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Raphael-GazzottiRaphael-Gazzotti
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V4: Removal of namespace in schema files. (#280)
* Removal of former namespace. * Version updated. * Removal of submodule name in path. * Keep the module prefix. * The SANDS prefix must be capitalized, which matches the schema_group attribute in the pipeline. * The SANDS prefix must be capitalized, which matches the schema_group attribute in the pipeline. * Revert, lower-case prefixes are more frequently used. --------- Co-authored-by: raphaelgazzotti <raphael.gazzotti@ebrains.eu>
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-116
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‎schemas/atlas/annotation.schema.tpl.json

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"maxItems": 3,
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"_instruction": "Enter the coordinates of the anchor point for this annotation (e.g., its centroid in two dimensional space as [x, y] or in three dimensional space as [x, y, z]).",
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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"core:QuantitativeValue"
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]
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},
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"criteria": {
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"_instruction": "Add the protocol execution defining the criteria that were applied to produce this annotation.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/ProtocolExecution"
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"core:ProtocolExecution"
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]
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},
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"criteriaQualityType": {
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"_instruction": "Add the quality type of the stated criteria used to define this annotation.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/CriteriaQualityType"
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"controlledTerms:CriteriaQualityType"
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]
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},
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"criteriaType": {
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"_instruction": "Add the criteria type for this annotation.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/AnnotationCriteriaType"
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"controlledTerms:AnnotationCriteriaType"
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]
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},
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"inspiredBy": {
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"uniqueItems": true,
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"_instruction": "Add all (source) files that inspired the definition of this annotation.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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"core:File"
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]
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},
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"internalIdentifier": {
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"uniqueItems": true,
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"_instruction": "Add one or both sides of the body, bilateral organ or bilateral organ part that this annotation is defined in.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/Laterality"
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"controlledTerms:Laterality"
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]
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},
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"preferredVisualization": {
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"_instruction": "Add the preferred viewer specification to visualize this annotation.",
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/sands/ViewerSpecification"
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"sands:ViewerSpecification"
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]
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},
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"type": {
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"_instruction": "Add the geometry type of this annotation.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/AnnotationType"
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"controlledTerms:AnnotationType"
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]
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}
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}

‎schemas/atlas/atlasAnnotation.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/sands/AtlasAnnotation",
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"_type": "sands:AtlasAnnotation",
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"_extends": "atlas/annotation.schema.tpl.json",
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"properties": {
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"specification": {
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"_instruction": "Add the non-parametric specification of this annotation.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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"core:File"
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]
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}
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}

‎schemas/atlas/brainAtlas.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/sands/BrainAtlas",
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"_type": "sands:BrainAtlas",
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"_extends": "/core/schemas/products/researchProduct.schema.tpl.json",
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"required": [
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"author",
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"digitalIdentifier": {
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"_instruction": "Add the globally unique and persistent digital identifier of this research product. Note that this digital identifier will be used to reference all attached research product versions.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/DOI",
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"https://openminds.ebrains.eu/core/ISBN",
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"https://openminds.ebrains.eu/core/RRID"
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"core:DOI",
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"core:ISBN",
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"core:RRID"
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]
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},
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"hasTerminology": {
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"_instruction": "Enter the parcellation terminology of this brain atlas.",
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/sands/ParcellationTerminology"
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"sands:ParcellationTerminology"
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]
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},
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"hasVersion": {
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"uniqueItems": true,
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"_instruction": "Add versions of this brain atlas.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/BrainAtlasVersion"
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"sands:BrainAtlasVersion"
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]
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},
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"ontologyIdentifier": {
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"usedSpecies": {
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"_instruction": "Add the species that was used for the creation of this brain atlas.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/Species"
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"controlledTerms:Species"
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]
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}
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}

‎schemas/atlas/brainAtlasVersion.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/sands/BrainAtlasVersion",
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"_type": "sands:BrainAtlasVersion",
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"_extends": "/core/schemas/products/researchProductVersion.schema.tpl.json",
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"required": [
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"coordinateSpace",
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"coordinateSpace": {
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"_instruction": "Add the specific common coordinate space in which this brain atlas version exists.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion"
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"sands:CommonCoordinateSpaceVersion"
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]
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},
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"digitalIdentifier": {
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"_instruction": "Add the globally unique and persistent digital identifier of this research product version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/DOI",
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"https://openminds.ebrains.eu/core/ISBN",
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"https://openminds.ebrains.eu/core/RRID"
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"core:DOI",
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"core:ISBN",
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"core:RRID"
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]
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},
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"hasTerminology": {
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"_instruction": "Enter the specific parcellation terminology of this brain atlas version.",
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/sands/ParcellationTerminologyVersion"
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"sands:ParcellationTerminologyVersion"
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]
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},
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"isAlternativeVersionOf": {
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"uniqueItems": true,
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"_instruction": "Add all brain atlas versions that can be used alternatively to this brain atlas version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/BrainAtlasVersion"
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"sands:BrainAtlasVersion"
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]
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},
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"isNewVersionOf": {
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"_instruction": "Add the brain atlas version preceding this brain atlas version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/BrainAtlasVersion"
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"sands:BrainAtlasVersion"
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]
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},
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"license": {
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"_instruction": "Add the license of this brain atlas version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/License"
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"core:License"
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]
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},
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"majorVersionIdentifier": {
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"type": {
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"_instruction": "Add the type of this brain atlas version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/AtlasType"
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"controlledTerms:AtlasType"
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]
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},
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"usedSpecimen": {
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"uniqueItems": true,
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"_instruction": "Add the specimen that was used for the creation of this brain atlas version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/Subject",
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"https://openminds.ebrains.eu/core/SubjectGroup",
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"https://openminds.ebrains.eu/core/TissueSample",
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"https://openminds.ebrains.eu/core/TissueSampleCollection"
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"core:Subject",
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"core:SubjectGroup",
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"core:TissueSample",
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"core:TissueSampleCollection"
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]
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}
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}

‎schemas/atlas/commonCoordinateSpace.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/sands/CommonCoordinateSpace",
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"_type": "sands:CommonCoordinateSpace",
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"_extends": "/core/schemas/products/researchProduct.schema.tpl.json",
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"_categories": [
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"coordinateSpace"
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"digitalIdentifier": {
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"_instruction": "Add the globally unique and persistent digital identifier of this research product. Note that this digital identifier will be used to reference all attached research product versions.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/DOI",
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"https://openminds.ebrains.eu/core/ISBN",
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"https://openminds.ebrains.eu/core/RRID"
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"core:DOI",
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"core:ISBN",
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"core:RRID"
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]
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},
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"hasVersion": {
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"uniqueItems": true,
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"_instruction": "Add all versions of this common coordinate space.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion"
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"sands:CommonCoordinateSpaceVersion"
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]
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},
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"ontologyIdentifier": {
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"usedSpecies": {
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"_instruction": "Add the species that was used for the creation of this common coordinate space.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/Species"
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"controlledTerms:Species"
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]
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}
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}

‎schemas/atlas/commonCoordinateSpaceVersion.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion",
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"_type": "sands:CommonCoordinateSpaceVersion",
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"_extends": "/core/schemas/products/researchProductVersion.schema.tpl.json",
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"_categories": [
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"coordinateSpace"
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"anatomicalAxesOrientation": {
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"_instruction": "Add the axes orientation denoted in standard anatomical terms of direction (stated as XYZ) for this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation"
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"controlledTerms:AnatomicalAxesOrientation"
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]
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},
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"author": {
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"uniqueItems": true,
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"_instruction": "Enter the origin (central point where all axes intersect) of this common coordinate space version for two-dimensional spaces as [x, y] or for three-dimensional space as [x, y, z].",
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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"core:QuantitativeValue"
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]
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},
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"defaultImage": {
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"uniqueItems": true,
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"_instruction": "Add all image files used as visual representation of this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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"core:File"
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]
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},
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"digitalIdentifier": {
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"_instruction": "Add the globally unique and persistent digital identifier of this research product version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/DOI",
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"https://openminds.ebrains.eu/core/ISBN",
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"https://openminds.ebrains.eu/core/RRID"
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"core:DOI",
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"core:ISBN",
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"core:RRID"
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]
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},
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"isAlternativeVersionOf": {
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"uniqueItems": true,
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"_instruction": "Add all common coordinate space versions that can be used alternatively to this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion"
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"sands:CommonCoordinateSpaceVersion"
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]
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},
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"isNewVersionOf": {
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"_instruction": "Add the common coordinate space version preceding this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion"
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"sands:CommonCoordinateSpaceVersion"
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]
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},
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"license": {
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"_instruction": "Add the license of this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/License"
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"core:License"
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]
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},
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"nativeUnit": {
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"_instruction": "Add the native unit that is used for this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement"
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"controlledTerms:UnitOfMeasurement"
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]
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},
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"ontologyIdentifier": {
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"uniqueItems": true,
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"_instruction": "Add the specimen that was used for the creation of this common coordinate space version.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/Subject",
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"https://openminds.ebrains.eu/core/SubjectGroup",
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"https://openminds.ebrains.eu/core/TissueSample",
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"https://openminds.ebrains.eu/core/TissueSampleCollection"
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"core:Subject",
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"core:SubjectGroup",
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"core:TissueSample",
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"core:TissueSampleCollection"
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]
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}
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}

‎schemas/atlas/parcellationEntity.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/sands/ParcellationEntity",
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"_type": "sands:ParcellationEntity",
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"_categories": [
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"anatomicalLocation",
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"studyTarget"
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"uniqueItems": true,
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"_instruction": "Add all anatomical parent structures for this parcellation entity as defined within the corresponding brain atlas.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/ParcellationEntity"
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"sands:ParcellationEntity"
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]
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},
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"hasVersion": {
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"uniqueItems": true,
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"_instruction": "Add all versions of this parcellation entity.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/ParcellationEntityVersion"
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"sands:ParcellationEntityVersion"
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]
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},
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"lookupLabel": {
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"relatedUBERONTerm":{
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"_instruction": "Add the related anatomical entity as defined by the UBERON ontology.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/Organ",
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"https://openminds.ebrains.eu/controlledTerms/UBERONParcellation"
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"controlledTerms:Organ",
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"controlledTerms:UBERONParcellation"
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]
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}
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}

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