Difference between revisions of "Data Object JSON v4"
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(Created page with "The current (version 4) form of the JSON schema for the Data object file is shown below. <br> This version was created in September 2020. <br><br> <div style="font-family: m...") |
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| (4 intermediate revisions by the same user not shown) | |||
| Line 7: | Line 7: | ||
{ | { | ||
"$schema": "http://json-schema.org/draft-07/schema#", | "$schema": "http://json-schema.org/draft-07/schema#", | ||
| − | "$id": "http://ecrin.org/json_schemas/mdrdataobject/ | + | "$id": "http://ecrin.org/json_schemas/mdrdataobject/v4.json", |
"title": "XDC Data Object definition", | "title": "XDC Data Object definition", | ||
"description": "ECRIN Metadata Repository for clinical research objects, Data Object JSON definition, version 4 September 2020", | "description": "ECRIN Metadata Repository for clinical research objects, Data Object JSON definition, version 4 September 2020", | ||
| Line 111: | Line 111: | ||
"url_last_checked": { | "url_last_checked": { | ||
"type": "string", | "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" | ||
}, | }, | ||
| Line 119: | Line 124: | ||
"description": "For dataset objects only, provides an indication of the types of keys used in the dataset, in particular if they are anonymous or pseudonymous", | "description": "For dataset objects only, provides an indication of the types of keys used in the dataset, in particular if they are anonymous or pseudonymous", | ||
"properties": { | "properties": { | ||
| − | " | + | "record_keys_type_id": { |
"type": "integer", | "type": "integer", | ||
"description": "An integer referencing the relevant record in the dataset_recordkey_types enumeration / lookup table" | "description": "An integer referencing the relevant record in the dataset_recordkey_types enumeration / lookup table" | ||
}, | }, | ||
| − | " | + | "record_keys_type": { |
"type": "string", | "type": "string", | ||
"description": "One of the allowed types, from the dataset_recordkey_types enumeration, e.g. 'Anonymised', or 'Pseudonymised'" | "description": "One of the allowed types, from the dataset_recordkey_types enumeration, e.g. 'Anonymised', or 'Pseudonymised'" | ||
}, | }, | ||
| − | " | + | "record_keys_details": { |
"type": "string", | "type": "string", | ||
"description": "Provides further details of the record key types, perhaps referring to dataset preparation, if available" | "description": "Provides further details of the record key types, perhaps referring to dataset preparation, if available" | ||
| Line 138: | Line 143: | ||
"description": "For dataset objects only, provides an indication of the level of identifiers in the dataset", | "description": "For dataset objects only, provides an indication of the level of identifiers in the dataset", | ||
"properties": { | "properties": { | ||
| − | " | + | "deident_type_id": { |
"type": "integer", | "type": "integer", | ||
"description": "An integer referencing the relevant record in the dataset_identifier_types enumeration / lookup table" | "description": "An integer referencing the relevant record in the dataset_identifier_types enumeration / lookup table" | ||
}, | }, | ||
| − | " | + | "deident_type": { |
"type": "string", | "type": "string", | ||
| − | "description": "One of the allowed types, from the | + | "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", | "type": "string", | ||
| − | "description": "Provides further details of the | + | "description": "Provides further details of the de-identification of the dataset, perhaps referring to other documents and / or a URL." |
} | } | ||
} | } | ||
| Line 157: | Line 182: | ||
"description": "For dataset objects only, provides an indication of the level of explicit consent for secondary use of the data", | "description": "For dataset objects only, provides an indication of the level of explicit consent for secondary use of the data", | ||
"properties": { | "properties": { | ||
| − | " | + | "consent_type_id": { |
"type": "integer", | "type": "integer", | ||
"description": "An integer referencing the relevant record in the dataset_consent_types enumeration / lookup table" | "description": "An integer referencing the relevant record in the dataset_consent_types enumeration / lookup table" | ||
}, | }, | ||
| − | " | + | "consent_type": { |
"type": "string", | "type": "string", | ||
| − | "description": "One of the allowed types, from the dataset_consent_types enumeration, e.g. ' | + | "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 research is restricted to genetic studies only" | ||
| + | } | ||
| + | "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", | "type": "string", | ||
| − | "description": "Provides further details of the consent for secondary use associated with the dataset, if available" | + | "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." |
} | } | ||
} | } | ||
Latest revision as of 09:45, 14 September 2020
The current (version 4) form of the JSON schema for the Data object file is shown below.
This version was created in September 2020.
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "http://ecrin.org/json_schemas/mdrdataobject/v4.json",
"title": "XDC Data Object definition",
"description": "ECRIN Metadata Repository for clinical research objects, Data Object JSON definition, version 4 September 2020",
"type": "object",
"required": ["id", "data_object_title", "class", "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 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",
"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, from the object_classes enumeration, e.g. 'Dataset', or 'Text'"
}
}
},
"object_type": {
"type": "object",
"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, from the object_types enumeration, e.g. 'Study Protocol', or 'IPD final analysis dataset (full study population)'"
}
}
},
"publication_year": {
"type": "integer",
"description": "A four digit number indicating the year the object was published, i.e. became available"
},
"language_code": {
"type": "array",
"items": {
"$ref": "#/definitions/lang_code"
}
},
"managing_organisation": {
"$ref": "#/definitions/organisation"
},
"access_type": {
"type": "object",
"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, e.g. 'Public download (self-attestation required)', or 'Case by case download'"
}
}
},
"access_details": {
"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."
},
"access_details_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 anonymous or pseudonymous",
"properties": {
"record_keys_type_id": {
"type": "integer",
"description": "An integer referencing the relevant record in the dataset_recordkey_types enumeration / lookup table"
},
"record_keys_type": {
"type": "string",
"description": "One of the allowed types, from the dataset_recordkey_types enumeration, e.g. 'Anonymised', or 'Pseudonymised'"
},
"record_keys_details": {
"type": "string",
"description": "Provides further details of the record key types, perhaps referring to dataset preparation, if available"
}
}
},
"dataset_identifiers": {
"type": "object",
"description": "For dataset objects only, provides an indication of the level of identifiers in 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_consents": {
"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 research is restricted to genetic studies only"
}
"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_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",
"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, from the identifier_types enumeration, e.g. 'Trial Registry ID', or 'Sponsor ID'"
}
}
},
"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'"
},
"identifier_org": {
"$ref": "#/definitions/organisation"
}
}
}
},
"object_titles": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the type and value of the 'other title'",
"required": ["id", "title_type", "title_text"],
"properties": {
"id": {
"type": "integer",
"description": "Other title record primary key, generated automatically in database"
},
"title_type": {
"type": "object",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the title_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types, from the title_types enumeration, e.g. 'Abbreviation or Acronym', or 'Translated Title'"
}
}
},
"title_text": {
"type": "string"
},
"lang_code": {
"$ref": "#/definitions/lang_code"
},
"contains_html": {
"type": "boolean"
"description": "Whether the title text has any embedded html tags, e.g. for super or subscripts"
},
"comments": {
"type": "string"
}
}
}
},
"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",
"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, from the contribution_types enumeration, e.g. 'Creator', or 'Trial Sponsor'"
}
}
},
"is_individual": {
"type": "boolean",
"description": "Indicates whether the contributor is an individual or an organisation, e.g. pharma company or research network."
},
"person": {
"type": "object",
"description": "A composite object that may include an id, but should have as a minimum either a last_name or full_name included. Not required if there is an organisation entry.",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the people table"
},
"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 first_name last_name"
},
"identifier": {
"type": "object",
"properties": {
"person_id": {
"type": "string",
"description": "The person's identifier within the identifier scheme"
},
"scheme_name": {
"type": "string",
"description": "A recognised identifier scheme name, most commonly ORCID"
}
}
},
"affiliation": {
"type": "object",
"properties": {
"affiliation": {
"type": "string",
"description": "The person's organisational affiliation as it appears in the source data"
},
"org_id": {
"type": "string",
"description": "The organisation's identifier within the identifier scheme"
},
"scheme_name": {
"type": "string",
"description": "A recognised identifier scheme name"
}
}
}
}
},
"organisation": {
"$ref": "#/definitions/organisation"
}
}
}
},
"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",
"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, from the date_types enumeration, e.g. 'Available', or 'Updated'"
}
}
},
"is_date_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",
"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",
"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_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",
"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, from the description_types enumeration, e.g. 'Table of Contents', or 'Abstract Section'"
}
}
},
"description_label": {
"type": "string",
"description": "A short label describing the nature of the description text"
},
"description_text": {
"type": "string",
"description": "The description text, as it appears in the source data"
},
"language_code": {
"$ref": "#/definitions/lang_code"
},
"contains_html": {
"type": "boolean"
"description": "Whether the title text has any embedded html tags, e.g. for super or subscripts"
},
}
}
},
"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",
"required": ["id", "repository_org", "file_type"],
"properties": {
"id": {
"type": "integer",
"description": "Object instance record primary key, generated automatically in database"
},
"repository_org": {
"$ref": "#/definitions/organisation"
},
"url":{
"type": "string",
"format": "uri",
"description": "The url where the object can be accessed, if one exists"
},
"url_direct_access":{
"type": "boolean",
"description": "Whether or not the access via the url is public and freely available"
},
"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_type": {
"type": "object",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the file_types enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types, from the file_types enumeration, e.g. 'PDF', or 'Excel Spreadsheet(s)'"
}
}
},
"resource_size":{
"type": "number",
"description": "A number (may be a real or an integer number) indicating the size of the resource"
},
"resource_size_unit":{
"type": "string",
"description": "One of the allowed types, from the size_units enumeration / look up table, e.g. 'Mb', or 'Pages'"
},
"resource_comment":{
"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_topics": {
"type": "array",
"items": {
"type": "object",
"description": "A composite object that indicates the topic name or keyword, and - if applicable - how it was classified in the source data, the controlled terminology system used, and the code for the topic in that system",
"required": ["id", "value"],
"properties": {
"id": {
"type": "integer",
"description": "Object topic record primary key, generated automatically in database"
},
"topic_value": {
"type": "string",
"description": "The topic name, as provided in the source data"
},
"topic_source_type": {
"type": "object",
"description": "How the topic was categorised in the source data, (or by using the controlled terminology, or using a category matching service)",
"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, from the topic_source_types enumeration, e.g. 'Condition', or 'Organism'"
}
}
},
"topic_ct": {
"type": "object",
"description": "If applicable, the controlled terminology system from which the topic name was taken",
"properties": {
"id": {
"type": "integer",
"description": "An integer referencing the relevant record in the topic_controlled_terminologies enumeration / lookup table"
},
"name": {
"type": "string",
"description": "One of the allowed types, from the topic_controlled_terminologies enumeration, e.g. 'MESH', or 'Cochrane PICO terminology'"
}
}
},
"topic_ct_code": {
"type": "string",
"description": "The code for the topic within the designated controlled terminology scheme"
}
}
}
},
"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"
},
"details":{
"type": "string",
"description": "The name of the rights applied, possibly including a detailed description"
},
"rights_url":{
"type": "string",
"format": "uri",
"description": "The url where details of the rights applied can be found, e.g. defintition of creative commons variant"
}
}
}
},
"related_objects": {
"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",
"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, e.g. 'Is metadata for', or 'Is supplement to'"
}
}
},
"target_object_id": {
"type": "integer",
"description": "The id, i.e. internal accession number, of the related object"
}
}
}
},
"related_studies": {
"type": "array",
"items": {
"type": "integer",
"description": "The id, i.e. internal accession number, of the linked study"
}
},
"provenance_data": {
"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"
},
},
"definitions": {
"lang_code": {
"type": "string",
"minLength": 2,
"maxLength": 2,
"description": "A two letter ISO 369-1 code indicating the language of the study",
"default": "en"
},
"organisation": {
"type": "object",
"required": ["name"],
"properties": {
"id": {
"type": "integer",
"description": "The id of the organisation within the ECRIN contextual database, if that id exists"
},
"name": {
"type": "array",
"description": "Either the name of the organisation as supplied by the source data, or the names (may be multiple) of the organisation within the ECRIN contextual database",
"minItems": 1,
"items": {
"type": "string"
}
}
}
}
}
}
