From 9d3ed733c65ed0959364ee0255877224f5167414 Mon Sep 17 00:00:00 2001 From: Raphael-Gazzotti <125291580+Raphael-Gazzotti@users.noreply.github.com> Date: Tue, 24 Sep 2024 21:07:20 +0200 Subject: [PATCH] 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 --- schemas/atlas/annotation.schema.tpl.json | 16 +++++----- schemas/atlas/atlasAnnotation.schema.tpl.json | 4 +-- schemas/atlas/brainAtlas.schema.tpl.json | 14 ++++----- .../atlas/brainAtlasVersion.schema.tpl.json | 28 ++++++++--------- .../commonCoordinateSpace.schema.tpl.json | 12 ++++---- ...mmonCoordinateSpaceVersion.schema.tpl.json | 30 +++++++++---------- .../atlas/parcellationEntity.schema.tpl.json | 10 +++---- .../parcellationEntityVersion.schema.tpl.json | 12 ++++---- .../parcellationTerminology.schema.tpl.json | 6 ++-- ...ellationTerminologyVersion.schema.tpl.json | 6 ++-- .../mathematicalShapes/circle.schema.tpl.json | 4 +-- .../ellipse.schema.tpl.json | 6 ++-- .../rectangle.schema.tpl.json | 6 ++-- .../anatomicalTargetPosition.schema.tpl.json | 6 ++-- .../coordinatePoint.schema.tpl.json | 8 ++--- ...litativeRelationAssessment.schema.tpl.json | 12 ++++---- ...titativeRelationAssessment.schema.tpl.json | 10 +++---- .../miscellaneous/singleColor.schema.tpl.json | 2 +- .../viewerSpecification.schema.tpl.json | 6 ++-- .../customAnatomicalEntity.schema.tpl.json | 12 ++++---- .../customAnnotation.schema.tpl.json | 10 +++---- .../customCoordinateSpace.schema.tpl.json | 10 +++---- version.txt | 2 +- 23 files changed, 116 insertions(+), 116 deletions(-) diff --git a/schemas/atlas/annotation.schema.tpl.json b/schemas/atlas/annotation.schema.tpl.json index d6d95c77e..075ce6a27 100644 --- a/schemas/atlas/annotation.schema.tpl.json +++ b/schemas/atlas/annotation.schema.tpl.json @@ -11,25 +11,25 @@ "maxItems": 3, "_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]).", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "criteria": { "_instruction": "Add the protocol execution defining the criteria that were applied to produce this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/ProtocolExecution" + "core:ProtocolExecution" ] }, "criteriaQualityType": { "_instruction": "Add the quality type of the stated criteria used to define this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/CriteriaQualityType" + "controlledTerms:CriteriaQualityType" ] }, "criteriaType": { "_instruction": "Add the criteria type for this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/AnnotationCriteriaType" + "controlledTerms:AnnotationCriteriaType" ] }, "inspiredBy": { @@ -38,7 +38,7 @@ "uniqueItems": true, "_instruction": "Add all (source) files that inspired the definition of this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File" + "core:File" ] }, "internalIdentifier": { @@ -52,19 +52,19 @@ "uniqueItems": true, "_instruction": "Add one or both sides of the body, bilateral organ or bilateral organ part that this annotation is defined in.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/Laterality" + "controlledTerms:Laterality" ] }, "preferredVisualization": { "_instruction": "Add the preferred viewer specification to visualize this annotation.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/ViewerSpecification" + "sands:ViewerSpecification" ] }, "type": { "_instruction": "Add the geometry type of this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/AnnotationType" + "controlledTerms:AnnotationType" ] } } diff --git a/schemas/atlas/atlasAnnotation.schema.tpl.json b/schemas/atlas/atlasAnnotation.schema.tpl.json index 1e167108a..fcd0f7867 100644 --- a/schemas/atlas/atlasAnnotation.schema.tpl.json +++ b/schemas/atlas/atlasAnnotation.schema.tpl.json @@ -1,11 +1,11 @@ { - "_type": "https://openminds.ebrains.eu/sands/AtlasAnnotation", + "_type": "sands:AtlasAnnotation", "_extends": "atlas/annotation.schema.tpl.json", "properties": { "specification": { "_instruction": "Add the non-parametric specification of this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File" + "core:File" ] } } diff --git a/schemas/atlas/brainAtlas.schema.tpl.json b/schemas/atlas/brainAtlas.schema.tpl.json index 836a14baf..450b429e6 100644 --- a/schemas/atlas/brainAtlas.schema.tpl.json +++ b/schemas/atlas/brainAtlas.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/BrainAtlas", + "_type": "sands:BrainAtlas", "_extends": "/core/schemas/products/researchProduct.schema.tpl.json", "required": [ "author", @@ -22,15 +22,15 @@ "digitalIdentifier": { "_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.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/DOI", - "https://openminds.ebrains.eu/core/ISBN", - "https://openminds.ebrains.eu/core/RRID" + "core:DOI", + "core:ISBN", + "core:RRID" ] }, "hasTerminology": { "_instruction": "Enter the parcellation terminology of this brain atlas.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationTerminology" + "sands:ParcellationTerminology" ] }, "hasVersion": { @@ -39,7 +39,7 @@ "uniqueItems": true, "_instruction": "Add versions of this brain atlas.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/BrainAtlasVersion" + "sands:BrainAtlasVersion" ] }, "ontologyIdentifier": { @@ -52,7 +52,7 @@ "usedSpecies": { "_instruction": "Add the species that was used for the creation of this brain atlas.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/Species" + "controlledTerms:Species" ] } } diff --git a/schemas/atlas/brainAtlasVersion.schema.tpl.json b/schemas/atlas/brainAtlasVersion.schema.tpl.json index e0f1f6dd0..c41cdfbab 100644 --- a/schemas/atlas/brainAtlasVersion.schema.tpl.json +++ b/schemas/atlas/brainAtlasVersion.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/BrainAtlasVersion", + "_type": "sands:BrainAtlasVersion", "_extends": "/core/schemas/products/researchProductVersion.schema.tpl.json", "required": [ "coordinateSpace", @@ -23,21 +23,21 @@ "coordinateSpace": { "_instruction": "Add the specific common coordinate space in which this brain atlas version exists.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion" + "sands:CommonCoordinateSpaceVersion" ] }, "digitalIdentifier": { "_instruction": "Add the globally unique and persistent digital identifier of this research product version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/DOI", - "https://openminds.ebrains.eu/core/ISBN", - "https://openminds.ebrains.eu/core/RRID" + "core:DOI", + "core:ISBN", + "core:RRID" ] }, "hasTerminology": { "_instruction": "Enter the specific parcellation terminology of this brain atlas version.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationTerminologyVersion" + "sands:ParcellationTerminologyVersion" ] }, "isAlternativeVersionOf": { @@ -46,19 +46,19 @@ "uniqueItems": true, "_instruction": "Add all brain atlas versions that can be used alternatively to this brain atlas version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/BrainAtlasVersion" + "sands:BrainAtlasVersion" ] }, "isNewVersionOf": { "_instruction": "Add the brain atlas version preceding this brain atlas version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/BrainAtlasVersion" + "sands:BrainAtlasVersion" ] }, "license": { "_instruction": "Add the license of this brain atlas version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/License" + "core:License" ] }, "majorVersionIdentifier": { @@ -75,7 +75,7 @@ "type": { "_instruction": "Add the type of this brain atlas version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/AtlasType" + "controlledTerms:AtlasType" ] }, "usedSpecimen": { @@ -84,10 +84,10 @@ "uniqueItems": true, "_instruction": "Add the specimen that was used for the creation of this brain atlas version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/Subject", - "https://openminds.ebrains.eu/core/SubjectGroup", - "https://openminds.ebrains.eu/core/TissueSample", - "https://openminds.ebrains.eu/core/TissueSampleCollection" + "core:Subject", + "core:SubjectGroup", + "core:TissueSample", + "core:TissueSampleCollection" ] } } diff --git a/schemas/atlas/commonCoordinateSpace.schema.tpl.json b/schemas/atlas/commonCoordinateSpace.schema.tpl.json index eed19a131..474bec4e7 100644 --- a/schemas/atlas/commonCoordinateSpace.schema.tpl.json +++ b/schemas/atlas/commonCoordinateSpace.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/CommonCoordinateSpace", + "_type": "sands:CommonCoordinateSpace", "_extends": "/core/schemas/products/researchProduct.schema.tpl.json", "_categories": [ "coordinateSpace" @@ -24,9 +24,9 @@ "digitalIdentifier": { "_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.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/DOI", - "https://openminds.ebrains.eu/core/ISBN", - "https://openminds.ebrains.eu/core/RRID" + "core:DOI", + "core:ISBN", + "core:RRID" ] }, "hasVersion": { @@ -35,7 +35,7 @@ "uniqueItems": true, "_instruction": "Add all versions of this common coordinate space.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion" + "sands:CommonCoordinateSpaceVersion" ] }, "ontologyIdentifier": { @@ -53,7 +53,7 @@ "usedSpecies": { "_instruction": "Add the species that was used for the creation of this common coordinate space.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/Species" + "controlledTerms:Species" ] } } diff --git a/schemas/atlas/commonCoordinateSpaceVersion.schema.tpl.json b/schemas/atlas/commonCoordinateSpaceVersion.schema.tpl.json index b0e6c46ce..80a603a57 100644 --- a/schemas/atlas/commonCoordinateSpaceVersion.schema.tpl.json +++ b/schemas/atlas/commonCoordinateSpaceVersion.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion", + "_type": "sands:CommonCoordinateSpaceVersion", "_extends": "/core/schemas/products/researchProductVersion.schema.tpl.json", "_categories": [ "coordinateSpace" @@ -17,7 +17,7 @@ "anatomicalAxesOrientation": { "_instruction": "Add the axes orientation denoted in standard anatomical terms of direction (stated as XYZ) for this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation" + "controlledTerms:AnatomicalAxesOrientation" ] }, "author": { @@ -36,7 +36,7 @@ "uniqueItems": true, "_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].", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "defaultImage": { @@ -45,15 +45,15 @@ "uniqueItems": true, "_instruction": "Add all image files used as visual representation of this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File" + "core:File" ] }, "digitalIdentifier": { "_instruction": "Add the globally unique and persistent digital identifier of this research product version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/DOI", - "https://openminds.ebrains.eu/core/ISBN", - "https://openminds.ebrains.eu/core/RRID" + "core:DOI", + "core:ISBN", + "core:RRID" ] }, "isAlternativeVersionOf": { @@ -62,25 +62,25 @@ "uniqueItems": true, "_instruction": "Add all common coordinate space versions that can be used alternatively to this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion" + "sands:CommonCoordinateSpaceVersion" ] }, "isNewVersionOf": { "_instruction": "Add the common coordinate space version preceding this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion" + "sands:CommonCoordinateSpaceVersion" ] }, "license": { "_instruction": "Add the license of this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/License" + "core:License" ] }, "nativeUnit": { "_instruction": "Add the native unit that is used for this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement" + "controlledTerms:UnitOfMeasurement" ] }, "ontologyIdentifier": { @@ -101,10 +101,10 @@ "uniqueItems": true, "_instruction": "Add the specimen that was used for the creation of this common coordinate space version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/Subject", - "https://openminds.ebrains.eu/core/SubjectGroup", - "https://openminds.ebrains.eu/core/TissueSample", - "https://openminds.ebrains.eu/core/TissueSampleCollection" + "core:Subject", + "core:SubjectGroup", + "core:TissueSample", + "core:TissueSampleCollection" ] } } diff --git a/schemas/atlas/parcellationEntity.schema.tpl.json b/schemas/atlas/parcellationEntity.schema.tpl.json index 71738f40b..c0b105670 100644 --- a/schemas/atlas/parcellationEntity.schema.tpl.json +++ b/schemas/atlas/parcellationEntity.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/ParcellationEntity", + "_type": "sands:ParcellationEntity", "_categories": [ "anatomicalLocation", "studyTarget" @@ -31,7 +31,7 @@ "uniqueItems": true, "_instruction": "Add all anatomical parent structures for this parcellation entity as defined within the corresponding brain atlas.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationEntity" + "sands:ParcellationEntity" ] }, "hasVersion": { @@ -40,7 +40,7 @@ "uniqueItems": true, "_instruction": "Add all versions of this parcellation entity.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" + "sands:ParcellationEntityVersion" ] }, "lookupLabel": { @@ -66,8 +66,8 @@ "relatedUBERONTerm":{ "_instruction": "Add the related anatomical entity as defined by the UBERON ontology.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/Organ", - "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation" + "controlledTerms:Organ", + "controlledTerms:UBERONParcellation" ] } } diff --git a/schemas/atlas/parcellationEntityVersion.schema.tpl.json b/schemas/atlas/parcellationEntityVersion.schema.tpl.json index 2c4a2816b..43cdc5731 100644 --- a/schemas/atlas/parcellationEntityVersion.schema.tpl.json +++ b/schemas/atlas/parcellationEntityVersion.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/ParcellationEntityVersion", + "_type": "sands:ParcellationEntityVersion", "_categories": [ "anatomicalLocation", "studyTarget" @@ -36,7 +36,7 @@ "uniqueItems": true, "_instruction": "Add all atlas annotations which define this parcellation entity version.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/AtlasAnnotation" + "sands:AtlasAnnotation" ] }, "hasParent": { @@ -45,8 +45,8 @@ "uniqueItems": true, "_instruction": "Add all anatomical parent structures (or version of the structures) for this parcellation entity as defined within corresponding brain atlas version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationEntity", - "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" + "sands:ParcellationEntity", + "sands:ParcellationEntityVersion" ] }, "lookupLabel": { @@ -75,8 +75,8 @@ "uniqueItems": true, "_instruction": "Add all relations (qualitative or quantitative) of this parcellation entity version to other anatomical entities.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/QualitativeRelationAssessment", - "https://openminds.ebrains.eu/sands/QuantitativeRelationAssessment" + "sands:QualitativeRelationAssessment", + "sands:QuantitativeRelationAssessment" ] }, "versionIdentifier": { diff --git a/schemas/atlas/parcellationTerminology.schema.tpl.json b/schemas/atlas/parcellationTerminology.schema.tpl.json index 58c7dd53b..e6902c670 100644 --- a/schemas/atlas/parcellationTerminology.schema.tpl.json +++ b/schemas/atlas/parcellationTerminology.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/ParcellationTerminology", + "_type": "sands:ParcellationTerminology", "required": [ "hasEntity" ], @@ -10,7 +10,7 @@ "uniqueItems": true, "_instruction": "Add the location of all files in which this parcellation terminology is stored.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File" + "core:File" ] }, "hasEntity": { @@ -19,7 +19,7 @@ "uniqueItems": true, "_instruction": "Add all parcellation entities which belong to this parcellation terminology.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationEntity" + "sands:ParcellationEntity" ] }, "ontologyIdentifier": { diff --git a/schemas/atlas/parcellationTerminologyVersion.schema.tpl.json b/schemas/atlas/parcellationTerminologyVersion.schema.tpl.json index 923331f7d..efd9b6d45 100644 --- a/schemas/atlas/parcellationTerminologyVersion.schema.tpl.json +++ b/schemas/atlas/parcellationTerminologyVersion.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/ParcellationTerminologyVersion", + "_type": "sands:ParcellationTerminologyVersion", "required": [ "hasEntity" ], @@ -10,7 +10,7 @@ "uniqueItems": true, "_instruction": "Add the location of all files in which this parcellation terminology version is stored.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File" + "core:File" ] }, "hasEntity": { @@ -19,7 +19,7 @@ "uniqueItems": true, "_instruction": "Add all parcellation entity versions which belong to this parcellation terminology version.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" + "sands:ParcellationEntityVersion" ] }, "ontologyIdentifier": { diff --git a/schemas/mathematicalShapes/circle.schema.tpl.json b/schemas/mathematicalShapes/circle.schema.tpl.json index 32a3928cf..2719a4474 100644 --- a/schemas/mathematicalShapes/circle.schema.tpl.json +++ b/schemas/mathematicalShapes/circle.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/Circle", + "_type": "sands:Circle", "_categories": [ "mathematicalShapes" ], @@ -10,7 +10,7 @@ "radius": { "_instruction": "Enter the radius of this circle.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] } } diff --git a/schemas/mathematicalShapes/ellipse.schema.tpl.json b/schemas/mathematicalShapes/ellipse.schema.tpl.json index f49a863e2..64f42e209 100644 --- a/schemas/mathematicalShapes/ellipse.schema.tpl.json +++ b/schemas/mathematicalShapes/ellipse.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/Ellipse", + "_type": "sands:Ellipse", "_categories": [ "mathematicalShapes" ], @@ -11,13 +11,13 @@ "semiMinorAxis": { "_instruction": "Enter the length of the semi-major axis of this ellipse.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "semiMajorAxis": { "_instruction": "Enter the length of the semi-minor axis of this ellipse.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] } } diff --git a/schemas/mathematicalShapes/rectangle.schema.tpl.json b/schemas/mathematicalShapes/rectangle.schema.tpl.json index 7a3e33a0f..bc7c2493c 100644 --- a/schemas/mathematicalShapes/rectangle.schema.tpl.json +++ b/schemas/mathematicalShapes/rectangle.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/Rectangle", + "_type": "sands:Rectangle", "_categories": [ "mathematicalShapes" ], @@ -11,13 +11,13 @@ "length": { "_instruction": "Enter the length of this rectangle.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "width": { "_instruction": "Enter the width of this rectangle.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] } } diff --git a/schemas/miscellaneous/anatomicalTargetPosition.schema.tpl.json b/schemas/miscellaneous/anatomicalTargetPosition.schema.tpl.json index a3f5b5991..a5106cdbc 100644 --- a/schemas/miscellaneous/anatomicalTargetPosition.schema.tpl.json +++ b/schemas/miscellaneous/anatomicalTargetPosition.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/AnatomicalTargetPosition", + "_type": "sands:AnatomicalTargetPosition", "required": [ "anatomicalTarget", "targetIdentificationType" @@ -24,13 +24,13 @@ "uniqueItems": true, "_instruction": "Add all coordinate points that describe the spatial location of the anatomical target structure(s).", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/CoordinatePoint" + "sands:CoordinatePoint" ] }, "targetIdentificationType": { "_instruction": "Add the target identification type that best describes how the this anatomical target position was identified.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/AnatomicalIdentificationType" + "controlledTerms:AnatomicalIdentificationType" ] } } diff --git a/schemas/miscellaneous/coordinatePoint.schema.tpl.json b/schemas/miscellaneous/coordinatePoint.schema.tpl.json index 0f2b5b0b0..6cd24274d 100644 --- a/schemas/miscellaneous/coordinatePoint.schema.tpl.json +++ b/schemas/miscellaneous/coordinatePoint.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/CoordinatePoint", + "_type": "sands:CoordinatePoint", "required": [ "coordinates", "coordinateSpace" @@ -11,14 +11,14 @@ "maxItems": 3, "_instruction": "Enter the coordinates of this point within the stated coordinate space for two-dimensonal spaces as [x, y] or for three-dimensional space as [x, y, z].", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "coordinateSpace": { "_instruction": "Add the coordinate space in which this coordinate point exists in.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion", - "https://openminds.ebrains.eu/sands/CustomCoordinateSpace" + "sands:CommonCoordinateSpaceVersion", + "sands:CustomCoordinateSpace" ] } } diff --git a/schemas/miscellaneous/qualitativeRelationAssessment.schema.tpl.json b/schemas/miscellaneous/qualitativeRelationAssessment.schema.tpl.json index f33014d43..26bf9c201 100644 --- a/schemas/miscellaneous/qualitativeRelationAssessment.schema.tpl.json +++ b/schemas/miscellaneous/qualitativeRelationAssessment.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/QualitativeRelationAssessment", + "_type": "sands:QualitativeRelationAssessment", "required": [ "inRelationTo", "qualitativeOverlap" @@ -8,21 +8,21 @@ "criteria": { "_instruction": "Add the protocol execution defining the criteria that were applied to determine this relation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/ProtocolExecution" + "core:ProtocolExecution" ] }, "inRelationTo": { "_instruction": "Add the anatomical entity to which the relation is described.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CustomAnatomicalEntity", - "https://openminds.ebrains.eu/sands/ParcellationEntity", - "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" + "sands:CustomAnatomicalEntity", + "sands:ParcellationEntity", + "sands:ParcellationEntityVersion" ] }, "qualitativeOverlap": { "_instruction": "Add the qualitative overlap that best describes the relation between the two anatomical entities.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/QualitativeOverlap" + "controlledTerms:QualitativeOverlap" ] } } diff --git a/schemas/miscellaneous/quantitativeRelationAssessment.schema.tpl.json b/schemas/miscellaneous/quantitativeRelationAssessment.schema.tpl.json index fd7c6289b..27a75c680 100644 --- a/schemas/miscellaneous/quantitativeRelationAssessment.schema.tpl.json +++ b/schemas/miscellaneous/quantitativeRelationAssessment.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/QuantitativeRelationAssessment", + "_type": "sands:QuantitativeRelationAssessment", "required": [ "inRelationTo", "quantitativeOverlap" @@ -8,20 +8,20 @@ "criteria": { "_instruction": "Add the protocol execution defining the criteria that were applied to determine this relation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/ProtocolExecution" + "core:ProtocolExecution" ] }, "inRelationTo": { "_instruction": "Add the parcellation entity version to which the relation is described.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/ParcellationEntityVersion" + "sands:ParcellationEntityVersion" ] }, "quantitativeOverlap": { "_instruction": "Enter the quantitative overlap between the two anatomical entities, preferably expressed in percentage.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue", - "https://openminds.ebrains.eu/core/QuantitativeValueRange" + "core:QuantitativeValue", + "core:QuantitativeValueRange" ] } } diff --git a/schemas/miscellaneous/singleColor.schema.tpl.json b/schemas/miscellaneous/singleColor.schema.tpl.json index 7895dc744..70eec1381 100644 --- a/schemas/miscellaneous/singleColor.schema.tpl.json +++ b/schemas/miscellaneous/singleColor.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/SingleColor", + "_type": "sands:SingleColor", "_categories": [ "color" ], diff --git a/schemas/miscellaneous/viewerSpecification.schema.tpl.json b/schemas/miscellaneous/viewerSpecification.schema.tpl.json index d28889d82..8eec1cea1 100644 --- a/schemas/miscellaneous/viewerSpecification.schema.tpl.json +++ b/schemas/miscellaneous/viewerSpecification.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/ViewerSpecification", + "_type": "sands:ViewerSpecification", "required": [ "anchorPoint" ], @@ -14,13 +14,13 @@ "maxItems": 3, "_instruction": "Enter the coordinates of the anchor point that a viewer should use. Either state the anchor point of the annotation again or state another coordinate point.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "cameraPosition": { "_instruction": "Enter the camera position that a viewer should use.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/CoordinatePoint" + "sands:CoordinatePoint" ] }, "preferredDisplayColor": { diff --git a/schemas/non-atlas/customAnatomicalEntity.schema.tpl.json b/schemas/non-atlas/customAnatomicalEntity.schema.tpl.json index 35f5764f7..7f1c2a423 100644 --- a/schemas/non-atlas/customAnatomicalEntity.schema.tpl.json +++ b/schemas/non-atlas/customAnatomicalEntity.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/CustomAnatomicalEntity", + "_type": "sands:CustomAnatomicalEntity", "_categories": [ "anatomicalLocation", "studyTarget" @@ -14,7 +14,7 @@ "uniqueItems": true, "_instruction": "Add all custom annotations which define this custom anatomical entity.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/CustomAnnotation" + "sands:CustomAnnotation" ] }, "name": { @@ -24,8 +24,8 @@ "relatedUBERONTerm":{ "_instruction": "Add the related anatomical entity as defined by the UBERON ontology.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/Organ", - "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation" + "controlledTerms:Organ", + "controlledTerms:UBERONParcellation" ] }, "relationAssessment": { @@ -34,8 +34,8 @@ "uniqueItems": true, "_instruction": "Add all relations (qualitative or quantitative) of this custom anatomical entity to other anatomical entities.", "_embeddedTypes": [ - "https://openminds.ebrains.eu/sands/QualitativeRelationAssessment", - "https://openminds.ebrains.eu/sands/QuantitativeRelationAssessment" + "sands:QualitativeRelationAssessment", + "sands:QuantitativeRelationAssessment" ] } } diff --git a/schemas/non-atlas/customAnnotation.schema.tpl.json b/schemas/non-atlas/customAnnotation.schema.tpl.json index e8dd4ae70..360d10437 100644 --- a/schemas/non-atlas/customAnnotation.schema.tpl.json +++ b/schemas/non-atlas/customAnnotation.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/CustomAnnotation", + "_type": "sands:CustomAnnotation", "_extends": "atlas/annotation.schema.tpl.json", "required": [ "coordinateSpace" @@ -8,15 +8,15 @@ "coordinateSpace": { "_instruction": "Add the coordinate space for this custom annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion", - "https://openminds.ebrains.eu/sands/CustomCoordinateSpace" + "sands:CommonCoordinateSpaceVersion", + "sands:CustomCoordinateSpace" ] }, "specification": { "_instruction": "Add the non-parametric or parametric specification of this annotation.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File", - "https://openminds.ebrains.eu/core/PropertyValueList" + "core:File", + "core:PropertyValueList" ] } } diff --git a/schemas/non-atlas/customCoordinateSpace.schema.tpl.json b/schemas/non-atlas/customCoordinateSpace.schema.tpl.json index addaddb19..bdf856e47 100644 --- a/schemas/non-atlas/customCoordinateSpace.schema.tpl.json +++ b/schemas/non-atlas/customCoordinateSpace.schema.tpl.json @@ -1,5 +1,5 @@ { - "_type": "https://openminds.ebrains.eu/sands/CustomCoordinateSpace", + "_type": "sands:CustomCoordinateSpace", "_categories": [ "coordinateSpace" ], @@ -13,7 +13,7 @@ "anatomicalAxesOrientation": { "_instruction": "Add the axes orientation denoted in standard anatomical terms of direction (stated as XYZ) for this custom coordinate space.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation" + "controlledTerms:AnatomicalAxesOrientation" ] }, "axesOrigin": { @@ -23,7 +23,7 @@ "uniqueItems": true, "_instruction": "Enter the origin (central point where all axes intersect) of this custom coordinate space for two-dimensional spaces as [x, y] or for three-dimensional space as [x, y, z].", "_embeddedTypes": [ - "https://openminds.ebrains.eu/core/QuantitativeValue" + "core:QuantitativeValue" ] }, "defaultImage": { @@ -32,7 +32,7 @@ "uniqueItems": true, "_instruction": "Add all image files used as visual representation of this custom coordinate space.", "_linkedTypes": [ - "https://openminds.ebrains.eu/core/File" + "core:File" ] }, "name": { @@ -42,7 +42,7 @@ "nativeUnit": { "_instruction": "Add the native unit that is used for this custom coordinate space.", "_linkedTypes": [ - "https://openminds.ebrains.eu/controlledTerms/UnitOfMeasurement" + "controlledTerms:UnitOfMeasurement" ] } } diff --git a/version.txt b/version.txt index 29ef827e8..c694117fd 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -v3 +v4