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add some mappings to DCAT
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@vemonet
vemonet committed Apr 9, 2024
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72 changes: 38 additions & 34 deletions cohort-explorer-ontology.ttl
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Expand Up @@ -6,102 +6,106 @@
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix vann: <http://purl.org/vocab/vann/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .

icare: a owl:Ontology ;
rdfs:label "iCARE4CVD ontology" ;
rdfs:label "iCARE4CVD ontology"@en ;
dcterms:license <https://creativecommons.org/licenses/by-sa/4.0/> ;
vann:preferredNamespacePrefix "icare" ;
vann:preferredNamespaceUri "https://w3id.org/icare4cvd/" ;
vann:preferredNamespacePrefix "icare"@en ;
vann:preferredNamespaceUri "https://w3id.org/icare4cvd/"@en ;
rdfs:comment "OWL ontology for the iCARE4CVD project, to represent Cohorts tabular file containing Variables for individuals in the cohort (metadata, measurement, etc)"@en .


# Classes
icare:Cohort a owl:Class ;
# rdfs:subClassOf owl:Thing ;
rdfs:label "Cohort" ;
rdfs:label "Cohort"@en ;
rdfs:comment "A study cohort, represented by a tabular data file (usually rows are for patients infos and measurements)"@en ;
owl:disjointWith icare:Variable, icare:VariableCategory ;
owl:sameAs dcat:Resource ;
rdfs:isDefinedBy icare: .

icare:Variable a owl:Class ;
rdfs:label "Variable" ;
rdfs:label "Variable"@en ;
rdfs:comment "A variable in a cohort, represented by a column in the cohort tabular data file"@en ;
owl:disjointWith icare:Cohort, icare:VariableCategory ;
rdfs:isDefinedBy icare: .

icare:VariableCategory a owl:Class ;
rdfs:label "Variable category" ;
rdfs:label "Variable category"@en ;
rdfs:comment "Categories for categorical variables"@en ;
owl:disjointWith icare:Cohort, icare:Variable ;
rdfs:isDefinedBy icare: .


# Cohort Properties
icare:institution a owl:DatatypeProperty ;
rdfs:label "Institution" ;
rdfs:label "Institution"@en ;
rdfs:comment "The institution that conducted the study"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
owl:sameAs dcterms:publisher ;
rdfs:isDefinedBy icare: .

icare:cohortType a owl:DatatypeProperty ;
rdfs:label "Cohort type" ;
rdfs:label "Cohort type"@en ;
rdfs:comment "The type of cohort"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:email a owl:DatatypeProperty ;
rdfs:label "Contact email" ;
rdfs:label "Contact email"@en ;
rdfs:comment "Email of the contact for this cohort"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
owl:sameAs dcat:contactPoint ;
rdfs:isDefinedBy icare: .

icare:studyType a owl:DatatypeProperty ;
rdfs:label "Study type" ;
rdfs:label "Study type"@en ;
rdfs:comment "The type of study"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:studyParticipants a owl:DatatypeProperty ;
rdfs:label "Number of study participants" ;
rdfs:label "Number of study participants"@en ;
rdfs:comment "The number of participants in the study"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:integer ;
rdfs:isDefinedBy icare: .

icare:studyDuration a owl:DatatypeProperty ;
rdfs:label "Study duration" ;
rdfs:label "Study duration"@en ;
rdfs:comment "The duration of the study"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:studyOngoing a owl:DatatypeProperty ;
rdfs:label "Ongoing study" ;
rdfs:label "Ongoing study"@en ;
rdfs:comment "Is the study ongoing? Either yes or no"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:studyPopulation a owl:DatatypeProperty ;
rdfs:label "Study population" ;
rdfs:label "Study population"@en ;
rdfs:comment "Description of the population studied"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:studyObjective a owl:DatatypeProperty ;
rdfs:label "Study objective" ;
rdfs:label "Study objective"@en ;
rdfs:comment "Description of the study objective"@en ;
rdfs:domain icare:Cohort ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:hasVariable a owl:ObjectProperty ;
rdfs:label "Has variable" ;
rdfs:label "Has variable"@en ;
rdfs:comment "The variables that are included in this cohort"@en ;
rdfs:domain icare:Cohort ;
rdfs:range icare:Variable ;
Expand All @@ -110,77 +114,77 @@ icare:hasVariable a owl:ObjectProperty ;
# Should we add inverse?
# icare:isVariableOf a owl:ObjectProperty ;
# owl:inverseOf icare:hasVariable ;
# rdfs:label "Is variable of" ;
# rdfs:label "Is variable of"@en ;
# rdfs:comment "The cohort this variable belongs to"@en ;
# rdfs:domain icare:Variable ;
# rdfs:range icare:Cohort .


# Variable Properties
icare:varType a owl:DatatypeProperty ;
rdfs:label "Variable type" ;
rdfs:label "Variable type"@en ;
rdfs:comment "The data type of the variable: STR, INT, FLOAT, DATETIME"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:count a owl:DatatypeProperty ;
rdfs:label "Value count" ;
rdfs:label "Value count"@en ;
rdfs:comment "The number of rows with values for this variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:integer ;
rdfs:isDefinedBy icare: .

icare:na a owl:DatatypeProperty ;
rdfs:label "n/a count" ;
rdfs:label "n/a count"@en ;
rdfs:comment "The number of n/a rows for this variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:integer ;
rdfs:isDefinedBy icare: .

icare:index a owl:DatatypeProperty ;
rdfs:label "Variable index" ;
rdfs:label "Variable index"@en ;
rdfs:comment "The index of the variable in the cohort tabular data file"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:integer ;
rdfs:isDefinedBy icare: .

icare:max a owl:DatatypeProperty ;
rdfs:label "Maximum value" ;
rdfs:label "Maximum value"@en ;
rdfs:comment "The maximum value for this variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:decimal . # int + float = decimal

icare:min a owl:DatatypeProperty ;
rdfs:label "Minimum value" ;
rdfs:label "Minimum value"@en ;
rdfs:comment "The minimum value for this variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:decimal ;
rdfs:isDefinedBy icare: .

icare:units a owl:DatatypeProperty ;
rdfs:label "Units" ;
rdfs:label "Units"@en ;
rdfs:comment "The units of the variable (e.g. kg, mmHg, etc)"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:formula a owl:DatatypeProperty ;
rdfs:label "Formula" ;
rdfs:label "Formula"@en ;
rdfs:comment "The formula used to calculate this variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:definition a owl:DatatypeProperty ;
rdfs:label "Definition" ;
rdfs:label "Definition"@en ;
rdfs:comment "A reference to the standard used to define this variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:visits a owl:DatatypeProperty ;
rdfs:label "Visits" ;
rdfs:label "Visits"@en ;
rdfs:comment "Details about the study visit for this variable (e.g. M1, M2, M6)"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:string ;
Expand All @@ -189,29 +193,29 @@ icare:visits a owl:DatatypeProperty ;

# Mapping properties
icare:conceptId a owl:ObjectProperty ;
rdfs:label "Concept ID" ;
rdfs:label "Concept ID"@en ;
rdfs:comment "The concept ID for this variable, as provided in the original cohort metadata file"@en ;
rdfs:domain icare:Variable ;
rdfs:range owl:Thing ;
rdfs:isDefinedBy icare: .

icare:mappedId a owl:ObjectProperty ;
rdfs:label "Mapped ID" ;
rdfs:label "Mapped ID"@en ;
rdfs:comment "The mapped concept ID for this variable or category, defined through the Cohort Explorer service"@en ;
rdfs:domain [ owl:unionOf ( icare:Variable icare:VariableCategory ) ] ;
rdfs:range owl:Thing ;
rdfs:isDefinedBy icare: .# Should we limit to OMOP concepts?


icare:omop a owl:DatatypeProperty ;
rdfs:label "OMOP domain" ;
rdfs:label "OMOP domain"@en ;
rdfs:comment "The OMOP domain for this variable, such as Measurement, Condition, etc"@en ;
rdfs:domain icare:Variable ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

icare:categories a owl:ObjectProperty ;
rdfs:label "Has categories" ;
rdfs:label "Has categories"@en ;
rdfs:comment "Categories for this variable, if it is a categorical variable"@en ;
rdfs:domain icare:Variable ;
rdfs:range icare:VariableCategory ;
Expand All @@ -220,7 +224,7 @@ icare:categories a owl:ObjectProperty ;

# Category Properties
rdf:value a owl:DatatypeProperty ;
rdfs:label "Category value" ;
rdfs:label "Category value"@en ;
rdfs:comment "Value for a category"@en ;
rdfs:domain icare:VariableCategory ;
rdfs:range xsd:string ;
Expand All @@ -229,14 +233,14 @@ rdf:value a owl:DatatypeProperty ;

# Misc. properties
rdfs:label a owl:DatatypeProperty ;
rdfs:label "Label" ;
rdfs:label "Label"@en ;
rdfs:comment "A concept label"@en ;
rdfs:domain owl:Thing ;
rdfs:range xsd:string ;
rdfs:isDefinedBy icare: .

dc:identifier a owl:DatatypeProperty ;
rdfs:label "Identifier" ;
rdfs:label "Identifier"@en ;
rdfs:comment "A variable or cohort identifier"@en ;
rdfs:domain [ owl:unionOf ( icare:Variable icare:Cohort ) ] ;
rdfs:range xsd:string .

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