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HDRDescriptiveMetadata.yml
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HDRDescriptiveMetadata.yml
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"$schema": "http://json-schema.org/draft-07/schema"
"$id": "https://raw.githubusercontent.com/HDRUK/schemata/master/schema/dataset/dataset.schema.json"
type: object
title: HDR UK Dataset
description: HDR UK Dataset Schema
version: "2.0.0"
required:
- identifier
- version
- revisions
- issued
- modified
- summary
- accessibility
additionalProperties: false
properties:
identifier:
"$id": "#/properties/identifier"
title: Dataset identifier
"$comment": "http://purl.org/dc/terms/identifier"
examples:
- ["226fb3f1-4471-400a-8c39-2b66d46a39b6"]
description: System dataset identifier
anyOf:
- "$ref": "#/definitions/uuidv4"
- type: string
format: uri
version:
"$id": "#/properties/version"
title: Dataset Version
description: Dataset metadata version
"$ref": "#/definitions/semver"
examples:
- "1.1.0"
revisions:
"$id": "#/properties/revisions"
title: Dataset Revisions
description: Revisions of Dataset metadata
type: array
items:
- "$ref": "#/definitions/revision"
issued:
"$id": "#/properties/issued"
title: Creation Date
"$comment": 'dcat:issued'
description: Dataset Metadata Creation Date
type: string
format: date-time
modified:
"$id": "#/properties/modified"
title: Modification Date
"$comment": 'dcat:modified'
description: Dataset Metadata Creation Date
type: string
format: date-time
summary:
"$id": "#/properties/summary"
title: Summary
description: Summary metadata must be completed by Data Custodians onboarding
metadata into the Innovation Gateway MVP.
"$ref": "#/definitions/summary"
documentation:
"$id": "#/properties/documentation"
title: Documentation
description: Documentation can include a rich text description of the dataset
or links to media such as documents, images, presentations, videos or links
to data dictionaries, profiles or dashboards. Organisations are required
to confirm that they have permission to distribute any additional media.
"$ref": "#/definitions/documentation"
coverage:
"$id": "#/properties/coverage"
title: Coverage
description: This information includes attributes for geographical and temporal
coverage, cohort details etc. to enable a deeper understanding of the dataset
content so that researchers can make decisions about the relevance of the
underlying data.
"$ref": "#/definitions/coverage"
provenance:
"$id": "#/properties/provenance"
title: Provenance
description: Provenance information allows researchers to understand data
within the context of its origins and can be an indicator of quality, authenticity
and timeliness.
"$ref": "#/definitions/provenance"
accessibility:
"$id": "#/properties/accessibility"
title: Accessibility
description: Accessibility information allows researchers to understand access,
usage, limitations, formats, standards and linkage or interoperability with
toolsets.
"$ref": "#/definitions/accessibility"
enrichmentAndLinkage:
"$id": "#/properties/enrichmentAndLinkage"
title: Enrichment and Linkage
description: 'This section includes information about related datasets that may have previously been linked, as well as indicating if there is the opportunity
to link to other datasets in the future. If a dataset has been enriched and/or derivations, scores and existing tools are available this section allows
providers to indicate this to researchers.'
"$ref": "#/definitions/enrichmentAndLinkage"
observations:
"$id": "#/properties/observations"
title: Observations
"$comment": https://schema.org/observation
description: 'Multiple observations about the dataset may be provided and
users are expected to provide at least one observation (1..*). We will
be supporting the schema.org observation model (https://schema.org/Observation)
with default values. Users will be encouraged to provide their own statistical
populations as the project progresses. Example: <b> Statistical
Population 1 </b> type: StatisticalPopulation populationType: Persons
numConstraints: 0 <b> Statistical Population 2 </b> type:
StatisticalPopulation populationType: Events numConstraints: 0 <b>
Statistical Population 3 </b> type: StatisticalPopulation populationType:
Findings numConstraints: 0 typeOf: Observation observedNode: <b>
Statistical Population 1 </b> measuredProperty: count measuredValue:
32937 observationDate: “2017”'
type: array
items:
allOf:
- "$ref": "#/definitions/observation"
definitions:
revision:
"$id": "#/definitions/revision"
required:
- version
- url
additionalProperties: false
properties:
version:
"$id": "#/definitions/revision/version"
description: Semantic Version
"$ref": "#/definitions/semver"
url:
"$id": "#/definitions/revision/url"
description: URL endpoint to obtain the version
"$ref": "#/definitions/url"
summary:
"$id": "#/definitions/summary"
required:
- title
- abstract
- publisher
- contactPoint
- keywords
additionalProperties: false
properties:
title:
"$id": "#/summary/title"
"$comment": "dct:title. title is reserved word in json schema"
title: Title
description: Title of the dataset limited to 80 characters. It should provide a
short description of the dataset and be unique across the gateway. If your title
is not unique, please add a prefix with your organisation name or identifier
to differentiate it from other datasets within the Gateway. Please avoid acronyms
wherever possible. Good titles should summarise the content of the dataset and
if relevant, the region the dataset covers.
examples:
- ["North West London COVID-19 Patient Level Situation Report"]
allOf:
- "$ref": "#/definitions/eightyCharacters"
abstract:
"$id": "#/summary/abstract"
title: Dataset Abstract
description: Provide a clear and brief descriptive signpost for researchers who
are searching for data that may be relevant to their research. The abstract
should allow the reader to determine the scope of the data collection and accurately
summarise its content. The optimal length is one paragraph (limited to 255 characters)
and effective abstracts should avoid long sentences and abbreviations where
possible
"$comment": dct:abstract
examples:
- CPRD Aurum contains primary care data contributed by General Practitioner
(GP) practices using EMIS Web® including patient registration information
and all care events that GPs have chosen to record as part of their usual
medical practice.
allOf:
- "$ref": "#/definitions/abstractText"
publisher:
"$id": "#/summary/publisher"
"$comment": Conforms to spec, but this MAY be an an object of organisation. https://schema.org/publisher
title: Dataset publisher
description: This is the organisation responsible for running or supporting the
data access request process, as well as publishing and maintaining the metadata.
In most this will be the same as the HDR UK Organisation (Hub or Alliance Member).
However, in some cases this will be different i.e. Tissue Directory are an HDR
UK Gateway organisation but coordinate activities across a number of data publishers
i.e. Cambridge Blood and Stem Cell Biobank.
allOf:
- "$ref": "#/definitions/organisation"
contactPoint:
"$id": "#/summary/contactPoint"
title: Contact Point
"$comment": dcat:contactPoint
default: Defaulted to the contact point of the primary organisation of the user however, can be overridden for specific datasets
examples:
description: 'Please provide a valid email address that can be used to coordinate
data access requests with the publisher. Organisations are expected to provide
a dedicated email address associated with the data access request process.
Notes: An employee’s email address can only be provided on a temporary basis
and if one is provided an explicit consent must be obtained for this purpose.'
allOf:
- "$ref": "#/definitions/emailAddress"
keywords:
"$id": "#/summary/keywords"
"$comment": dcat:keyword. May be an array of strings or comma seperated list.
title: Keywords
description: 'Please provide relevant and specific keywords that can improve
the SEO of your dataset as a comma separated list. Notes: Onboarding portal
will suggest keywords based on title, abstract and description. We are compiling
a standardised list of keywords and synonyms across datasets to make filtering
easier for users.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/eightyCharacters"
uniqueItems: true
minItems: 1
alternateIdentifiers:
"$id": "#/summary/alternateIdentifiers"
"$comment": 'DATA-CITE alternate-identifiers used. Note, will support comma separated list for backwards compatibility with other systems'
title: Alternate dataset identifiers
description: Alternate dataset identifiers or local identifiers
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/shortDescription"
uniqueItems: true
minItems: 1
doiName:
"$id": "#/summary/doiName"
title: Digital Object Identifier
description: All HDR UK registered datasets should either have a Digital Object
Identifier (DOI) or be working towards obtaining one. If a DOI is available,
please provide the DOI.
allOf:
- "$ref": "#/definitions/doi"
"$comment": 'Vocabulary: DOI Data Dictionary '
examples:
- 10.3399/bjgp17X692645
organisation:
"$id": "#/definitions/organisation"
type: object
required:
- name
- contactPoint
title: Organisation Metadata
description: Describes an organisation for purposes of discovery and identification.
properties:
identifier:
"$id": "#/organisation/identifier"
title: Organisation Identifier
description: "Please provide a Grid.ac identifier (see https://www.grid.ac/institutes)
for your organisation. If your organisation does not have a Grid.ac identifier please
use the “suggest and institute” function here: https://www.grid.ac/institutes#"
"$comment": https://schema.org/identifier
allOf:
- "$ref": "#/definitions/url"
name:
"$id": "#/organisation/name"
title: Organisation Name
description: Name of the organisation
"$comment": https://schema.org/name
allOf:
- "$ref": "#/definitions/eightyCharacters"
logo:
"$id": "#/organisation/logo"
title: Organisation Logo
description: Please provide a logo associated with the Gateway Organisation using a
valid URL. The following formats will be accepted .jpg, .png or .svg.
"$comment": https://schema.org/logo
allOf:
- "$ref": "#/definitions/url"
description:
"$id": "#/organisation/description"
title: Organisation Description
description: Please provide a URL that describes the organisation.
"$comment": https://schema.org/description
allOf:
- "$ref": "#/definitions/description"
contactPoint:
"$id": "#/organisation/contactPoint"
title: Organisation Contact Point
description: Organisation contact point(s)
"$comment": https://schema.org/contactPoint
anyOf:
- "$ref": "#/definitions/emailAddress"
- type: array
items:
allOf:
- "$ref": "#/definitions/emailAddress"
memberOf:
"$id": "#/organisation/memberOf"
title: Organisation Membership
description: Please indicate if the organisation is an Alliance Member or a Hub.
"$comment": https://schema.org/memberOf
allOf:
- "$ref": "#/definitions/memberOf"
accessRights:
"$id": "#/organisation/accessRights"
title: Organisation Default Access Rights
"$comment": dct:access_rights
description: The URL of a webpage where the data access request process and/or
guidance is provided. If there is more than one access process i.e. industry
vs academic please provide both.
anyOf:
- type: string
format: uri
- type: array
items:
type: string
format: uri
deliveryLeadTime:
"$id": "#/member/deliveryLeadTime"
title: Access Request Duration
"$comment": https://schema.org/deliveryLeadTime
description: "Please provide an indication of the typical processing times based
on the types of requests typically received. Note: This value will be used as
default access request duration for all datasets submitted by the organisation.
However, there will be the opportunity to overwrite this value for each dataset."
allOf:
- "$ref": "#/definitions/deliveryLeadTime"
accessService:
"$id": "#/member/accessService"
title: Organisation Access Service
"$comment": dcat:accessService
examples:
- https://cnfl.extge.co.uk/display/GERE/Research+Environment+User+Guide
description: 'Please provide a brief description of the data access services that are available including: environment that is currently available to researchers;additional consultancy and services;any indication of costs associated.
If no environment is currently available, please indicate the current plans and timelines when and how data will be made available to researchers
Note: This value will be used as default access environment for all datasets submitted by the organisation. However, there will be the opportunity to overwrite this value for each dataset.'
allOf:
- "$ref": "#/definitions/longDescription"
accessRequestCost:
"$id": "#/member/accessRequestCost"
title: Organisation Access Request Cost
"$comment": No standard identified
description: "Please provide link(s) to a webpage detailing the commercial model for processing data access requests for the organisation (if available) Definition: Indication of commercial model or cost (in GBP) for processing each data access request by the data custodian."
allOf:
- "$ref": "#/definitions/longDescription"
dataUseLimitation:
"$id": "#/member/dataUseLimitation"
title: Data Use Limitation
"$comment": https://www.ebi.ac.uk/ols/ontologies/duo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000001
description: "Please provide an indication of consent permissions for datasets and/or
materials, and relates to the purposes for which datasets and/or material might be
removed, stored or used. Notes: where there are existing data-sharing arrangements
such as the HDR UK HUB data sharing agreement or the NIHR HIC data sharing agreement
this should be indicated within access rights. This value will be used as terms for
all datasets submitted by the organisation. However, there will be the opportunity
to overwrite this value for each dataset."
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/dataUseLimitation"
uniqueItems: true
minItems: 1
dataUseRequirements:
"$id": "#/member/dataUseRequirements"
title: Data Use Requirements
description: Please indicate fit here are any additional conditions set
for use if any, multiple requirements may be provided. Please ensure that
these restrictions are documented in access rights information.
"$comment": https://www.ebi.ac.uk/ols/ontologies/duo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000001
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/dataUseRequirements"
uniqueItems: true
minItems: 1
documentation:
"$id": "#/definitions/member"
additionalProperties: false
properties:
description:
"$id": "#/properties/documentation/description"
title: Description
"$comment": dc:description, https://schema.org/description
description: A free-text description of the record.
allOf:
- "$ref": "#/definitions/description"
associatedMedia:
"$id": "#/properties/documentation/associatedMedia"
title: Associated Media
"$comment": https://schema.org/associatedMedia
examples:
- PDF Document that describes study protocol
description: 'Please provide any media associated with the Gateway Organisation
using a valid URI for the content. This is an opportunity to provide additional
context that could be useful for researchers wanting to understand more
about the dataset and its relevance to their research question. The following
formats will be accepted .jpg, .png or .svg, .pdf, .xslx or .docx. Note:
media asset can be hosted by the organisation or uploaded using the onboarding
portal.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/url"
uniqueItems: true
minItems: 1
isPartOf:
"$id": "#/properties/documentation/isPartOf"
title: Group
"$comment": "https://schema.org/isPartOf NOTE: we may make Groups first class citizens so the are navigable"
default: NOT APPLICABLE
examples:
- Hospital Episodes Statistics datasets (A&E, APC, OP, AC MSDS).
description: Please complete only if the dataset is part of a group or family
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
anyOf:
- "$ref": "#/definitions/url"
- "$ref": "#/definitions/eightyCharacters"
- type: string
enum:
- NOT APPLICABLE
uniqueItems: true
minItems: 1
coverage:
"$id": "#/definitions/coverage"
additionalProperties: false
properties:
spatial:
"$id": "#/properties/coverage/spatial"
title: Geographic Coverage
"$comment": dct:spatial
description: The geographical area covered by the dataset. It is recommended that links are to entries in a well-maintained gazetteer such as https://www.geonames.org/ or https://what3words.com/daring.lion.race.
examples:
- 'https://www.geonames.org/2635167/united-kingdom-of-great-britain-and-northern-ireland.html'
allOf:
- "$ref": "#/definitions/url"
typicalAgeRange:
"$id": "#/properties/coverage/typicalAgeRange"
title: Age Range
"$comment": https://schema.org/typicalAgeRange
description: Please indicate the age range in whole years of participants in the
dataset. Please provide range in the following format ‘[min age] – [max age]’
where both the minimum and maximum are whole numbers (integers).
allOf:
- "$ref": "#/definitions/ageRange"
physicalSampleAvailability:
"$id": "#/properties/coverage/physicalSampleAvailability"
title: Physical Sample Availability
"$comment": No standard identified. Used enumeration from the UK Tissue Directory.
examples:
- BONE MARROW
description: Availability of physical samples associated with the dataset.
If samples are available, please indicate the types of samples that are
available. More than one type may be provided. If sample are not yet available,
please provide “AVAILABILITY TO BE CONFIRMED”. If samples are not available,
then please provide “NOT AVAILABLE”.
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
contains:
"$ref": "#/definitions/physicalSampleAvailability"
uniqueItems: true
minItems: 1
followup:
"$id": "#/properties/coverage/followup"
title: Followup
"$comment": No standard identified
default: UNKNOWN
description: If known, what is the typical time span that a patient appears
in the dataset (follow up period)
allOf:
- "$ref": "#/definitions/followup"
pathway:
"$id": "#/properties/coverage/pathway"
title: Pathway
"$comment": No standard identified
description: Please indicate if the dataset is representative of the patient
pathway and any limitations the dataset may have with respect to pathway
coverage. This could include if the dataset is from a single speciality
or area, a single tier of care, linked across two tiers (e.g. primary and
secondary care), or an integrated care record covering the whole patient
pathway.
allOf:
- "$ref": "#/definitions/description"
provenance:
"$id": "#/definitions/provenance"
required:
- temporal
additionalProperties: false
properties:
origin:
"$id": "#/definitions/provenance/origin"
allOf:
- "$ref": "#/definitions/origin"
temporal:
"$id": "#/definitions/provenance/temporal"
allOf:
- "$ref": "#/definitions/temporal"
origin:
"$id": "#/definitions/origin"
additionalProperties: false
properties:
purpose:
"$id": "#/properties/provenance/origin/purpose"
title: Purpose
"$comment": https://ddialliance.org/Specification/DDI-Lifecycle/3.3/XMLSchema/FieldLevelDocumentation/
description: Pleases indicate the purpose(s) that the dataset was collected.
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
- "$ref": "#/definitions/purpose"
uniqueItems: true
minItems: 1
source:
"$id": "#/properties/provenance/origin/source"
title: Source
"$comment": https://dublincore.org/specifications/dublin-core/dcmi-terms/#source
description: Pleases indicate the source of the data extraction
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
- "$ref": "#/definitions/source"
uniqueItems: true
minItems: 1
collectionSituation:
"$id": "#/properties/provenance/origin/collectionSituation"
title: Setting
"$comment": https://ddialliance.org/Specification/DDI-Lifecycle/3.2/XMLSchema/FieldLevelDocumentation/
description: Pleases indicate the setting(s) where data was collected. Multiple
settings may be provided
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
- "$ref": "#/definitions/setting"
uniqueItems: true
minItems: 1
temporal:
"$id": "#/definitions/temporal"
required:
- accrualPeriodicity
- timeLag
- startDate
additionalProperties: false
properties:
accrualPeriodicity:
"$id": "#/properties/provenance/temporal/accrualPeriodicity"
title: Periodicity
"$comment": dct:accrualPeriodicity
default: ''
description: 'Please indicate the frequency of publishing. If a dataset is
published regularly please choose a publishing periodicity from the constrained
list and indicate the next release date. When the release date becomes historical,
a new release date will be calculated based on the publishing periodicity.
If a dataset has been published and will remain static please indicate that
it is static and indicated when it was released. If a dataset is released
on an irregular basis or “on-demand” please indicate that it is Irregular
and leave release date as null. If a dataset can be published in real-time
or near-real-time please indicate that it is continuous and leave release
date as null. Notes: see https://www.dublincore.org/specifications/dublin-core/collection-description/frequency/'
allOf:
- "$ref": "#/definitions/periodicity"
distributionReleaseDate:
"$id": "#/properties/provenance/temporal/distributionReleaseDate"
title: Release Date
"$comment": dcat:distribution_release_date
description: 'Date of the latest release of the dataset. If this is a regular
release i.e. quarterly, or this is a static dataset please complete this
alongside Periodicity. If this is Irregular or Continuously released please
leave this blank. Notes: Periodicity and release date will be used to determine
when the next release is expected. E.g. if the release date is documented as 01/01/2020
and it is now 20/04/2020 and there is a quarterly release schedule, the
latest release will be calculated as 01/04/2020.'
anyOf:
- type: string
format: date
- type: string
format: date-time
startDate:
"$id": "#/properties/provenance/temporal/startDate"
title: Start Date
"$comment": dcat:startDate
description: The start of the time period that the dataset provides coverage
for. If there are multiple cohorts in the dataset with varying start dates,
please provide the earliest date and use the description or the media attribute
to provide more information.
anyOf:
- type: string
format: date
- type: string
format: date-time
endDate:
"$id": "#/properties/provenance/temporal/endDate"
title: End Date
"$comment": dcat:endDate
description: The end of the time period that the dataset provides coverage
for. If the dataset is “Continuous” and has no known end date, please leave
blank. If there are multiple cohorts in the dataset with varying end dates,
please provide the latest date and use the description or the media attribute
to provide more information.
anyOf:
- type: string
format: date
- type: string
format: date-time
- type: string
enum:
- NOT APPLICABLE
timeLag:
"$id": "#/properties/provenance/temporal/timeLag"
title: Time Lag
"$comment": No standard identified
description: Please indicate the typical time-lag between an event and the
data for that event appearing in the dataset
allOf:
- "$ref": "#/definitions/timeLag"
accessibility:
"$id": "#/definitions/accessibility"
required:
- access
additionalProperties: false
properties:
usage:
"$id": "#/definitions/accessibility/usage"
title: Usage
description: This section includes information about how the data can be used and how it is currently being used
"$ref": "#/definitions/usage"
access:
"$id": "#/definitions/accessibility/access"
title: Access
description: This section includes information about data access
"$ref": "#/definitions/access"
formatAndStandards:
"$id": "#/definitions/accessibility/formatAndStandards"
title: Format and Standards
description: Section includes technical attributes for language vocabularies, sizes etc. and gives researchers facts about and processing the underlying data in the dataset.
"$ref": "#/definitions/formatAndStandards"
usage:
"$id": "#/definitions/usage"
additionalProperties: false
properties:
dataUseLimitation:
"$id": "#/properties/accessibility/usage/dataUseLimitation"
title: Data Use Limitation
"$comment": https://www.ebi.ac.uk/ols/ontologies/duo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000001
description: 'Please provide an indication of consent permissions for datasets
and/or materials, and relates to the purposes for which datasets and/or
material might be removed, stored or used. NOTE: we have extended the DUO
to include a value for NO LINKAGE'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/dataUseLimitation"
uniqueItems: true
minItems: 1
dataUseRequirements:
"$id": "#/properties/accessibility/usage/dataUseRequirements"
title: Data Use Requirements
description: Please indicate fit here are any additional conditions set
for use if any, multiple requirements may be provided. Please ensure that
these restrictions are documented in access rights information.
"$comment": https://www.ebi.ac.uk/ols/ontologies/duo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000001
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/dataUseRequirements"
uniqueItems: true
minItems: 1
resourceCreator:
"$id": "#/properties/accessibility/usage/resourceCreator"
title: Citation Requirements
"$comment": dct:creator
description: Please provide the text that you would like included as part of any citation that credits this dataset. This is typically just the name of the publisher. No employee details should be provided.
allOf:
- "$ref": "#/definitions/shortDescription"
investigations:
title: Investigations
"$comment": No standard identified
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/url"
isReferencedBy:
title: Citations
"$comment": 'dct:isReferencedBy '
description: Please provide the keystone paper associated with the dataset.
Also include a list of known citations, if available and should be links
to existing resources where the dataset has been used or referenced. Please
provide multiple entries, or if you are using a csv upload please provide
them as a tab separated list. [Author] ([Year]) [Title] . [DOI] . [Source]
anyOf:
- "$ref": "#/definitions/doi"
- type: array
items:
- "$ref": "#/definitions/doi"
access:
"$id": "#/definitions/access"
required:
- accessRights
- jurisdiction
- dataController
additionalProperties: false
properties:
accessRights:
"$id": "#/properties/accessibility/access/accessRights"
title: Access Rights
"$comment": 'dct:access_rights NOTE: need to ensure that this is consistent across the organisation info and the dataset info'
anyOf:
- type: string
pattern: "^In Progress$"
- type: string
format: uri
- type: array
items:
type: string
format: uri
accessService:
"$id": "#/properties/accessibility/access/accessService"
title: Access Service
"$comment": 'dcat:accessService '
examples:
- https://cnfl.extge.co.uk/display/GERE/Research+Environment+User+Guide
description: 'Please provide a brief description of the data access services that are available including: environment that is currently available to researchers;additional consultancy and services;any indication of costs associated.
If no environment is currently available, please indicate the current plans and timelines when and how data will be made available to researchers
Note: This value will be used as default access environment for all datasets submitted by the organisation. However, there will be the opportunity to overwrite this value for each dataset.'
allOf:
- "$ref": "#/definitions/longDescription"
accessRequestCost:
"$id": "#/member/accessRequestCost"
title: Organisation Access Request Cost
"$comment": No standard identified
description: "Please provide link(s) to a webpage detailing the commercial model for processing data access requests for the organisation (if available) Definition: Indication of commercial model or cost (in GBP) for processing each data access request by the data custodian."
allOf:
- "$ref": "#/definitions/longDescription"
deliveryLeadTime:
"$id": "#/properties/accessibility/access/deliveryLeadTime"
title: Access Request Duration
"$comment": https://schema.org/deliveryLeadTime
description: Please provide an indication of the typical processing times based on the types of requests typically received.
allOf:
- "$ref": "#/definitions/deliveryLeadTime"
jurisdiction:
"$id": "#/properties/accessibility/access/jurisdiction"
title: Jurisdiction
default: GB-ENG
"$comment": 'http://purl.org/dc/terms/Jurisdiction FIXME: Add ISO 3166-2 Subdivision code pattern'
description: 'Please use country code from ISO 3166-1 country codes and the associated
ISO 3166-2 for regions, cities, states etc. for the country/state under whose
laws the data subjects’ data is collected, processed and stored.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/isocountrycode"
dataController:
"$id": "#/properties/accessibility/access/dataController"
title: Data Controller
"$comment": " dpv:DataController"
description: Data Controller means a person/entity who (either alone or jointly or in common with other persons/entities) determines the purposes for which and the way any Data Subject data, specifically personal data or are to be processed.
allOf:
- "$ref": "#/definitions/longDescription"
dataProcessor:
"$id": "#/properties/accessibility/access/dataProcessor"
title: Data Processor
"$comment": dpv:DataProcessor
description: A Data Processor, in relation to any Data Subject data, specifically personal data, means any person/entity (other than an employee of the data controller) who processes the data on behalf of the data controller.
allOf:
- "$ref": "#/definitions/longDescription"
formatAndStandards:
"$id": "#/definitions/formatAndStandards"
additionalProperties: false
required:
- vocabularyEncodingScheme
- conformsTo
- language
- format
properties:
vocabularyEncodingScheme:
"$id": "#/properties/accessibility/formatAndStandards/vocabularyEncodingScheme"
title: Controlled Vocabulary
"$comment": 'https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/dcam/VocabularyEncodingScheme'
default: LOCAL
description: 'List any relevant terminologies / ontologies / controlled
vocabularies, such as ICD 10 Codes, NHS Data Dictionary National Codes
or SNOMED CT International, that are being used by the dataset. If the
controlled vocabularies are local standards, please make that explicit.
If you are using a standard that has not been included in the list, please
use “other” and contact support desk to ask for an addition. Notes: More
than one vocabulary may be provided.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/controlledVocabulary"
minItems: 0
conformsTo:
"$id": "#/properties/accessibility/formatAndStandards/conformsTo"
title: Conforms To
"$comment": 'dct:conformsTo'
default: LOCAL
description: 'List standardised data models that the dataset has been stored
in or transformed to, such as OMOP or FHIR. If the data is only available
in a local format, please make that explicit. If you are using a standard
that has not been included in the list, please use “other” and contact support
desk to ask for an addition.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
- "$ref": "#/definitions/standardisedDataModels"
language:
"$id": "#/properties/accessibility/formatAndStandards/language"
title: Language
description: This should list all the languages in which the dataset metadata
and underlying data is made available.
default: en
"$comment": 'dct:language. FIXME: Conforms to spec, but may be a list of strings given cardinality
1:*. Validate against external list of languages. Resources defined by the Library
of Congress (ISO 639-1, ISO 639-2) SHOULD be used.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/language"
minItems: 1
format:
"$id": "#/properties/accessibility/formatAndStandards/format"
title: Format
description: 'If multiple formats are available please specify. See application,
audio, image, message, model, multipart, text, video, https://www.iana.org/assignments/media-types/media-types.xhtml
Note: If your file format is not included in the current list of formats,
please indicate other. If you are using the HOP you will be directed to
a service desk page where you can request your additional format. If not
please go to: https://metadata.atlassian.net/servicedesk/customer/portal/4
to request your format.'
"$comment": 'http://purl.org/dc/terms/format'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/format"
minItems: 1
enrichmentAndLinkage:
"$id": "#/definitions/enrichmentAndLinkage"
additionalProperties: false
properties:
qualifiedRelation:
"$id": "#/properties/enrichmentAndLinkage/qualifiedRelation"
title: Linked Datasets
"$comment": 'dcat:qualifiedRelation'
description: 'If applicable, please provide the DOI of other datasets that
have previously been linked to this dataset and their availability. If
no DOI is available, please provide the title of the datasets that can
be linked, where possible using the same title of a dataset previously
onboarded to the HOP. Note: If all the datasets from Gateway organisation
can be linked please indicate “ALL” and the onboarding portal will automate
linkage across the datasets submitted.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/url"
derivation:
title: Derivations
"$comment": 'prov:Derivation'
description: 'Indicate if derived datasets or predefined extracts are available
and the type of derivation available. Notes. Single or multiple dimensions
can be provided as a derived extract alongside the dataset.'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/abstractText"
tools:
"$id": "#/properties/enrichmentAndLinkage/tools"
title: Tools
"$comment": 'No standard identified. We encourage users to adopt a model along
the lines of https://www.ga4gh.org/news/tool-registry-service-api-enabling-an-interoperable-library-of-genomics-analysis-tools/'
description: 'Please provide the URL of any analysis tools or models that
have been created for this dataset and are available for further use.
Multiple tools may be provided. Note: We encourage users to adopt a model
along the lines of https://www.ga4gh.org/news/tool-registry-service-api-enabling-an-interoperable-library-of-genomics-analysis-tools/'
anyOf:
- "$ref": "#/definitions/commaSeparatedValues"
- type: array
items:
allOf:
- "$ref": "#/definitions/url"
minItems: 0
observation:
"$id": "#/definitions/observation"
required:
- observedNode
- measuredValue
- observationDate
- measuredProperty
additionalProperties: false
properties:
observedNode:
"$id": "#/properties/observation/observedNode"