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ERC000052.json
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ERC000052.json
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{"id": "ERC000052", "dataTypeId": "samples", "displayName": "HoloFood Checklist", "description": "Minimum information required for reporting HoloFood samples. HoloFood is a 'hologenomic' approach that will improve the efficiency of food production systems by understanding the biomolecular and physiological processes affected by incorporating feed additives and novel sustainable feeds in farmed animals (https://www.holofood.eu/).", "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}, "project name": {"required": true, "allowUnits": false, "allowTerms": false}, "sample volume or weight for DNA extraction": {"required": true, "allowUnits": false, "allowTerms": false}, "nucleic acid extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "pcr primers": {"required": false, "allowUnits": false, "allowTerms": false}, "adapters": {"required": false, "allowUnits": false, "allowTerms": false}, "sequencing method": {"required": true, "allowUnits": false, "allowTerms": false}, "reference host genome for decontamination": {"required": true, "allowUnits": false, "allowTerms": false}, "collection date": {"required": false, "allowUnits": false, "allowTerms": false}, "geographic location (country and/or sea)": {"required": false, "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}, "trial length": {"required": false, "allowUnits": false, "allowTerms": false}, "trial timepoint": {"required": true, "allowUnits": false, "allowTerms": false}, "sample storage temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage location": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage buffer": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage container": {"required": false, "allowUnits": false, "allowTerms": false}, "host disease status": {"required": false, "allowUnits": false, "allowTerms": false}, "host common name": {"required": true, "allowUnits": false, "allowTerms": false}, "host subject id": {"required": true, "allowUnits": false, "allowTerms": false}, "host taxid": {"required": true, "allowUnits": false, "allowTerms": false}, "host body site": {"required": true, "allowUnits": false, "allowTerms": false}, "host length": {"required": false, "allowUnits": false, "allowTerms": false}, "host total mass": {"required": false, "allowUnits": false, "allowTerms": false}, "host sex": {"required": false, "allowUnits": false, "allowTerms": false}, "host scientific name": {"required": false, "allowUnits": false, "allowTerms": false}, "host breed": {"required": false, "allowUnits": false, "allowTerms": false}, "host gutted mass": {"required": false, "allowUnits": false, "allowTerms": false}, "host diet": {"required": false, "allowUnits": false, "allowTerms": false}, "host diet treatment": {"required": true, "allowUnits": false, "allowTerms": false}, "host diet treatment concentration": {"required": false, "allowUnits": false, "allowTerms": false}, "host storage container": {"required": false, "allowUnits": false, "allowTerms": false}, "host storage container pH": {"required": false, "allowUnits": false, "allowTerms": false}, "host storage container temperature": {"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": {"$ref": "#/definitions/terms"}, "units": {"minLength": 1, "type": "string"}}}}, "terms": {"type": "array", "items": {"required": ["url"], "type": "object", "properties": {"url": {"format": "uri", "type": "string"}}}}, "properties": {"attributes": {"required": [], "type": "object", "description": "Attributes for describing a sample.", "patternProperties": {"^.*$": {"$ref": "#/definitions/attribute"}}, "properties": {}}}}, "description": "Minimum information required for reporting HoloFood samples. HoloFood is a 'hologenomic' approach that will improve the efficiency of food production systems by understanding the biomolecular and physiological processes affected by incorporating feed additives and novel sustainable feeds in farmed animals (https://www.holofood.eu/).", "properties": {"attributes": {"required": ["project name", "sample volume or weight for DNA extraction", "sequencing method", "reference host genome for decontamination", "trial timepoint", "host common name", "host subject id", "host taxid", "host body site", "host diet treatment"], "properties": {"reference host genome for decontamination": {"maxItems": 1, "description": "Reference host genome that was mapped against for host decontamination (in the form of a valid assembly accession - e.g. in the format GCA_xxxxxxx.x)", "items": {"properties": {"value": {"pattern": "(^(E|D|S)RZ[0-9]{6,}$)|(^GCA_[0-9]{9}.[0-9]+$|^[A-Z]{1}[0-9]{5}.[0-9]+$|^[A-Z]{2}[0-9]{6}.[0-9]+$|^[A-Z]{2}[0-9]{8}$|^[A-Z]{4}[0-9]{2}S?[0-9]{6,8}$|^[A-Z]{6}[0-9]{2}S?[0-9]{7,9}$)"}}}}, "host diet treatment": {"maxItems": 1, "description": "Experimental diet treatment/additive to normal host feed e.g. Probiotic (GalliPro EPB5)", "items": {}}, "trial timepoint": {"maxItems": 1, "description": "Timepoint of the trial when the sample was collected - length of time after the beginning of the trial", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host storage container pH": {"maxItems": 1, "description": "pH of the medium in which the host organism is kept before sampling (e.g. pH of water in tank)", "items": {"properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample storage container": {"maxItems": 1, "description": "Container that sample was stored in e.g. tube type", "items": {}}, "host breed": {"maxItems": 1, "description": "Breed of the host (e.g. COBB-500)", "items": {}}, "pcr primers": {"maxItems": 1, "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters", "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$)|(^restricted access$)"}}}}, "host length": {"maxItems": 1, "description": "the length of subject", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host storage container": {"maxItems": 1, "description": "storage container that the host organism is kept in before sampling (e.g. cage, water tank, pen) including details of size and type", "items": {}}, "host total mass": {"maxItems": 1, "description": "total mass of the host at collection, the unit depends on host", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host body site": {"maxItems": 1, "description": "name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA", "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"]}}}}, "host diet treatment concentration": {"maxItems": 1, "description": "Concentration of experimental diet treatment/additive to normal host feed as a percentage of the mass of the feed (e.g. 20%)", "items": {"required": ["units"], "properties": {"value": {"pattern": "^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"}}}}, "sample volume or weight for DNA extraction": {"maxItems": 1, "description": "Volume (mL) or weight (g) of sample processed for DNA extraction", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host disease status": {"maxItems": 1, "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": {"maxItems": 1, "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": {"maxItems": 1, "description": "NCBI taxon id of the host, e.g. 9606", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "adapters": {"maxItems": 1, "description": "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters", "items": {}}, "sequencing method": {"maxItems": 1, "description": "Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid", "items": {}}, "sample storage buffer": {"maxItems": 1, "description": "buffer used for sample storage (e.g. RNAlater)", "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$)"}}}}, "project name": {"maxItems": 1, "description": "Name of the project within which the sequencing was organized", "items": {}}, "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]+)?"}}}}, "host gutted mass": {"maxItems": 1, "description": "total mass of the host after gutting, the unit depends on host", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "trial length": {"maxItems": 1, "description": "Length of time from the beginning of the trial until the end of the trial", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "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": {}}, "host diet": {"maxItems": 1, "description": "type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types", "items": {}}, "host storage container temperature": {"maxItems": 1, "description": "temperature at which the host is kept before sampling", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "host common name": {"maxItems": 1, "description": "common name of the host, e.g. human", "items": {}}, "host subject id": {"maxItems": 1, "description": "a unique identifier by which each subject can be referred to, de-identified, e.g. #131", "items": {}}, "host scientific name": {"maxItems": 1, "description": "Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.", "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": "ERC000052", "type": "object", "title": "HoloFood Checklist", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000052"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000052"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000052/spreadsheet.csv"}}}