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labra/ctsa.json-schema

Last active September 5, 2019 16:42
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ctsa.json-schema
{
"@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#",
"bts": "http://discovery.biothings.io/bts/"
},
"@graph": [{
"@id": "bts:CTSADataset",
"@type": "rdfs:Class",
"rdfs:comment": "A schema describing Dataset from CTSA center",
"rdfs:label": "CTSADataset",
"rdfs:subClassOf": {
"@id": "schema:Dataset"
},
"$validation": {
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"name": {
"$comment": "the starting of inherented fields from schema:Dataset",
"description": "The name of the CTSA Dataset",
"type": "string"
},
"description": {
"description": "A description of the CTSA Dataset",
"type": "string"
},
"url": {
"description": "URL of the Dataset page if available.",
"type": "string",
"format": "uri"
},
"sameAs": {
"description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.",
"type": "uri"
},
"keywords": {
"description": "Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.",
"type": "array",
"items": {
"type": "string"
}
},
"datePublished": {
"description": "Date of first publication of this dataset.",
"oneOf": [{
"type": "string",
"format": "date-time"
},
{
"type": "string",
"format": "date"
}
]
},
"dateModified": {
"description": "The date on which the dataset was most recently modified.",
"oneOf": [{
"type": "string",
"format": "date-time"
},
{
"type": "string",
"format": "date"
}
]
},
"version": {
"description": "The version of the dataset.",
"type": "string"
},
"identifier": {
"description": "The identifier of the dataset if available, e.g. ID from repositories GEO, EGA.",
"type": "string"
},
"measurementTechnique": {
"description": "The technique or method used to produce the Dataset.",
"enum": [
"whole-genome sequencing",
"whole-exome sequencing",
"mass spectrum"
]
},
"creator": {
"description": "The creater (often the primary contact) of this dataset.",
"$ref": "#/definitions/person"
},
"contributor": {
"description": "The other contributor(s) of this dataset, besides the creator",
"oneOf": [{
"$ref": "#/definitions/person"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/person"
}
}
]
},
"publisher": {
"description": "The organization publish this dataset, usually the host institute.",
"type": "object",
"properties": {
"name": {
"type": "string"
},
"url": {
"type": "string",
"format": "uri"
}
},
"required": ["name"]
},
"license": {
"description": "Specify the data access license",
"type": "object",
"properties": {
"text": {
"type": "string"
},
"url": {
"type": "string",
"format": "uri"
}
},
"required": ["url"]
},
"citation": {
"description": "The citation of this dataset.",
"type": "object",
"properties": {
"text": {
"type": "string"
},
"url": {
"type": "string",
"format": "uri"
},
"identifier": {
"type": "string",
"description": "use PubMed id here"
}
},
"required": ["text"]
},
"samples": {
"description": "sample info of this dataset."
},
"funder": {
"description": "funder info of this dataset."
},
"includedInDataCatalog": {
"description": "This is a fixed CTSA DataCatalog.",
"type": "object",
"properties": {
"name": {
"const": "CTSA Datasets"
},
"url": {
"const": "https://ctsa.ncats.nih.gov/cd2h/"
}
}
}
},
"required": [
"name",
"description",
"creator",
"publisher",
"identifier"
],
"definitions": {
"person": {
"description": "Reusable person definition",
"type": "object",
"properties": {
"name": {
"type": "string"
},
"url": {
"type": "string",
"format": "uri"
}
},
"required": ["name"]
}
}
}
},
{
"@id": "bts:samples",
"@type": "rdf:Property",
"rdfs:comment": "Sample information including size, organism, tissus, etc.",
"rdfs:label": "samples",
"schema:domainIncludes": {
"@id": "bts:CTSADataset"
},
"schema:rangeIncludes": {
"@id": "bts:DataSamples"
}
},
{
"@id": "bts:funder",
"@type": "rdf:Property",
"rdfs:comment": "Funder information",
"rdfs:label": "funder",
"schema:domainIncludes": {
"@id": "bts:CTSADataset"
},
"schema:rangeIncludes": {
"@id": "bts:BioMedicalGrant"
}
},
{
"@id": "bts:DataSamples",
"@type": "rdfs:Class",
"rdfs:comment": "Sample information including size, organism, tissue, etc.",
"rdfs:label": "DataSamples",
"rdfs:subClassOf": {
"@id": "schema:Thing"
},
"$validation": {
"type": "object",
"properties": {
"size": {
"description": "the number of samples",
"type": "integer",
"minimum": 1
},
"organism": {
"description": "the organism of samples come from",
"oneOf": [{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
]
},
"tissue": {
"description": "the tissue of samples come from",
"oneOf": [{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
]
}
}
}
},
{
"@id": "bts:size",
"@type": "rdf:Property",
"rdfs:comment": "Sample size",
"rdfs:label": "size",
"schema:domainIncludes": {
"@id": "bts:DataSamples"
},
"schema:rangeIncludes": {
"@id": "schema:Integer"
}
},
{
"@id": "bts:organism",
"@type": "rdf:Property",
"rdfs:comment": "Sample organism",
"rdfs:label": "organism",
"schema:domainIncludes": {
"@id": "bts:DataSamples"
},
"schema:rangeIncludes": {
"@id": "schema:Text"
}
},
{
"@id": "bts:tissue",
"@type": "rdf:Property",
"rdfs:comment": "Sample tissue",
"rdfs:label": "tissue",
"schema:domainIncludes": {
"@id": "bts:DataSamples"
},
"schema:rangeIncludes": {
"@id": "schema:Text"
}
},
{
"@id": "bts:BioMedicalGrant",
"@type": "rdfs:Class",
"rdfs:comment": "BioMedical Grant information, typically from NIH or NSF",
"rdfs:label": "BioMedicalGrant",
"rdfs:subClassOf": {
"@id": "schema:Grant"
},
"$validation": {
"type": "object",
"properties": {
"identifier": {
"description": "the grant identifier, grant number or FAIN",
"type": "string"
},
"institute": {
"description": "The name of the funding institute, e.g. NIH or NSF",
"oneOf": [{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
]
},
"agency": {
"description": "The agency under the funding institute, e.g. NCATS, NHGRI, NCI etc.",
"oneOf": [{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
]
}
}
}
},
{
"@id": "bts:institute",
"@type": "rdf:Property",
"rdfs:comment": "The name of the funding institute, e.g. NIH or NSF",
"rdfs:label": "institute",
"schema:domainIncludes": {
"@id": "bts:BioMedicalGrant"
},
"schema:rangeIncludes": {
"@id": "schema:Text"
}
},
{
"@id": "bts:agency",
"@type": "rdf:Property",
"rdfs:comment": "The agency under the funding institute, e.g. NCATS, NHGRI, NCI etc.",
"rdfs:label": "agency",
"schema:domainIncludes": {
"@id": "bts:BioMedicalGrant"
},
"schema:rangeIncludes": {
"@id": "schema:Text"
}
}
]
}
Raw
ctsa.shex
prefix schema: <http://schema.org/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix bts: <http://discovery.biothings.io/bts/>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix dct: <http://purl.org/dc/terms/>
bts:CTSADatasetShape {
schema:name xsd:string // dct:description "The name of the CTSA Dataset" ;
schema:description xsd:string // dct:description "A description of the CTSA Dataset" ;
schema:url IRI
;
schema:sameAs IRI* ;
schema:keywords xsd:string * ;
schema:datePublished schema:Date ;
schema:dateModified schema:Date or schema:DateTime ;
schema:citation @bts:Citation ;
schema:version xsd:string ;
schema:identifier xsd:string ;
schema:measurementTechnique [
"whole-genome sequencing"
"whole-exome sequencing"
"mass spectrum"
] ;
schema:creator @bts:Person * ;
schema:contributor @bts:Person * ;
schema:publisher @bts:Publisher ;
schema:license . ? ; # TODO
schema:citation . *; # TODO
schema:samples . * ; # TODO
schema:funder . ?; # TODO
schema:includedInDataCatalog @bts:Catalog
}
bts:Person {
schema:name xsd:string ;
schema:url IRI
} // dct:description "Reusable person definition"
bts:Publisher {
schema:name xsd:string ;
schema:url IRI
}
bts:Citation {
schema:identifier .
}
bts:Catalog {
schema:name [ "CTSA Datasets" ] ;
schema:url [ <https://ctsa.ncats.nih.gov/cd2h/> ]
}
Raw
ctsa_abstract_model (json)
{
"type" : "Schema",
"@context" : "http://www.w3.org/ns/shex.jsonld",
"shapes" : [
{
"type" : "Shape",
"id" : "http://discovery.biothings.io/bts/CTSADatasetShape",
"expression" : {
"type" : "EachOf",
"expressions" : [
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/name",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"annotations" : [
{
"type" : "Annotation",
"predicate" : "http://purl.org/dc/terms/description",
"object" : {
"value" : "The name of the CTSA Dataset"
}
}
]
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/description",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"annotations" : [
{
"type" : "Annotation",
"predicate" : "http://purl.org/dc/terms/description",
"object" : {
"value" : "A description of the CTSA Dataset"
}
}
]
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/url",
"valueExpr" : {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}
},
{
"predicate" : "http://schema.org/sameAs",
"valueExpr" : {
"type" : "NodeConstraint",
"nodeKind" : "iri"
},
"min" : 0,
"max" : -1,
"type" : "TripleConstraint"
},
{
"predicate" : "http://schema.org/keywords",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
},
"min" : 0,
"max" : -1,
"type" : "TripleConstraint"
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/datePublished",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://schema.org/Date"
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/dateModified",
"valueExpr" : {
"type" : "ShapeOr",
"shapeExprs" : [
{
"type" : "NodeConstraint",
"datatype" : "http://schema.org/Date"
},
{
"type" : "NodeConstraint",
"datatype" : "http://schema.org/DateTime"
}
]
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/citation",
"valueExpr" : "http://discovery.biothings.io/bts/Citation"
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/version",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/identifier",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/measurementTechnique",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [
{
"value" : "whole-genome sequencing"
},
{
"value" : "whole-exome sequencing"
},
{
"value" : "mass spectrum"
}
]
}
},
{
"predicate" : "http://schema.org/creator",
"valueExpr" : "http://discovery.biothings.io/bts/Person",
"min" : 0,
"max" : -1,
"type" : "TripleConstraint"
},
{
"predicate" : "http://schema.org/contributor",
"valueExpr" : "http://discovery.biothings.io/bts/Person",
"min" : 0,
"max" : -1,
"type" : "TripleConstraint"
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/publisher",
"valueExpr" : "http://discovery.biothings.io/bts/Publisher"
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/license",
"min" : 0,
"max" : 1
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/citation",
"min" : 0,
"max" : -1
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/samples",
"min" : 0,
"max" : -1
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/funder",
"min" : 0,
"max" : 1
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/includedInDataCatalog",
"valueExpr" : "http://discovery.biothings.io/bts/Catalog"
}
]
}
},
{
"type" : "Shape",
"id" : "http://discovery.biothings.io/bts/Person",
"expression" : {
"type" : "EachOf",
"expressions" : [
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/name",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/url",
"valueExpr" : {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}
}
]
},
"annotations" : [
{
"type" : "Annotation",
"predicate" : "http://purl.org/dc/terms/description",
"object" : {
"value" : "Reusable person definition"
}
}
]
},
{
"type" : "Shape",
"id" : "http://discovery.biothings.io/bts/Publisher",
"expression" : {
"type" : "EachOf",
"expressions" : [
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/name",
"valueExpr" : {
"type" : "NodeConstraint",
"datatype" : "http://www.w3.org/2001/XMLSchema#string"
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/url",
"valueExpr" : {
"type" : "NodeConstraint",
"nodeKind" : "iri"
}
}
]
}
},
{
"type" : "Shape",
"id" : "http://discovery.biothings.io/bts/Citation",
"expression" : {
"type" : "TripleConstraint",
"predicate" : "http://schema.org/identifier"
}
},
{
"type" : "Shape",
"id" : "http://discovery.biothings.io/bts/Catalog",
"expression" : {
"type" : "EachOf",
"expressions" : [
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/name",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [
{
"value" : "CTSA Datasets"
}
]
}
},
{
"type" : "TripleConstraint",
"predicate" : "http://schema.org/url",
"valueExpr" : {
"type" : "NodeConstraint",
"values" : [
"https://ctsa.ncats.nih.gov/cd2h/"
]
}
}
]
}
}
]
}
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