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NDE_schema.jsonld
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{
"@context": {
"schema": "http://schema.org/",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"bioschemas": "https://discovery.biothings.io/view/bioschemas/",
"niaid": "https://discovery.biothings.io/view/niaid/",
"nde": "https://discovery.biothings.io/view/nde/"
},
"@graph": [
{
"@id": "nde:Dataset",
"@type": "rdfs:Class",
"rdfs:comment": "Datasets contained in the NIAID Data Ecosystem. A dataset is a collection of data of a particular experimental type. The NIAID Data Ecosystem is an environment to find and access and infectious and immune-mediated disease data and computational tools to speed the development of diagnostics, therapeutics, and vaccines. The NIAID Data Ecosystem Discovery Portal harvests metadata from dataset repository and harmonizes them to this schema to enable easy cross-platform dataset searching and filtering.",
"abstract": "Datasets contained in the NIAID Data Ecosystem. A dataset is a collection of data of a particular experimental type.",
"rdfs:label": "Dataset",
"rdfs:subClassOf": {
"@id": "niaid:Dataset"
},
"$validation": {
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"citedBy": {
"description": "Publications, datasets, or computational tools that cite the work.",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
],
"owl:cardinality": "many"
},
"date": {
"description": "Date the work has changed: most recent date of dateModified, datePublished, and dateCreated.",
"abstract": "date changed",
"format": "date",
"type": "string",
"owl:cardinality": "one"
},
"doi": {
"description": "Digital Object Identifier (DOI) for the work, not any associated publications.",
"abstract": "digital object identifier",
"type": "string",
"owl:cardinality": "one"
},
"isRelatedTo": {
"description": "Datasets which are related to the given dataset; often datasets involved in the same study. These linkages are created via human curation.",
"abstract": "related datasets (via curation)",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
],
"owl:cardinality": "many"
},
"isSimilarTo": {
"description": "Datasets or computational tools which are similar to the work, based on terms in the names, descriptions, authors, measurementTechniques, infectiousAgents, healthConditions, etc.",
"abstract": "similar datasets (auto-assigned)",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
],
"owl:cardinality": "many"
},
"isBasisFor": {
"description": "A dataset which reuses the dataset.",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
],
"owl:cardinality": "many"
},
"nctid": {
"description": "ClinicalTrials.gov identifier associated with the dataset.",
"abstract": "ClinicalTrials.gov ID",
"type": "string",
"owl:cardinality": "many"
},
"relationship": {
"description": "How an associated work is related to the dataset.",
"type": "string",
"owl:cardinality": "one"
},
"topicCategory": {
"description": "Topic of the work. This topic may be assigned by a human curator or through automated algorithms.",
"abstract": "topic",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/topic"
}
},
{
"$ref": "#/definitions/topic"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedterm"
}
},
{
"$ref": "#/definitions/definedterm"
}
],
"owl:cardinality": "many"
},
"infectiousAgent": {
"description": "Infectious agent(s) / pathogen(s) which are the focus of the work (like SARS-CoV-2).",
"abstract": "infectious agent / pathogen",
"anyOf": [
{
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"],
"ontology": ["ncbitaxon"]
}
},
{
"items": {
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_10239", "http://purl.obolibrary.org/obo/NCBITaxon_2"],
"ontology": ["ncbitaxon"]
}
},
"type": "array"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedterm"
}
},
{
"$ref": "#/definitions/definedterm"
}
],
"owl:cardinality": "many"
},
"healthCondition": {
"description": "The health condition(s) /infectious disease(s) which are the focus of the work (like COVID-19, coronavirus).",
"abstract": "health condition/disease",
"anyOf": [
{
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001",
"http://purl.obolibrary.org/obo/DOID_4",
"http://purl.obolibrary.org/obo/HP_0000001",
"http://purl.obolibrary.org/obo/NCIT_C7057"],
"ontology": ["mondo","hpo","doid","ncit"]
}
},
{
"items": {
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://purl.obolibrary.org/obo/MONDO_0000001",
"http://purl.obolibrary.org/obo/DOID_4",
"http://purl.obolibrary.org/obo/HP_0000001",
"http://purl.obolibrary.org/obo/NCIT_C7057"],
"ontology": ["mondo","hpo","doid","ncit"]
}
},
"type": "array"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedterm"
}
},
{
"$ref": "#/definitions/definedterm"
}
],
"owl:cardinality": "many"
},
"funding": {
"description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution.",
"abstract": "funding source (grant, contract, etc.)",
"oneOf": [
{
"type": "object",
"@type": "MonetaryGrant",
"description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution",
"properties": {
"funder": {
"description": "An organization associated with a creator or funder of a dataset",
"oneOf": [
{
"type": "object",
"@type": "Organization",
"description": "Information about a single funder",
"properties": {
"name": {
"type": "string",
"description": "An organization associated with a creator or funder of a dataset"
},
"parentOrganization": {
"type": "string",
"description": "name of the parent funding organization"
}
},
"required": [
"name"
]
},
{
"type": "array",
"items": {
"type": "object",
"@type": "Organization",
"description": "Information about a single funder",
"properties": {
"name": {
"type": "string",
"description": "An organization associated with a creator or funder of a dataset"
},
"parentOrganization": {
"type": "string",
"description": "name of the parent funding organization"
}
},
"required": [
"name"
]
}
}
]
},
"description": {
"type": "string",
"description": "description about the funding award / grant"
},
"url": {
"type": "string",
"description": "award / grant URL"
},
"identifier": {
"type": "string",
"description": "Unique identifier(s) for the grant(s) used to fund the Dataset"
}
},
"required": [
"funder",
"identifier"
]
},
{
"type": "array",
"items": {
"type": "object",
"@type": "MonetaryGrant",
"description": "Funding that supports (sponsors) the collection of this dataset through some kind of financial contribution",
"properties": {
"funder": {
"description": "An organization associated with a creator or funder of a dataset",
"oneOf": [
{
"type": "object",
"@type": "Organization",
"description": "Information about a single funder",
"properties": {
"name": {
"type": "string",
"description": "An organization associated with a creator or funder of a dataset"
},
"parentOrganization": {
"type": "string",
"description": "name of the parent funding organization"
}
},
"required": [
"name"
]
},
{
"type": "array",
"items": {
"type": "object",
"@type": "Organization",
"description": "Information about a single funder",
"properties": {
"name": {
"type": "string",
"description": "An organization associated with a creator or funder of a dataset"
},
"parentOrganization": {
"type": "string",
"description": "name of the parent funding organization"
}
},
"required": [
"name"
]
}
}
]
},
"description": {
"type": "string",
"description": "description about the funding award / grant"
},
"url": {
"type": "string",
"description": "award / grant URL"
},
"identifier": {
"type": "string",
"description": "Unique identifier(s) for the grant(s) used to fund the Dataset"
}
},
"required": [
"funder",
"identifier"
]
}
}
],
"owl:cardinality": "many"
},
"species": {
"description": "Species / host organism from which the dataset has been collected.",
"abstract": "species/host organism",
"anyOf": [
{
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"],
"ontology": ["ncbitaxon"]
}
},
{
"items": {
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://purl.obolibrary.org/obo/NCBITaxon_131567", "http://purl.obolibrary.org/obo/NCBITaxon_10239"],
"ontology": ["ncbitaxon"]
}
},
"type": "array"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedterm"
}
},
{
"$ref": "#/definitions/definedterm"
}
],
"owl:cardinality": "many"
},
"distribution": {
"description": "A downloadable form of this dataset, at a specific location, in a specific format.",
"abstract": "download link",
"oneOf": [
{
"items": {
"@type": "DataDownload",
"description": "A dataset in downloadable form.",
"properties": {
"contentUrl": {
"format": "uri",
"type": "string"
},
"encodingFormat": {
"description": "file type (ex: XLSX)",
"type": "string"
},
"dateModified": {
"format": "date",
"description": "date the file was modified",
"type": "string"
}
},
"required": ["dateModified", "contentUrl"],
"type": "object"
},
"type": "array"
},
{
"@type": "DataDownload",
"description": "A dataset in downloadable form.",
"properties": {
"contentUrl": {
"format": "uri",
"type": "string"
},
"encodingFormat": {
"description": "file type (ex: XLSX)",
"type": "string"
},
"dateModified": {
"format": "date",
"description": "date the file was modified",
"type": "string"
}
},
"required": ["dateModified", "contentUrl"],
"type": "object"
}
],
"owl:cardinality": "many"
},
"includedInDataCatalog": {
"description": "Data or tool catalog where the work is published; original source of the metadata.",
"abstract": "catalog containing the work",
"oneOf": [
{
"$ref": "#/definitions/catalog"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/catalog"
}
}
],
"owl:cardinality": "one"
},
"measurementTechnique": {
"description": "A technique or technology used in a dataset corresponding to the method used for measuring the corresponding variable(s) (described using variableMeasured). For example, if variableMeasured is molecule concentration, measurementTechnique could be: \"mass spectrometry\" or \"nmr spectroscopy\" or \"colorimetry\" or \"immunofluorescence\".",
"abstract": "measurement technique used to collect the dataset",
"anyOf": [
{
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://edamontology.org/topic_3361",
"http://purl.obolibrary.org/obo/NCIT_C20368",
"http://purl.obolibrary.org/obo/MMO_0000000",
"http://www.ebi.ac.uk/efo/EFO_0000001"],
"ontology": ["edam", "ncit", "mmo","efo"]
}
},
{
"items": {
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://edamontology.org/topic_3361",
"http://purl.obolibrary.org/obo/NCIT_C20368",
"http://purl.obolibrary.org/obo/MMO_0000000",
"http://www.ebi.ac.uk/efo/EFO_0000001"],
"ontology": ["edam", "ncit", "mmo","efo"]
}
},
"type": "array"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedterm"
}
},
{
"$ref": "#/definitions/definedterm"
}
],
"owl:cardinality": "many"
},
"variableMeasured": {
"description": "Variables measured within the dataset.",
"oneOf": [
{
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001",
"http://purl.obolibrary.org/obo/CMO_0000000",
"http://purl.obolibrary.org/obo/NCIT_C25209"],
"ontology": ["efo", "cmo","ncit"]
}
},
{
"items": {
"description": "collection of vocabulary terms defined in ontologies",
"strict": false,
"type": "string",
"vocabulary": {
"children_of": ["http://www.ebi.ac.uk/efo/EFO_0000001",
"http://purl.obolibrary.org/obo/CMO_0000000",
"http://purl.obolibrary.org/obo/NCIT_C25209"],
"ontology": ["efo", "cmo","ncit"]
}
},
"type": "array"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedterm"
}
},
{
"$ref": "#/definitions/definedterm"
}
],
"owl:cardinality": "many"
},
"abstract": {
"description": "Short description that summarizes a work.",
"abstract": "short description",
"type": "string",
"owl:cardinality": "one"
},
"aggregateRating": {
"description": "The overall rating, based on a collection of reviews or ratings, of the work. These ratings can be collected based on user reviews or through Altmetric scores of web-based citations.",
"abstract": "rating of the work",
"oneOf": [
{
"items": {
"@type": "AggregateRating",
"type": "object",
"properties": {
"ratingCount": {
"description": "Total number of ratings",
"type": "integer"
},
"ratingValue": {
"description": "Average rating",
"type": "string"
},
"itemReviewed": {
"description": "What is being reviewed",
"type": "string"
}
},
"required": ["ratingValue"],
"recommended": ["ratingCount", "itemReviewed"]
},
"type": "array"
},
{
"@type": "AggregateRating",
"type": "object",
"properties": {
"ratingCount": {
"description": "Total number of ratings",
"type": "integer"
},
"ratingValue": {
"description": "Average rating",
"type": "string"
},
"itemReviewed": {
"description": "What is being reviewed",
"type": "string"
}
},
"required": ["ratingValue"],
"recommended": ["ratingCount", "itemReviewed"]
}
],
"owl:cardinality": "many"
},
"author": {
"description": "Author or creator of the work. The default field for the author or creator of the work.",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/person"
}
},
{
"$ref": "#/definitions/person"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/organization"
}
},
{
"$ref": "#/definitions/organization"
}
],
"owl:cardinality": "many"
},
"citation": {
"description": "A citation or reference to a publication, dataset, or computational tool which uses the dataset. Examples: a publication which describes the collection/analysis of the dataset, a publication which reuses the dataset in a secondary analysis, a dataset which extends the existing dataset, or a computational tool which relies on the dataset.",
"abstract": "citation to the work",
"owl:cardinality": "many",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
]
},
"conditionsOfAccess": {
"description": "Conditions that affect the availability of, or method(s) of access to, the work. Options include open (freely available), restricted (may include restrictions such as on use), closed (requires registration to access), or embargoed (unpublished).",
"abstract": "accessibility of the work",
"type": "string",
"enum": ["Closed", "Open", "Restricted", "Embargoed"],
"owl:cardinality": "one"
},
"creator": {
"description": "The creator/author of this work; equivalent to author. Please use author by default. Use creator if author/creator in a record of this work submitted elsewhere differs from the author/creator entered into the author field.",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/person"
}
},
{
"$ref": "#/definitions/person"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/organization"
}
},
{
"$ref": "#/definitions/organization"
}
],
"owl:cardinality": "many"
},
"dateCreated": {
"description": "Date the work was created.",
"format": "date",
"type": "string",
"owl:cardinality": "one"
},
"dateModified": {
"description": "Date the work was modified.",
"format": "date",
"type": "string",
"owl:cardinality": "one"
},
"datePublished": {
"description": "Date the work was first published.",
"format": "date",
"type": "string",
"owl:cardinality": "one"
},
"hasPart": {
"description": "Associated materials for the dataset, including data dictionaries and data limitation descriptions.",
"abstract": "data limitations or dictionaries",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
],
"owl:cardinality": "many"
},
"inLanguage": {
"description": "The language of the content of the dataset.",
"owl:cardinality": "many",
"oneOf": [
{
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "language of the work"
},
"alternateName": {
"type": "string"
}
},
"required": ["name"],
"recommended": ["alternateName"]
},
"type": "array"
},
{
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "language of the work"
},
"alternateName": {
"type": "string"
}
},
"required": ["name"],
"recommended": ["alternateName"]
}
]
},
"interactionStatistic": {
"description": "The number of interactions with the work, such as page views or tool downloads.",
"abstract": "views or downloads",
"oneOf": [
{
"items": {
"@type": "InteractionCounter",
"type": "object",
"properties": {
"interactionType": {
"type": "string"
},
"userInteractionCount": {
"type": "integer"
}
},
"required": ["interactionType", "userInteractionCount"]
},
"type": "array"
},
{
"@type": "InteractionCounter",
"type": "object",
"properties": {
"interactionType": {
"type": "string"
},
"userInteractionCount": {
"type": "integer"
}
},
"required": ["interactionType", "userInteractionCount"]
}
],
"owl:cardinality": "many"
},
"isAccessibleForFree": {
"description": "A flag to signal that the work is accessible for free.",
"abstract": "accessible without charge",
"type": "boolean",
"owl:cardinality": "one"
},
"isBasedOn": {
"description": "A dataset, publication, or computational tool from which this work is derived, modified, or adapted.",
"abstract": "dataset, publication, or tool used to create the work",
"owl:cardinality": "many",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
]
},
"isPartOf": {
"description": "Indicates a broader study, project, or collection the work is part of.",
"abstract": "study or project including the work",
"owl:cardinality": "many",
"anyOf": [
{
"type": "array",
"items": {
"$ref": "#/definitions/citation"
}
},
{
"$ref": "#/definitions/citation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
},
{
"$ref": "#/definitions/creativework"
}
]
},
"keywords": {
"description": "Keywords or tags used to describe this work.",
"abstract": "keywords or tags",
"oneOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "string"
}
],
"owl:cardinality": "many"
},
"license": {
"description": "A license document that applies to this work, typically indicated by URL.",
"abstract": "license for use",
"format": "uri",
"owl:cardinality": "one",
"type": "string"
},
"sdPublisher": {
"description": "Original publisher of the dataset metadata (like GenBank, ImmPort, etc.).",
"abstract": "original metadata source",
"oneOf": [
{
"$ref": "#/definitions/catalog"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/catalog"
}
}
],
"owl:cardinality": "many"
},
"spatialCoverage": {
"description": "The place(s) which are the focus of the dataset.",
"abstract": "geographic focus of the work",
"oneOf": [
{
"items": {
"@type": "AdministrativeArea",
"description": "Location information",
"properties": {
"administrativeType": {
"description": "the type of administrative area, such as country, state, county, or city",
"enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"],
"type": "string"
},
"alternateName": {
"description": "An alias for the location",
"oneOf": [
{
"type": "string"
},
{
"items": {
"type": "string"
},
"type": "array"
}
]
},
"identifier": {
"description": "An identifier for the location, preferably a Wikidata ID",
"type": "string"
},
"locationType": {
"description": "Categorization of how the location relates to the dataset",
"oneOf": [
{
"enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"],
"type": "string"
},
{
"items": {
"enum": ["residence", "exposure", "collection", "screening", "treatment", "study location", "other", "unknown"],
"type": "string"
},
"type": "array"
}
]
},
"name": {
"description": "The name of the location",
"type": "string"
}
},
"type": "object"
},
"type": "array"
},
{
"@type": "AdministrativeArea",
"description": "Location information",
"properties": {
"administrativeType": {
"description": "the type of administrative area, such as country, state, county, or city",
"enum": ["province", "district", "chiefdom", "village", "city", "country", "prefecture", "sub-prefecture", "clan", "Federal Capital Territory", "state", "Local Government Area", "ward"],
"type": "string"
},
"alternateName": {
"description": "An alias for the location",
"oneOf": [
{
"type": "string"