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 <[email protected]>
openMetadataInitiative · Sep 24, 2024 · 9d3ed73 · 9d3ed73
1 parent 6f4ad53
commit 9d3ed73
Show file tree

Hide file tree

Showing 23 changed files with 116 additions and 116 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"
       ]
     }
   }