude)", "geographic location (longitude)", "environmental_sample", "host health state", "host scientific name", "Is the sequenced pathogen host associated?", "isolate"], "properties": {"host description": {"description": "Other descriptive information relating to the host.", "items": {}}, "isolation source host-associated": {"description": "Name of host tissue or organ sampled for analysis. Example: tracheal tissue", "items": {}}, "sample storage conditions": {"description": "Conditions at which sample was stored, usually storage temperature, duration and location", "items": {}}, "geographic location (depth)": {"description": "Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "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"]}}}}, "clinical setting": {"maxItems": 1, "description": "The timing of the clinic visit in relation to travel.", "items": {"properties": {"value": {"enum": ["after travel", "during travel"]}}}}, "pathotype": {"description": "name or code for pathotype of organism", "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"]}}}}, "host life stage": {"description": "description of life stage of host", "items": {}}, "passage_history": {"description": "details of passage of culture between time of isolation and sequencing", "items": {}}, "host disease outcome": {"description": "Disease outcome in the host.", "items": {"properties": {"value": {"enum": ["dead", "recovered", "recovered with sequelae"]}}}}, "amount or size of sample collected": {"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]+)?"}}}}, "travel-relation": {"maxItems": 1, "description": "Designates the relation of the main diagnosis to the patient's travel.", "items": {"properties": {"value": {"enum": ["not ascertainable", "not travel-related", "travel-related"]}}}}, "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": {}}, "collected_by": {"description": "name of persons or institute who collected the specimen", "items": {}}, "geographic location (latitude)": {"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$)"}}}}, "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": {}}, "host disease status": {"description": "list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text", "items": {}}, "host sex": {"description": "Gender or sex of the host.", "items": {"properties": {"value": {"enum": ["female", "hermaphrodite", "male", "neuter", "not applicable", "not collected", "not provided", "other", "restricted access"]}}}}, "host taxid": {"description": "NCBI taxon id of the host, e.g. 9606", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "culture_collection": {"description": "institution code and identifier for the culture from which the sample was obtained, with optional collection code.", "items": {}}, "isolation source non-host-associated": {"description": "Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soil", "items": {}}, "identified_by": {"description": "name of the expert who identified the specimen taxonomically", "items": {}}, "genotype": {"description": "name or code for genotype of organism", "items": {}}, "country of travel": {"maxItems": 1, "description": "The name of the country of patient's travel.", "items": {"properties": {"value": {"enum": ["Afghanistan", "Albania", "Algeria", "American Samoa", "Andorra", "Angola", "Anguilla", "Antarctica", "Antigua and Barbuda", "Argentina", "Armenia", "Aruba", "Ashmore and Cartier Islands", "Australia", "Austria", "Azerbaijan", "Bahamas", "Bahrain", "Baker Island", "Bangladesh", "Barbados", "Bassas da India", "Belarus", "Belgium", "Belize", "Benin", "Bermuda", "Bhutan", "Bolivia", "Bosnia and Herzegovina", "Botswana", "Bouvet Island", "Brazil", "British Virgin Islands", "Brunei", "Bulgaria", "Burkina Faso", "Burma", "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", "Cyprus", "Czech Republic", "Czechoslovakia", "Democratic Republic of the Congo", "Denmark", "Djibouti", "Dominica", "Dominican Republic", "Ecuador", "Egypt", "El Salvador", "Equatorial Guinea", "Eritrea", "Estonia", "Ethiopia", "Europa Island", "Falkland Islands", "Faroe Islands", "Federal Republic of Germany", "Fiji", "Finland", "Former Yugoslav Republic of Macedonia", "France", "French Guiana", "French Polynesia", "French Southern and Antarctic Lands", "GDR", "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", "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", "Kingman Reef", "Kiribati", "Korea", "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", "Mexico", "Micronesia", "Midway Islands", "Moldova", "Monaco", "Mongolia", "Montenegro", "Montserrat", "Morocco", "Mozambique", "Namibia", "Nauru", "Navassa Island", "Nepal", "Netherlands", "Netherlands Antilles", "New Caledonia", "New Zealand", "Nicaragua", "Niger", "Nigeria", "Niue", "Norfolk Island", "North Korea", "Northern Mariana Islands", "Norway", "Oman", "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", "Russia", "Rwanda", "Saint Barthelemy", "Saint Helena", "Saint Kitts and Nevis", "Saint Lucia", "Saint Martin", "Saint Pierre and Miquelon", "Saint Vincent and the Grenadines", "Samoa", "San Marino", "Sao Tome and Principe", "Saudi Arabia", "Senegal", "Serbia", "Serbia and Montenegro", "Seychelles", "Sierra Leone", "Singapore", "Slovakia", "Slovenia", "Solomon Islands", "Somalia", "South Africa", "South Georgia and the South Sandwich Islands", "South Korea", "South Sudan", "Spain", "Spratly Islands", "Sri Lanka", "State of Palestine", "Sudan", "Suriname", "Svalbard", "Swaziland", "Sweden", "Switzerland", "Syria", "Taiwan", "Tajikistan", "Tanzania", "Thailand", "Timor-Leste", "Togo", "Tokelau", "Tonga", "Trinidad and Tobago", "Tromelin Island", "Tunisia", "Turkey", "Turkmenistan", "Turks and Caicos Islands", "Tuvalu", "USA", "USSR", "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"]}}}}, "geographic location (altitude)": {"description": "The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "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$)"}}}}, "subject exposure": {"maxItems": 1, "description": "Exposure of the subject to infected human or animals, such as poultry, wild bird or swine. If multiple exposures are applicable, please state them separated by semicolon. Example: poultry; wild bird", "items": {}}, "isolate": {"description": "individual isolate from which the sample was obtained", "items": {}}, "geographic location (longitude)": {"description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "serovar": {"description": "serological variety of a species (usually a prokaryote) characterized by its antigenic properties", "items": {}}, "host age": {"description": "age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host disease stage": {"description": "disease stage of host", "items": {}}, "Is the sequenced pathogen host associated?": {"description": "Is the sequenced pathogen host associated? ('Yes' or 'No')", "items": {"properties": {"value": {"enum": ["No", "Yes"]}}}}, "sub_group": {"description": "name of sub-group of organism from which sample was obtained", "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": {}}, "sub_type": {"description": "name of sub-type of organism from which 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 subject id": {"description": "a unique identifier by which each subject can be referred to, de-identified, e.g. #131", "items": {}}, "subject exposure duration": {"maxItems": 1, "description": "Duration of the exposure of the subject to an infected human or animal. If multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. Example: 1 day; 0.33 days", "items": {}}, "host scientific name": {"description": "Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.", "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": {}}}}}, "required": ["attributes"], "id": "ERC000029", "type": "object", "title": "ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000029"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000029"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000029/spreadsheet.csv"}}}