Difference between revisions of "JSON Schema for Objects"
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| Line 1: | Line 1: | ||
| − | The current (version | + | <p style="color:blue; text-align:right"><small>'''''Last updated: 20/09/2022'''''</small></p> |
| + | The current (version 7) form of the JSON schema for the Data Object file is shown below. | ||
<br> | <br> | ||
| − | This version was created in | + | This version was created in September 2022. |
<br><br> | <br><br> | ||
<div style="font-family: monospace; font-size: 13px" > | <div style="font-family: monospace; font-size: 13px" > | ||
| Line 7: | Line 8: | ||
{ | { | ||
"$schema": "http://json-schema.org/draft-07/schema#", | "$schema": "http://json-schema.org/draft-07/schema#", | ||
| − | "$id": "http://ecrin.org/json_schemas/mdrdataobject/ | + | "$id": "http://ecrin.org/json_schemas/mdrdataobject/v7.json", |
"title": "XDC Data Object definition", | "title": "XDC Data Object definition", | ||
| − | "description": "ECRIN Metadata Repository for clinical research objects, Data Object JSON definition, version | + | "description": "ECRIN Metadata Repository for clinical research objects, Data Object JSON definition, version 7 September 2022", |
"type": "object", | "type": "object", | ||
"required": ["id", "data_object_title", "object_class", "object_type", "publication_year", "access_type"], | "required": ["id", "data_object_title", "object_class", "object_type", "publication_year", "access_type"], | ||
| Line 444: | Line 445: | ||
"contribution_type": { | "contribution_type": { | ||
"type": "object", | "type": "object", | ||
| − | "description": "The type of contribution made, by an individual or organisation, | + | "description": "The type of contribution made, by an individual or organisation, usually 'Creator', |
"properties": { | "properties": { | ||
"id": { | "id": { | ||
| Line 458: | Line 459: | ||
"is_individual": { | "is_individual": { | ||
"type": "boolean", | "type": "boolean", | ||
| − | "description": "Indicates whether the contributor is an individual, e.g. | + | "description": "Indicates whether the contributor is an individual, e.g., paper author, or an organisation, e.g., a research collaboration. |
| + | If an organisation the person object will be null. If a person, the organisation object will be null." | ||
}, | }, | ||
"organisation": { | "organisation": { | ||
| Line 552: | Line 554: | ||
"mesh_code": { | "mesh_code": { | ||
"type": "string", | "type": "string", | ||
| − | "description": "The MESH code for the topic if | + | "description": "The MESH code for the topic, if coding to MESH has been possible or was already present in the source data" |
}, | }, | ||
"mesh_value": { | "mesh_value": { | ||
"type": "string", | "type": "string", | ||
| − | "description": "The topic or keyword | + | "description": "The MESH term for the topic or keyword, if coding to MESH has been possible or was already present in the source data" |
| + | }, | ||
| + | "ct_type": { | ||
| + | "type": "object", | ||
| + | "description": "The controlled terminology system (if any) used for the topic term in the source data", | ||
| + | "properties": { | ||
| + | "id": { | ||
| + | "type": "integer", | ||
| + | "description": "An integer referencing the relevant record in the topic_vocabularies enumeration / lookup table" | ||
| + | }, | ||
| + | "name": { | ||
| + | "type": "string", | ||
| + | "description": "One of the allowed types listed in the topic_vocabularies enumeration" | ||
| + | } | ||
| + | } | ||
| + | }, | ||
| + | "ct_code": { | ||
| + | "type": "string", | ||
| + | "description": "The original code used for the topic or keyword, if a controlled terminology was used in the source data" | ||
}, | }, | ||
"original_value": { | "original_value": { | ||
Latest revision as of 11:31, 11 November 2022
Last updated: 20/09/2022
The current (version 7) form of the JSON schema for the Data Object file is shown below.
This version was created in September 2022.
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "http://ecrin.org/json_schemas/mdrdataobject/v7.json",
"title": "XDC Data Object definition",
"description": "ECRIN Metadata Repository for clinical research objects, Data Object JSON definition, version 7 September 2022",
"type": "object",
"required": ["id", "data_object_title", "object_class", "object_type", "publication_year", "access_type"],
"additionalProperties": false,
"properties": {
"file_type": {
"type": "string",
"description": "always 'data_object'"
},
"id": {
"type": "integer",
"description": "Internal accession number of the data object within the MDR database"
},
"doi": {
"type": "string",
"description": "The doi (without prefixes, beginning with '10...') of the object, if it has one"
},
"display_title": {
"type": "string",
"description": "The title of the object - if a unique title is not part of the source title it may be a composite of the study title and the object type"
},
"version": {
"type": "string",
"description": "Indication of version if there is one, in the format of the source data"
},
"object_class": {
"type": "object",
"description": "The broad type of object, e.g. 'Dataset', or 'Text'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the object_classes enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types in the object_classes enumeration"
}
}
},
"object_type": {
"type": "object",
"description": "A more detailed classification of the object type, e.g. 'Study Protocol', or 'IPD dataset’",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the object_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types in the object_types enumeration"
}
}
},
"publication_year": {
"type": "integer",
"description": "A four digit number indicating the year the object was published, i.e. became available"
},
"lang_code": {
"type": "string",
"description": "A two letter ISO 369-1 code indicating the language of the data object. Occasionaly - especially with journal articles - two or more such codes, separated by a comma"
},
"managing_organisation": {
"type": "object",
"description": "The organisation managing the object, in particular that determines access to it",
"properties": {
"id": {
"type": "integer",
"description": "The id of the organisation within the ECRIN context database, if that id exists"
},
"name": {
"type": "string",
"description": "The default name of the organisation within the ECRIN context database, if it exists, or the name of the organisation as supplied by the source data"
}
"ror_id": {
"type": "string",
"description": "The id of the organisation, if known, within the ROR (Research Organisation Registry) system. This is a URL linking to the ROR resource."
}
}
},
"access_type": {
"type": "object",
"description": "The type of access to the object, e.g. 'Public download (self-attestation required)', or 'Case by case download'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the object_access_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types from the object_access_types enumeration"
}
}
},
"access_details": {
"type": "object",
"description": "Further details of the access (especially if non public)",
"properties": {
"description": {
"type": "string",
"description": "A textual description of the access being offered, for example identifying the groups to which access is granted, the criteria on which a case-by-case decision would be based, any further restrictions on on-screen access, etc."
},
"url": {
"type": "string",
"format" : "uri",
"description": "A url of a web page that provides details of the accesss available, possibly including the practical details required or a form to use to apply for access"
},
"url_last_checked": {
"type": "string",
"format": "date",
"description": "If a check has been carried out, the date the url last responded with a 200 (success) message, as a string (yyyy MMM dd)"
}
}
},
"eosc_category": {
"type": "integer",
"description": "An integer between 0 and 3 inclusive, representing the type of data object / access management required, using a recommended eosc categorisation"
},
"dataset_record_keys": {
"type": "object",
"description": "For dataset objects only, provides an indication of the types of keys used in the dataset, in particular if they are claimed to be anonymous or pseudonymous",
"properties": {
"keys_type_id": {
"type": "integer",
"description": "An integer referencing the relevant record in the dataset_recordkey_types enumeration / lookup table"
},
"keys_type": {
"type": "string",
"description": "One of the allowed types, from the dataset_recordkey_types enumeration"
},
"keys_details": {
"type": "string",
"description": "Provides further details of the record key types, perhaps referring to dataset preparation, if available"
}
}
},
"dataset_deident_level": {
"type": "object",
"description": "For dataset objects only, provides an indication of the level of deidentification of the dataset",
"properties": {
"deident_type_id": {
"type": "integer",
"description": "An integer referencing the relevant record in the dataset_identifier_types enumeration / lookup table"
},
"deident_type": {
"type": "string",
"description": "One of the allowed types, from the dataset_de-identification_levels enumeration, e.g. 'De-identification applied'"
},
"deident_direct": {
"type": "boolean",
"description": "If direct Identifiers were removed from the data set"
},
"deident_hipaa": {
"type": "boolean",
"description": "If the US HIPAA de-identification rules have been applied"
},
"deident_dates": {
"type": "boolean",
"description": "If dates have been rebased and / or replaced by integers"
},
"deident_nonarr": {
"type": "boolean",
"description": "If narrative text fields have been removed"
},
"deident_kanon": {
"type": "boolean",
"description": "if k-anonymisation (k>=2) has been achieved"
},
"deident_details": {
"type": "string",
"description": "Provides further details of the de-identification of the dataset, perhaps referring to other documents and / or a URL."
}
}
},
"dataset_consent": {
"type": "object",
"description": "For dataset objects only, provides an indication of the level of explicit consent for secondary use of the data",
"properties": {
"consent_type_id": {
"type": "integer",
"description": "An integer referencing the relevant record in the dataset_consent_types enumeration / lookup table"
},
"consent_type": {
"type": "string",
"description": "One of the allowed types, from the dataset_consent_types enumeration, e.g. 'No explicit consent', or 'General research use'"
},
"consent_noncommercial": {
"type": "boolean",
"description": "If further use restricted to non-commercial users"
},
"consent_geog_restrict": {
"type": "boolean",
"description": "If any geographical restrictions apply to further use"
},
"consent_research_type": {
"type": "boolean",
"description": "If further use is restricted to specific type(s) of research"
},
"consent_genetic_only": {
"type": "boolean",
"description": "If further use is restricted to specific type(s) of research"
},
"consent_no_methods": {
"type": "boolean",
"description": "If the data cannot be used for work that is purely for methodological / algorithmic development"
},
"consents_details": {
"type": "string",
"description": "Provides further details of the consent for secondary use associated with the dataset, if available, and in particular any details associated with the specific restrictions listed above."
}
}
},
"object_instances": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the nature of a specific instance of a data object, e.g. a file or a web page",
"properties": {
"id": {
"type": "integer",
"description": "Object instance record primary key, generated automatically in database"
},
"repository_org": {
"type": "object",
"description": "The organisation hosting the instance",
"properties": {
"id": {
"type": "integer",
"description": "The id of the organisation within the ECRIN context database, if that id exists"
},
"name": {
"type": "string",
"description": "The default name of the organisation within the ECRIN context database, if it exists, or the name of the organisation as supplied by the source data"
}
}
},
"access_details":{
"type": "object",
"description": "Basic details of the access available to the instance",
"properties": {
"direct_access":{
"type": "boolean",
"description": "Whether or not the access is public and freely available, or restricted in some way"
},
"url": {
"type": "string",
"format": "uri",
"description": "The url where the object can be publicly accessed, if one exists"
},
"url_last_checked": {
"type": "string",
"format": "date",
"description": "If a check has been carried out, the date the url last responded with a 200 (success) message, as a string (yyyy MMM dd)"
}
}
},
"resource_details": {
"type": "object",
"description": "Details of the instance, considered as a physical resource",
"properties": {
"type_id": {
"type": "integer",
"description": "An integer referencing the relevant record in the file_types enumeration / lookup table"
},
"type_name": {
"type": "string",
"description": "One of the allowed types, from the file_types enumeration, e.g. 'PDF', or 'Excel Spreadsheet(s)'"
},
"size":{
"type": "number",
"description": "A number (may be a real or an integer number) indicating the size of the resource"
},
"size_unit":{
"type": "string",
"description": "One of the allowed types, from the size_units enumeration / look up table, e.g. 'Mb', or 'Pages', but note expressed only as a string"
},
"comments":{
"type": "string",
"description": "Holds further details of the resource, in particular to support machine processing. These could include the schema used for XML files, and / or the character coding used for text files (e.g. UTF-8 versus UTF-16) or the presence and types of any byte order marks."
}
}
}
}
}
},
"object_titles": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the type and value of the 'other title'",
"required": ["id", "title_type", "title_text"],
"properties": {
"id": {
"type": "integer",
"description": "Other title record primary key, generated automatically in database"
},
"title_type": {
"type": "object",
"description": "Type of the title, e.g. 'Translated Title'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the title_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the types listed in the title_types enumeration"
}
}
},
"title_text": {
"type": "string",
"description": "The text of the title, verbatim"
},
"lang_code": {
"type": "string",
"description": "A two letter ISO 369-1 code indicating the language of the title"
},
"comments": {
"type": "string",
"description": "Any additional comments regarding the source or derivation of the title"
}
}
}
},
"object_dates": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the date and its type",
"required": ["id", "date_type", "is_date_range", "start"],
"properties": {
"id": {
"type": "integer",
"description": "Object date record primary key, generated automatically in database"
},
"date_type": {
"type": "object",
"description": "The type of the date, e.g. 'Available', or 'Updated'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the date_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types in the date_types enumeration"
}
}
},
"date_is_range": {
"type": "boolean",
"default": false,
"description": "If true both start and end dates should be considered, otherwise just the start date"
},
"date_as_string": {
"type": "string",
"description": "String representation of the date, used for all dates including partial dates and date ranges "
},
"start_date": {
"type": "object",
"description": "The date, or the start date of a range",
"properties": {
"start_year": {
"type": "integer",
"description": "A 4 digit integer indicating the year"
},
"start_month": {
"type": "integer",
"description": "An integer indicating the month"
},
"start_day": {
"type": "integer",
"description": "An integer indicating the day"
}
}
},
"end_date": {
"type": "object",
"description": "The end date of a date range",
"properties": {
"end_year": {
"type": "integer",
"description": "A 4 digit integer indicating the year"
},
"end_month": {
"type": "integer",
"description": "An integer indicating the month"
},
"end_day": {
"type": "integer",
"description": "An integer indicating the day"
}
}
},
"comments": {
"type": "string",
"description": "Additional comments or information about the date"
}
}
}
},
"object_contributors": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the people and / or organisations that contributed to the data object, directly or indirectly",
"required": ["id", "contribution_type"],
"properties": {
"id": {
"type": "integer",
"description": "Object contributor record primary key, generated automatically in database"
},
"contribution_type": {
"type": "object",
"description": "The type of contribution made, by an individual or organisation, usually 'Creator',
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the contribution_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types in the contribution_types enumeration"
}
}
},
"is_individual": {
"type": "boolean",
"description": "Indicates whether the contributor is an individual, e.g., paper author, or an organisation, e.g., a research collaboration.
If an organisation the person object will be null. If a person, the organisation object will be null."
},
"organisation": {
"type": "object",
"description": "The organisation providing the contribution - not required if the contributor is an individual.",
"properties": {
"id": {
"type": "integer",
"description": "The id of the organisation, within the ECRIN context database, if that id exists"
},
"name": {
"type": "string",
"description": "The default name of the organisation, within the ECRIN context database, if it exists, or the name of the organisation as supplied by the source data"
},
"ror_id": {
"type": "string",
"description": "The id of the organisation, if known, within the ROR (Research Organisation Registry) system. This is a URL linking to the ROR resource."
}
}
},
"person": {
"type": "object",
"description": "A composite object that should include as a minimum a full_name. Not required if there is an organisation entry",
"properties": {
"family_name": {
"type": "string",
"description": "The person's family name, the 'key' name under which they are listed - usually the last name in Western cultures"
},
"given_name": {
"type": "string",
"description": "The person's given name, or the first name by which they are nornally known. May be replaced by initials"
},
"full_name": {
"type": "string",
"description": "The person's full name, in the order of given_name family_name"
},
"orcid": {
"type": "string",
"description": "The person's ORCID identifier, if known"
},
"affiliation_string": {
"type": "string",
"description": "The person's organisational affiliation as it appears in the source data"
},
"affiliation_org_id": {
"type": "integer",
"description": "The id of the organisation within the MDR, if it can be identified from the affiliation string."
},
"affiliation_org_name": {
"type": "string",
"description": "The name of the organisation to which the person is affiliated, as deduced from the affiliation string."
},
"affiliation_org_ror_id": {
"type": "string",
"description": "The id of the organisation to which the person is affiliated, if known, within the ROR (Research Organisation Registry) system. This is a URL linking to the ROR resource."
}
}
}
}
}
},
"object_topics": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the topic name or keyword, and - where available - the MESH coding for that term",
"required": ["id", "value"],
"properties": {
"id": {
"type": "integer",
"description": "Study topic record primary key, generated automatically in database"
},
"topic_type": {
"type": "object",
"description": "How the topic was categorised in the source data, e.g. 'Condition', or 'Organism'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the topic_source_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types listed in the topic_source_types enumeration"
}
}
},
"mesh_coded": {
"type": "boolean",
"description": "Whether or not the topic has been MESH coded"
},
"mesh_code": {
"type": "string",
"description": "The MESH code for the topic, if coding to MESH has been possible or was already present in the source data"
},
"mesh_value": {
"type": "string",
"description": "The MESH term for the topic or keyword, if coding to MESH has been possible or was already present in the source data"
},
"ct_type": {
"type": "object",
"description": "The controlled terminology system (if any) used for the topic term in the source data",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the topic_vocabularies enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types listed in the topic_vocabularies enumeration"
}
}
},
"ct_code": {
"type": "string",
"description": "The original code used for the topic or keyword, if a controlled terminology was used in the source data"
},
"original_value": {
"type": "string",
"description": "The original value of the term, whether coded or not"
}
}
}
},
"object_identifiers": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the value and type of the identifier, and optionally its date and organisation of origin",
"required": ["id", "value", "type"],
"properties": {
"id": {
"type": "integer",
"description": "Data object identifier record primary key, generated automatically in database"
},
"identifier_value": {
"type": "string",
"description": "The identifier value, in a standardised format (for each identifier type)"
},
"identifier_type": {
"type": "object",
"description": "The type of identifier, e.g. ‘Publisher ID’",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the identifier_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types in the identifier_types enumeration"
}
}
},
"identifier_org": {
"type": "object",
"description": "The organisation providing the identifier",
"properties": {
"id": {
"type": "integer",
"description": "The id of the organisation within the ECRIN context database, if that id exists"
},
"name": {
"type": "string",
"description": "The default name of the organisation within the ECRIN context database, if it exists, or the name of the organisation as supplied by the source data"
},
"ror_id": {
"type": "string",
"description": "The id of the organisation, if known, within the ROR (Research Organisation Registry) system. This is a URL linking to the ROR resource."
}
}
},
"identifier_date": {
"type": "string",
"description": "The date the identifier was allocated, if known, in a string 'yyyy MMM dd' format, e.g. '2015 Dec 12'"
}
}
}
},
"object_descriptions": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the description and its type",
"required": ["id", "description_type", "description_text"],
"properties": {
"id": {
"type": "integer",
"description": "Object description record primary key, generated automatically in database"
},
"description_type": {
"type": "object",
"description": "The type of description (or description section), e.g. 'Table of Contents', or 'Abstract Section'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the description_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types in the description_types enumeration"
}
}
},
"description_label": {
"type": "string",
"description": "A short label describing the nature of the description text, designed to be used as a possible sub-header in a display"
},
"description_text": {
"type": "string",
"description": "The description text, as it appears in the source data"
},
"lang_code": {
"type": "string",
"description": "A two letter ISO 369-1 code indicating the language of the description."
},
}
}
},
"object_rights": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates any usage and copyright rights associated with the data object",
"required": ["id", "details"],
"properties": {
"id":{
"type": "integer",
"description": "Object rights record primary key, generated automatically in database"
},
"rights_name":{
"type": "string",
"description": "The name of the rights applied"
},
"rights_url":{
"type": "string",
"format": "uri",
"description": "The url where details of the rights applied can be found, e.g. defintition of a creative commons variant"
},
"comments":{
"type": "string",
"description": "Any additional comments, or a more detailed description of the rights regime"
}
}
}
},
"object_relationships": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates any related data object and the nature of the relationship",
"required": ["id", "relationship_type", "target_object_id"],
"properties": {
"id": {
"type": "integer",
"description": "Object relationships record primary key, generated automatically in database"
},
"relationship_type": {
"type": "object",
"description": "The nature of the relationship, e.g. e.g. 'Is metadata for', or 'Is supplement to'",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the object_relationship_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types from the object_relationship_types enumeration"
}
}
},
"target_object_id": {
"type": "integer",
"description": "The id, i.e. internal accession number, of the related object"
}
}
}
},
"linked_studies": {
"type": "array",
"items": {
"type": "integer",
"description": "The id, i.e. internal accession number, of a linked study"
}
},
"provenance_string": {
"type": "string",
"description": "A listing of the source or sources from which the data for the data object has been drawn, and the date-time(s) when the data was last downloaded"
}
}
}
