diff --git a/openbis-pmd.ttl b/openbis-pmd.ttl new file mode 100644 index 0000000..f877c05 --- /dev/null +++ b/openbis-pmd.ttl @@ -0,0 +1,28 @@ +@prefix rdfs: . +@prefix owl: . +@prefix openbis: . +@prefix pmdco: . +@prefix rdf: . +@prefix xsd: . + + a owl:Ontology ; + owl:imports pmdco: . + +# ================================================================= +# Alignments between OpenBIS-Ontology and PMDco +# ================================================================= + +### Example Alignments (replace with your actual alignments) + +openbis:Experiment rdfs:subClassOf pmdco:Process . + +openbis:Sample rdfs:subClassOf pmdco:Material . + +openbis:Instrument rdfs:subClassOf pmdco:Device . + +openbis:DataSet rdfs:subClassOf pmdco:Result . + +# Add more alignments below this line after reviewing the full ontologies +# For example: +# openbis:SomeOtherClass rdfs:subClassOf pmdco:AnotherClass . +# openbis:hasSomeProperty rdfs:subPropertyOf pmdco:hasAnotherProperty . diff --git a/openbis.ttl b/openbis.ttl index 5cb08cf..b1bc148 100644 --- a/openbis.ttl +++ b/openbis.ttl @@ -10,90 +10,89 @@ @prefix skos: . @prefix vann: . @prefix dcterms: . +@prefix pmdco: . +@prefix dcat: . @base . rdf:type owl:Ontology ; - owl:versionIRI ; - dc:contributor "Andre Valdestilhas (Bundesanstalt für Materalprüfung und -forschung BAM)"@en , - "Mariam Rizkallah (Fraunhofer IFAM)"@en , - "Rasmus Antons (Fraunhofer IWM)"@en , - "Thomas Hanke (Fraunhofer IWM)"@en ; - dcterms:bibliographicCitation "obis: MatoLab openbis ontology. Version 1.0.0, http://w3id.org/matolab/ontology/" ; - dcterms:created "2024-01-15" ; - dcterms:creator "Matolab OpenBISmatic Team"@en ; - dcterms:description "A simple ontology with the scope to represent the database items of an OpenBIS instance semantically."@en ; - dcterms:license ; - dcterms:title "Matolab OpenBIS Ontology (OpenBISOnt)"@en ; - vann:preferredNamespacePrefix "obis"@en ; - vann:preferredNamespaceUri "http://w3id.org/matolab/openbis" ; - rdfs:comment "This is a simple Ontology expaining the data model of OpenBIS."@en ; - owl:versionInfo "1.0.0"@en . + owl:versionIRI ; + owl:imports pmdco: ; + dc:contributor "Andre Valdestilhas (Bundesanstalt für Materalprüfung und -forschung BAM)"@en , + "Mariam Rizkallah (Fraunhofer IFAM)"@en , + "Rasmus Antons (Fraunhofer IWM)"@en , + "Thomas Hanke (Fraunhofer IWM)"@en ; + dcterms:bibliographicCitation "obis: MatoLab openbis ontology. Version 1.0.0, http://w3id.org/matolab/ontology/" ; + dcterms:created "2024-01-15" ; + dcterms:creator "Matolab OpenBISmatic Team"@en ; + dcterms:description "A simple ontology with the scope to represent the database items of an OpenBIS instance semantically."@en ; + dcterms:license ; + dcterms:title "Matolab OpenBIS Ontology (OpenBISOnt)"@en ; + vann:preferredNamespacePrefix "obis"@en ; + vann:preferredNamespaceUri "http://w3id.org/matolab/openbis" ; + rdfs:comment "This is a simple Ontology expaining the data model of OpenBIS."@en ; + owl:versionInfo "1.0.0" . + +# ================================================================= +# Alignments between OpenBIS-Ontology and PMDco +# ================================================================= + +# Class alignments based on the descriptions and altLabels in the OpenBIS ontology. +:Collection rdfs:subClassOf pmdco:Process . + +:Object rdfs:subClassOf pmdco:Material . + +dcat:Dataset rdfs:subClassOf pmdco:Data . + +:Project rdfs:subClassOf pmdco:Workflow . + +# An OpenBIS Space does not have a clear direct equivalent in PMDco and can remain as a subclass of prov:Entity. + ################################################################# # Annotation properties ################################################################# -### http://purl.org/dc/elements/1.1/contributor +### http://purl.org/dc/elements/1.1/contributor dc:contributor rdf:type owl:AnnotationProperty . - -### http://purl.org/dc/terms/bibliographicCitation +### http://purl.org/dc/terms/bibliographicCitation dcterms:bibliographicCitation rdf:type owl:AnnotationProperty . - -### http://purl.org/dc/terms/created +### http://purl.org/dc/terms/created dcterms:created rdf:type owl:AnnotationProperty ; - :openbis_json_key "registrationDate" . + :openbis_json_key "registrationDate" . - -### http://purl.org/dc/terms/creator +### http://purl.org/dc/terms/creator dcterms:creator rdf:type owl:AnnotationProperty . - -### http://purl.org/dc/terms/description +### http://purl.org/dc/terms/description dcterms:description rdf:type owl:AnnotationProperty . - -### http://purl.org/dc/terms/license +### http://purl.org/dc/terms/license dcterms:license rdf:type owl:AnnotationProperty . - -### http://purl.org/dc/terms/title +### http://purl.org/dc/terms/title dcterms:title rdf:type owl:AnnotationProperty . - -### http://purl.org/vocab/vann/preferredNamespacePrefix +### http://purl.org/vocab/vann/preferredNamespacePrefix vann:preferredNamespacePrefix rdf:type owl:AnnotationProperty . - -### http://purl.org/vocab/vann/preferredNamespaceUri +### http://purl.org/vocab/vann/preferredNamespaceUri vann:preferredNamespaceUri rdf:type owl:AnnotationProperty . - -### http://w3id.org/matolab/openbis/code +### http://w3id.org/matolab/openbis/code :code rdf:type owl:AnnotationProperty ; :openbis_json_key "code" ; rdfs:range xsd:string . - -### http://w3id.org/matolab/openbis/openbis_json_key +### http://w3id.org/matolab/openbis/openbis_json_key :openbis_json_key rdf:type owl:AnnotationProperty ; rdfs:range xsd:string . - -### http://www.w3.org/2000/01/rdf-schema#comment -rdfs:comment :openbis_json_key "description" . - - -### http://www.w3.org/2000/01/rdf-schema#label -rdfs:label :openbis_json_key "label" . - - -### http://www.w3.org/2004/02/skos/core#altLabel +### http://www.w3.org/2004/02/skos/core#altLabel skos:altLabel rdf:type owl:AnnotationProperty . - -### http://www.w3.org/2004/02/skos/core#definition +### http://www.w3.org/2004/02/skos/core#definition skos:definition rdf:type owl:AnnotationProperty . @@ -101,7 +100,7 @@ skos:definition rdf:type owl:AnnotationProperty . # Datatypes ################################################################# -### https://www.w3.org/2000/01/rdf-schema#Resource +### https://www.w3.org/2000/01/rdf-schema#Resource rdf:type rdfs:Datatype . @@ -109,30 +108,27 @@ skos:definition rdf:type owl:AnnotationProperty . # Object Properties ################################################################# -### http://purl.org/dc/elements/1.1/creator +### http://purl.org/dc/elements/1.1/creator dc:creator rdf:type owl:ObjectProperty ; rdfs:domain prov:Entity ; rdfs:range prov:Agent ; :openbis_json_key "registrator" . - -### http://purl.org/dc/terms/contributor +### http://purl.org/dc/terms/contributor dcterms:contributor rdf:type owl:ObjectProperty ; rdfs:subPropertyOf owl:topObjectProperty ; rdfs:domain prov:Entity ; rdfs:range prov:Agent ; :openbis_json_key "modifier" . - -### http://w3id.org/matolab/openbis/dataset_permid +### http://w3id.org/matolab/openbis/dataset_permid :dataset_permid rdf:type owl:ObjectProperty ; - rdfs:domain ; + rdfs:domain dcat:Distribution ; rdfs:range :PermanentIdentifier ; :openbis_json_key "dataSetId" ; rdfs:label "dataset permId" . - -### http://w3id.org/matolab/openbis/has_child +### http://w3id.org/matolab/openbis/has_child :has_child rdf:type owl:ObjectProperty ; owl:inverseOf :has_parent ; rdfs:domain :Object ; @@ -141,19 +137,17 @@ dcterms:contributor rdf:type owl:ObjectProperty ; rdfs:label "has child"@en ; skos:definition "Relation towards the child of an Object." . - -### http://w3id.org/matolab/openbis/has_identifier +### http://w3id.org/matolab/openbis/has_identifier :has_identifier rdf:type owl:ObjectProperty ; owl:inverseOf :is_identifier_of ; rdfs:domain prov:Entity ; rdfs:range :Identifier ; :openbis_json_key "filePath" , - "permId" ; + "permId" ; rdfs:label "has identifier"@en ; skos:definition "Relation pointing to an Identifier concretizing the Identity of the entity further." . - -### http://w3id.org/matolab/openbis/has_parent +### http://w3id.org/matolab/openbis/has_parent :has_parent rdf:type owl:ObjectProperty ; rdfs:domain :Object ; rdfs:range :Object ; @@ -161,8 +155,7 @@ dcterms:contributor rdf:type owl:ObjectProperty ; rdfs:label "has parent"@en ; skos:definition "Inverse of has_child." . - -### http://w3id.org/matolab/openbis/has_tag +### http://w3id.org/matolab/openbis/has_tag :has_tag rdf:type owl:ObjectProperty ; owl:inverseOf :is_tag_of ; rdfs:domain prov:Entity ; @@ -171,154 +164,147 @@ dcterms:contributor rdf:type owl:ObjectProperty ; rdfs:label "has tag"@en ; skos:definition "Relation pointing to an Tag concretizing the Category of the entity." . - -### http://w3id.org/matolab/openbis/is_identifier_of +### http://w3id.org/matolab/openbis/is_identifier_of :is_identifier_of rdf:type owl:ObjectProperty ; rdfs:domain :Identifier ; rdfs:range prov:Entity ; rdfs:label "is identifier of"@en ; skos:definition "Inverse of has_identifier." . - -### http://w3id.org/matolab/openbis/is_tag_of +### http://w3id.org/matolab/openbis/is_tag_of :is_tag_of rdf:type owl:ObjectProperty ; rdfs:domain :Identifier ; rdfs:range prov:Entity ; rdfs:label "is tag of"@en ; skos:definition "Inverse of has_tag." . - -### http://w3id.org/matolab/openbis/relates_to +### http://w3id.org/matolab/openbis/relates_to :relates_to rdf:type owl:ObjectProperty , - owl:SymmetricProperty ; + owl:SymmetricProperty ; rdfs:domain :Collection , :DataStore , :Object , :Project , :Space , - ; + dcat:Dataset ; rdfs:range :Collection , :Object , :Project , :Space ; :openbis_json_key "attachments" , - "components" , - "dataSets" , - "dataStore" , - "experiment" , - "experiments" , - "files" , - "project" , - "projects" , - "samples" , - "space" ; + "components" , + "dataSets" , + "dataStore" , + "experiment" , + "experiments" , + "files" , + "project" , + "projects" , + "samples" , + "space" ; rdfs:label "relates to"@en ; skos:definition "A general relation of OpenBIS instance marking them related to each other." . - -### http://www.w3.org/ns/dcat#distribution - rdf:type owl:ObjectProperty ; - rdfs:domain ; - rdfs:range ; - rdfs:label "distribution" . +### http://www.w3.org/ns/dcat#distribution +dcat:distribution rdf:type owl:ObjectProperty ; + rdfs:domain dcat:Dataset ; + rdfs:range dcat:Distribution ; + rdfs:label "distribution" . ################################################################# # Data properties ################################################################# -### http://w3id.org/matolab/openbis/file_path +### http://w3id.org/matolab/openbis/file_path :file_path rdf:type owl:DatatypeProperty ; - rdfs:domain ; + rdfs:domain dcat:Distribution ; rdfs:range xsd:string ; :openbis_json_key "path" . +### http://www.w3.org/ns/dcat#byteSize +dcat:byteSize rdf:type owl:DatatypeProperty ; + rdfs:domain dcat:Distribution ; + rdfs:range xsd:nonNegativeInteger ; + :openbis_json_key "fileLength" . -### http://www.w3.org/ns/dcat#byteSize - rdf:type owl:DatatypeProperty ; - rdfs:domain ; - rdfs:range xsd:nonNegativeInteger ; - :openbis_json_key "fileLength" . - - -### http://www.w3.org/ns/dcat#downloadURL - rdf:type owl:DatatypeProperty ; - rdfs:subPropertyOf owl:topDataProperty ; - rdfs:domain ; - rdfs:range . - +### http://www.w3.org/ns/dcat#downloadURL +dcat:downloadURL rdf:type owl:DatatypeProperty ; + rdfs:subPropertyOf owl:topDataProperty ; + rdfs:domain dcat:Distribution ; + rdfs:range . -### http://www.w3.org/ns/dcat#endpointURL - rdf:type owl:DatatypeProperty ; - rdfs:subPropertyOf owl:topDataProperty ; - rdfs:domain ; - rdfs:range ; - :openbis_json_key "downloadUrl" . +### http://www.w3.org/ns/dcat#endpointURL +dcat:endpointURL rdf:type owl:DatatypeProperty ; + rdfs:subPropertyOf owl:topDataProperty ; + rdfs:domain dcat:DataService ; + rdfs:range ; + :openbis_json_key "downloadUrl" . ################################################################# # Classes ################################################################# -### http://w3id.org/matolab/openbis/Collection +### http://w3id.org/matolab/openbis/Collection :Collection rdf:type owl:Class ; - rdfs:subClassOf prov:Entity ; + rdfs:subClassOf prov:Entity , pmdco:Process ; :openbis_json_key "as.dto.experiment.Experiment" ; rdfs:label "Collection" ; skos:altLabel "Experiment" ; skos:definition "An OpenBIS Collection of Objects and DataSets." . -### http://w3id.org/matolab/openbis/DataStore +### http://w3id.org/matolab/openbis/DataStore :DataStore rdf:type owl:Class ; - rdfs:subClassOf ; + rdfs:subClassOf dcat:DataService ; :openbis_json_key "as.dto.datastore.DataStore" ; rdfs:label "OpenBIS Data Store" ; skos:definition "A openBIS database service hosting files." . -### http://w3id.org/matolab/openbis/Identifier +### http://w3id.org/matolab/openbis/Identifier :Identifier rdf:type owl:Class ; rdfs:subClassOf prov:Entity ; :openbis_json_key "as.dto.experiment.id.ExperimentIdentifier" , - "as.dto.project.id.ProjectIdentifier" , - "as.dto.sample.id.SampleIdentifier" ; + "as.dto.project.id.ProjectIdentifier" , + "as.dto.sample.id.SampleIdentifier" ; rdfs:label "Identifier" ; skos:definition "A String as additional Identifier." . -### http://w3id.org/matolab/openbis/Object +### http://w3id.org/matolab/openbis/Object :Object rdf:type owl:Class ; - rdfs:subClassOf prov:Entity ; + rdfs:subClassOf prov:Entity , pmdco:Material ; :openbis_json_key "as.dto.sample.Sample" ; rdfs:label "Object" ; skos:altLabel "Sample" ; skos:definition "An OpenBIS entity of an object." . -### http://w3id.org/matolab/openbis/PermanentIdentifier +### http://w3id.org/matolab/openbis/PermanentIdentifier :PermanentIdentifier rdf:type owl:Class ; rdfs:subClassOf :Identifier ; :openbis_json_key "as.dto.dataset.id.DataSetPermId" , - "as.dto.entitytype.id.EntityTypePermId" , - "as.dto.experiment.id.ExperimentPermId" , - "as.dto.person.id.PersonPermId" , - "as.dto.project.id.ProjectPermId" , - "as.dto.sample.id.SamplePermId" , - "as.dto.space.id.SpacePermId" ; + "as.dto.entitytype.id.EntityTypePermId" , + "as.dto.experiment.id.ExperimentPermId" , + "as.dto.person.id.PersonPermId" , + "as.dto.project.id.ProjectPermId" , + "as.dto.sample.id.SamplePermId" , + "as.dto.space.id.SpacePermId" ; rdfs:label "Permanent Identifier" ; skos:definition "A additional String given by the OpenBIS data storage which will never be changed." . -### http://w3id.org/matolab/openbis/Project +### http://w3id.org/matolab/openbis/Project :Project rdf:type owl:Class ; - rdfs:subClassOf prov:Entity ; + rdfs:subClassOf prov:Entity , pmdco:Workflow ; :openbis_json_key "as.dto.project.Project" ; rdfs:label "Project" ; skos:definition "An OpenBIS Project." . -### http://w3id.org/matolab/openbis/Space +### http://w3id.org/matolab/openbis/Space :Space rdf:type owl:Class ; rdfs:subClassOf prov:Entity ; :openbis_json_key "as.dto.space.Space" ; @@ -326,7 +312,7 @@ dcterms:contributor rdf:type owl:ObjectProperty ; skos:definition "An OpenBIS Space." . -### http://w3id.org/matolab/openbis/User +### http://w3id.org/matolab/openbis/User :User rdf:type owl:Class ; owl:equivalentClass prov:Agent ; rdfs:subClassOf foaf:Person ; @@ -335,40 +321,40 @@ dcterms:contributor rdf:type owl:ObjectProperty ; skos:definition "An named openBIS user." . -### http://www.w3.org/ns/dcat#DataService - rdf:type owl:Class ; - rdfs:subClassOf prov:SoftwareAgent ; - rdfs:label "Data Service" . +### http://www.w3.org/ns/dcat#DataService +dcat:DataService rdf:type owl:Class ; + rdfs:subClassOf prov:SoftwareAgent ; + rdfs:label "Data Service" . -### http://www.w3.org/ns/dcat#Dataset - rdf:type owl:Class ; - rdfs:subClassOf prov:Entity ; - :openbis_json_key "as.dto.dataset.DataSet" ; - rdfs:label "Data Set" ; - skos:definition "An folder where data files are stored. A data set has user-defined properties." . +### http://www.w3.org/ns/dcat#Dataset +dcat:Dataset rdf:type owl:Class ; + rdfs:subClassOf prov:Entity, pmdco:Data ; + :openbis_json_key "as.dto.dataset.DataSet" ; + rdfs:label "Data Set" ; + skos:definition "An folder where data files are stored. A data set has user-defined properties." . -### http://www.w3.org/ns/dcat#Distribution - rdf:type owl:Class ; - rdfs:subClassOf prov:Entity ; - :openbis_json_key "dss.dto.datasetfile.DataSetFile" ; - rdfs:label "Distribution"@en . +### http://www.w3.org/ns/dcat#Distribution +dcat:Distribution rdf:type owl:Class ; + rdfs:subClassOf prov:Entity ; + :openbis_json_key "dss.dto.datasetfile.DataSetFile" ; + rdfs:label "Distribution"@en . -### http://www.w3.org/ns/prov#Agent +### http://www.w3.org/ns/prov#Agent prov:Agent rdf:type owl:Class . -### http://www.w3.org/ns/prov#Entity +### http://www.w3.org/ns/prov#Entity prov:Entity rdf:type owl:Class . -### http://www.w3.org/ns/prov#SoftwareAgent +### http://www.w3.org/ns/prov#SoftwareAgent prov:SoftwareAgent rdf:type owl:Class . -### http://xmlns.com/foaf/0.1/Person +### http://xmlns.com/foaf/0.1/Person foaf:Person rdf:type owl:Class . @@ -376,27 +362,27 @@ foaf:Person rdf:type owl:Class . # Individuals ################################################################# -### http://w3id.org/matolab/openbis/GeneralProtocols +### http://w3id.org/matolab/openbis/GeneralProtocols :GeneralProtocols rdf:type owl:NamedIndividual , - :Collection ; + :Collection ; rdfs:label "General Protocols Collection, a default OpenBIS collection to contain the lab proceedures generally used in the lab." . -### http://w3id.org/matolab/openbis/Materials +### http://w3id.org/matolab/openbis/Materials :Materials rdf:type owl:NamedIndividual , - :Space ; + :Space ; rdfs:label "Materials Space, a default OpenBIS space for material entities." . -### http://w3id.org/matolab/openbis/Methods +### http://w3id.org/matolab/openbis/Methods :Methods rdf:type owl:NamedIndividual , - :Space ; + :Space ; rdfs:label "Methods Space, a default OpenBIS space for methods and proceedures." . -### http://w3id.org/matolab/openbis/Protocols +### http://w3id.org/matolab/openbis/Protocols :Protocols rdf:type owl:NamedIndividual , - :Project ; + :Project ; rdfs:label "Protocols Project, a default OpenBIS project for proceedures." . @@ -406,31 +392,17 @@ foaf:Person rdf:type owl:Class . dcterms:modified :openbis_json_key "modificationDate" . - rdf:type :openbis_json_key "type" . - rdf:value :openbis_json_key "identifier" , - "permId" . - - -owl:Class :openbis_json_key "as.dto.dataset.DataSetType" , - "as.dto.experiment.ExperimentType" , - "as.dto.sample.SampleType" . - - -owl:ObjectProperty :openbis_json_key "as.dto.property.PropertyType" . - + "permId" . foaf:family_name :openbis_json_key "lastName" . - foaf:givenname :openbis_json_key "firstName" . - foaf:mbox :openbis_json_key "email" . - ################################################################# # General axioms ################################################################# @@ -446,4 +418,4 @@ foaf:mbox :openbis_json_key "email" . ] . -### Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi