bia_mifa_models.shacl.ttl

@prefix WIKIDATA_PROPERTY: <https://www.wikidata.org/prop/> .
@prefix bia_mifa_models: <https://w3id.org/BioImage-Archive/bia-mifa-models/> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix schema1: <http://schema.org/> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

bia_mifa_models:Annotations a sh:NodeShape ;
    sh:closed true ;
    sh:description "A set of annotations for an AI-ready dataset" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:FileLevelMetadata ;
            sh:description "a collection of the file level metadata for each annotation" ;
            sh:nodeKind sh:IRI ;
            sh:order 6 ;
            sh:path bia_mifa_models:file_metadata ],
        [ sh:datatype xsd:string ;
            sh:description "Which images from the dataset were annotated, and what percentage of the data has been annotated from what is available" ;
            sh:maxCount 1 ;
            sh:order 3 ;
            sh:path bia_mifa_models:annotation_coverage ],
        [ sh:datatype xsd:string ;
            sh:description "Confidence on annotation accuracy" ;
            sh:maxCount 1 ;
            sh:order 4 ;
            sh:path bia_mifa_models:annotation_confidence_level ],
        [ sh:class bia_mifa_models:Author ;
            sh:description "a collection of the authors of a study" ;
            sh:nodeKind sh:BlankNode ;
            sh:order 5 ;
            sh:path bia_mifa_models:authors ],
        [ sh:datatype xsd:string ;
            sh:description "Rules used to generate annotations" ;
            sh:maxCount 1 ;
            sh:order 2 ;
            sh:path bia_mifa_models:annotation_criteria ],
        [ sh:datatype xsd:string ;
            sh:description "Short descriptive summary indicating the type of annotation and how it was generated" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path bia_mifa_models:annotation_overview ],
        [ sh:datatype xsd:string ;
            sh:description "Description of how the annotations were created. For example, were the annotations crowdsourced or expertly annotated,  produced by  a human or software, what software was used, when were the annotations created,  protocols used for consensus and quality assurance" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path bia_mifa_models:annotation_method ] ;
    sh:targetClass bia_mifa_models:Annotations .

bia_mifa_models:AuthorCollection a sh:NodeShape ;
    sh:closed false ;
    sh:description "A holder for Author objects" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:Author ;
            sh:description "a collection of the authors of a study" ;
            sh:nodeKind sh:BlankNode ;
            sh:order 0 ;
            sh:path bia_mifa_models:authors ] ;
    sh:targetClass bia_mifa_models:AuthorCollection .

bia_mifa_models:FileLevelMetadataCollection a sh:NodeShape ;
    sh:closed false ;
    sh:description "A holder for FileLevelMetadata objects" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:FileLevelMetadata ;
            sh:description "a collection of the file level metadata for each annotation" ;
            sh:nodeKind sh:IRI ;
            sh:order 0 ;
            sh:path bia_mifa_models:file_metadata ] ;
    sh:targetClass bia_mifa_models:FileLevelMetadataCollection .

bia_mifa_models:GrantReferenceCollection a sh:NodeShape ;
    sh:closed false ;
    sh:description "A holder for GrantReference objects" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:GrantReference ;
            sh:description "a collection of grant ids and funder names associated with the study" ;
            sh:nodeKind sh:IRI ;
            sh:order 0 ;
            sh:path bia_mifa_models:grants ] ;
    sh:targetClass bia_mifa_models:GrantReferenceCollection .

bia_mifa_models:Links a sh:NodeShape ;
    sh:closed false ;
    sh:description "Links related to the study" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:datatype xsd:string ;
            sh:description "The description of the linked content" ;
            sh:order 1 ;
            sh:path bia_mifa_models:link_description ],
        [ sh:description "URL of relevant link" ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path bia_mifa_models:link_url ] ;
    sh:targetClass bia_mifa_models:Links .

bia_mifa_models:OrganisationInfoCollection a sh:NodeShape ;
    sh:closed false ;
    sh:description "A holder for OrganisationInfo objects" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:OrganisationInfo ;
            sh:description "a collection of the name and address of organisations authors are affiliated with" ;
            sh:nodeKind sh:BlankNode ;
            sh:order 0 ;
            sh:path bia_mifa_models:organisation ] ;
    sh:targetClass bia_mifa_models:OrganisationInfoCollection .

bia_mifa_models:PublicationsCollection a sh:NodeShape ;
    sh:closed false ;
    sh:description "A holder for Publications objects" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:Publications ;
            sh:description "a collection of publications associated with a study" ;
            sh:nodeKind sh:IRI ;
            sh:order 0 ;
            sh:path bia_mifa_models:publications ] ;
    sh:targetClass bia_mifa_models:PublicationsCollection .

bia_mifa_models:Study a sh:NodeShape ;
    sh:closed true ;
    sh:description "General information about the study" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:datatype xsd:string ;
            sh:description "Description of how the study was funded" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 6 ;
            sh:path bia_mifa_models:funding_statement ],
        [ sh:datatype xsd:string ;
            sh:description "The description of the linked content" ;
            sh:order 10 ;
            sh:path bia_mifa_models:link_description ],
        [ sh:datatype xsd:string ;
            sh:description "Keywords or tags used to describe the dataset" ;
            sh:minCount 1 ;
            sh:order 2 ;
            sh:path schema1:keywords ],
        [ sh:datatype xsd:string ;
            sh:description "Brief description of the detaset. Must contain the biological application of the dataset" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path schema1:description ],
        [ sh:description "Link to the models that have been trained with this dataset (if any). This could be links to GitHub or repositories like the BioImage Zoo." ;
            sh:order 4 ;
            sh:path bia_mifa_models:ai_models_trained ],
        [ sh:datatype xsd:string ;
            sh:description "The title for your dataset. This will be displayed when search results including your data are shown. Often this will be the same as an associated publication." ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path schema1:title ],
        [ sh:class bia_mifa_models:Author ;
            sh:description "a collection of the authors of a study" ;
            sh:nodeKind sh:BlankNode ;
            sh:order 8 ;
            sh:path bia_mifa_models:authors ],
        [ sh:description "URL of relevant link" ;
            sh:minCount 1 ;
            sh:order 9 ;
            sh:path bia_mifa_models:link_url ],
        [ sh:description "The license under which the data are available" ;
            sh:in ( <https://creativecommons.org/publicdomain/zero/1.0/> <https://creativecommons.org/licenses/by/4.0/> ) ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 3 ;
            sh:path schema1:license ],
        [ sh:class bia_mifa_models:Publications ;
            sh:description "a collection of publications associated with a study" ;
            sh:nodeKind sh:IRI ;
            sh:order 7 ;
            sh:path bia_mifa_models:publications ],
        [ sh:datatype xsd:string ;
            sh:description "Any people or groups that should be acknowledged as part of the dataset" ;
            sh:maxCount 1 ;
            sh:order 5 ;
            sh:path bia_mifa_models:acknowledgements ],
        [ sh:class bia_mifa_models:GrantReference ;
            sh:description "a collection of grant ids and funder names associated with the study" ;
            sh:nodeKind sh:IRI ;
            sh:order 11 ;
            sh:path bia_mifa_models:grants ] ;
    sh:targetClass bia_mifa_models:Study .

bia_mifa_models:Version a sh:NodeShape ;
    sh:closed true ;
    sh:description "Information about the dataset version" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:datatype xsd:dateTime ;
            sh:description "Date and time when the version was created" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path pav:authoredOn ],
        [ sh:datatype xsd:string ;
            sh:description "Textual description of changes compared to previous version" ;
            sh:maxCount 1 ;
            sh:order 2 ;
            sh:path bia_mifa_models:changes ],
        [ sh:datatype xsd:string ;
            sh:description "Unique version number" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path pav:version ],
        [ sh:description "Pointer to previous version" ;
            sh:maxCount 1 ;
            sh:order 3 ;
            sh:path pav:previousVersion ] ;
    sh:targetClass bia_mifa_models:Version .

bia_mifa_models:FileLevelMetadata a sh:NodeShape ;
    sh:closed true ;
    sh:description "metadata atributes that must be detailed at the file level" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:datatype xsd:string ;
            sh:description "The identifier for the annotation" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path schema1:identifier ],
        [ sh:datatype xsd:dateTime ;
            sh:description "Date and time when the annotation was created" ;
            sh:maxCount 1 ;
            sh:order 5 ;
            sh:path pav:authoredOn ],
        [ sh:description "Annotation type, for example class labels, segmentation masks, counts..." ;
            sh:in ( "class_labels" "bounding_boxes" "counts" "derived_annotations" "geometrical_annotations" "graphs" "point_annotations" "segmentation_mask" "tracks" "weak_annotations" "other" ) ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path bia_mifa_models:annotation_type ],
        [ sh:datatype xsd:string ;
            sh:description "Spatial information for non-pixel annotations" ;
            sh:maxCount 1 ;
            sh:order 4 ;
            sh:path bia_mifa_models:spatial_information ],
        [ sh:datatype xsd:string ;
            sh:description "Any transformations required to link the images to the annotations" ;
            sh:maxCount 1 ;
            sh:order 3 ;
            sh:path bia_mifa_models:transformations ],
        [ sh:datatype xsd:string ;
            sh:description "identifier of the source image from which the annotation originated" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 2 ;
            sh:path bia_mifa_models:source_image_id ] ;
    sh:targetClass bia_mifa_models:FileLevelMetadata .

bia_mifa_models:GrantReference a sh:NodeShape ;
    sh:closed true ;
    sh:description "Information about grant ID and funding body that funded the study" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:datatype xsd:string ;
            sh:description "The identifier for the grant" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path schema1:identifier ],
        [ sh:datatype xsd:string ;
            sh:description "The funding body provididing support" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path schema1:funder ] ;
    sh:targetClass bia_mifa_models:GrantReference .

bia_mifa_models:OrganisationInfo a sh:NodeShape ;
    sh:closed true ;
    sh:description "Information about the organisation the author is affiliated with" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:datatype xsd:string ;
            sh:description "Organisation address" ;
            sh:maxCount 1 ;
            sh:order 1 ;
            sh:path schema1:name ],
        [ sh:datatype xsd:string ;
            sh:description "Organisation name" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path schema1:name ],
        [ sh:description "Identifier for the Research Organization Registry" ;
            sh:maxCount 1 ;
            sh:order 2 ;
            sh:path WIKIDATA_PROPERTY:P6782 ] ;
    sh:targetClass bia_mifa_models:OrganisationInfo .

bia_mifa_models:Publications a sh:NodeShape ;
    sh:closed true ;
    sh:description "Information about any publications associated with the dataset" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:description "Identifier for journal articles/abstracts in PubMed" ;
            sh:maxCount 1 ;
            sh:order 4 ;
            sh:path WIKIDATA_PROPERTY:P698 ],
        [ sh:datatype xsd:string ;
            sh:description "Authors of associated publication" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path schema1:author ],
        [ sh:description "Digital Object Identifier (DOI)" ;
            sh:maxCount 1 ;
            sh:order 2 ;
            sh:path WIKIDATA_PROPERTY:P356 ],
        [ sh:datatype xsd:string ;
            sh:description "Year of publication" ;
            sh:maxCount 1 ;
            sh:order 3 ;
            sh:path bia_mifa_models:publication_year ],
        [ sh:datatype xsd:string ;
            sh:description "The title for a publication associated to the dataset" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path schema1:title ] ;
    sh:targetClass bia_mifa_models:Publications .

bia_mifa_models:Author a sh:NodeShape ;
    sh:closed true ;
    sh:description "Information about the authors" ;
    sh:ignoredProperties ( rdf:type ) ;
    sh:property [ sh:class bia_mifa_models:OrganisationInfo ;
            sh:description "a collection of the name and address of organisations authors are affiliated with" ;
            sh:nodeKind sh:BlankNode ;
            sh:order 5 ;
            sh:path bia_mifa_models:organisation ],
        [ sh:description "A unique identifier for an author" ;
            sh:maxCount 1 ;
            sh:order 3 ;
            sh:path WIKIDATA_PROPERTY:P496 ],
        [ sh:datatype xsd:string ;
            sh:description "Email address of a person" ;
            sh:maxCount 1 ;
            sh:order 2 ;
            sh:path schema1:email ;
            sh:pattern "^\\S+@[\\S+\\.]+\\S+" ],
        [ sh:datatype xsd:string ;
            sh:description "First name for an author" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 0 ;
            sh:path schema1:name ],
        [ sh:datatype xsd:string ;
            sh:description "Last name for an author" ;
            sh:maxCount 1 ;
            sh:minCount 1 ;
            sh:order 1 ;
            sh:path schema1:name ],
        [ sh:datatype xsd:string ;
            sh:description "Role of the author when creating the dataset" ;
            sh:order 4 ;
            sh:path schema1:roleName ] ;
    sh:targetClass bia_mifa_models:Author .