Merge main and run build.

schema/v1.1.0/dataset_config_materialized.yaml

@@ -345,6 +345,20 @@ types:
     base: str
     pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$
 enums:
+  annotation_file_source_enum:
+    name: annotation_file_source_enum
+    description: How the annotation file was acquired
+    from_schema: cdp-dataset-config
+    permissible_values:
+      dataset_author:
+        text: dataset_author
+        description: Annotation submitted by dataset author
+      community:
+        text: community
+        description: Annotation submitted by community member
+      portal_standard:
+        text: portal_standard
+        description: Annotation submitted by portal standardization
   annotation_method_type_enum:
     name: annotation_method_type_enum
     description: Describes how the annotations were generated.
@@ -498,8 +512,8 @@ enums:
       raw:
         text: raw
         description: Tomogram was not processed
-  tomogrom_reconstruction_method_enum:
-    name: tomogrom_reconstruction_method_enum
+  tomogram_reconstruction_method_enum:
+    name: tomogram_reconstruction_method_enum
     description: Tomogram reconstruction method
     from_schema: cdp-dataset-config
     permissible_values:
@@ -526,6 +540,17 @@ enums:
       CANONICAL:
         text: CANONICAL
         description: Canonical tomogram (basis geometry for all annotations)
+  alignment_type_enum:
+    name: alignment_type_enum
+    description: Type of alignment
+    from_schema: cdp-dataset-config
+    permissible_values:
+      LOCAL:
+        text: LOCAL
+        description: per-section non-rigid alignment available
+      GLOBAL:
+        text: GLOBAL
+        description: only per-section rigid alignment available
 classes:
   Container:
     name: Container

schema/v1.1.0/dataset_config_models.py

@@ -472,6 +472,19 @@ def __contains__(self, key: str) -> bool:
 )
 
 
+class AnnotationFileSourceEnum(str, Enum):
+    """
+    How the annotation file was acquired
+    """
+
+    # Annotation submitted by dataset author
+    dataset_author = "dataset_author"
+    # Annotation submitted by community member
+    community = "community"
+    # Annotation submitted by portal standardization
+    portal_standard = "portal_standard"
+
+
 class AnnotationMethodTypeEnum(str, Enum):
     """
     Describes how the annotations were generated.
@@ -605,7 +618,7 @@ class TomogramProcessingEnum(str, Enum):
     raw = "raw"
 
 
-class TomogromReconstructionMethodEnum(str, Enum):
+class TomogramReconstructionMethodEnum(str, Enum):
     """
     Tomogram reconstruction method
     """
@@ -631,6 +644,17 @@ class TomogramTypeEnum(str, Enum):
     CANONICAL = "CANONICAL"
 
 
+class AlignmentTypeEnum(str, Enum):
+    """
+    Type of alignment
+    """
+
+    # per-section non-rigid alignment available
+    LOCAL = "LOCAL"
+    # only per-section rigid alignment available
+    GLOBAL = "GLOBAL"
+
+
 class PicturePath(ConfiguredBaseModel):
     """
     A set of paths to representative images of a piece of data.
@@ -2133,13 +2157,13 @@ class Tomogram(AuthoredEntity):
             }
         },
     )
-    reconstruction_method: Optional[Union[TomogromReconstructionMethodEnum, str]] = Field(
+    reconstruction_method: Optional[Union[TomogramReconstructionMethodEnum, str]] = Field(
         None,
         description="""Describe reconstruction method (WBP, SART, SIRT)""",
         json_schema_extra={
             "linkml_meta": {
                 "alias": "reconstruction_method",
-                "any_of": [{"range": "tomogrom_reconstruction_method_enum"}, {"range": "StringFormattedString"}],
+                "any_of": [{"range": "tomogram_reconstruction_method_enum"}, {"range": "StringFormattedString"}],
                 "domain_of": ["Tomogram"],
             }
         },
@@ -6175,3 +6199,4 @@ class TomogramHeader(ConfiguredBaseModel):
 VoxelSpacingSource.model_rebuild()
 VoxelSpacingLiteral.model_rebuild()
 TomogramHeader.model_rebuild()
+

schema/v1.1.0/dataset_config_models.schema.json

@@ -1,5 +1,14 @@
 {
     "$defs": {
+        "AlignmentTypeEnum": {
+            "description": "Type of alignment",
+            "enum": [
+                "LOCAL",
+                "GLOBAL"
+            ],
+            "title": "AlignmentTypeEnum",
+            "type": "string"
+        },
         "Annotation": {
             "additionalProperties": false,
             "description": "Metadata describing an annotation.",
@@ -136,6 +145,16 @@
             "title": "AnnotationFileShapeTypeEnum",
             "type": "string"
         },
+        "AnnotationFileSourceEnum": {
+            "description": "How the annotation file was acquired",
+            "enum": [
+                "dataset_author",
+                "community",
+                "portal_standard"
+            ],
+            "title": "AnnotationFileSourceEnum",
+            "type": "string"
+        },
         "AnnotationInstanceSegmentationFile": {
             "additionalProperties": false,
             "description": "File and sourcing data for an instance segmentation annotation. Annotation that identifies individual instances of object shapes.",
@@ -2081,7 +2100,7 @@
                 "reconstruction_method": {
                     "anyOf": [
                         {
-                            "$ref": "#/$defs/TomogromReconstructionMethodEnum"
+                            "$ref": "#/$defs/TomogramReconstructionMethodEnum"
                         },
                         {
                             "pattern": "^[ ]*\\{[a-zA-Z0-9_-]+\\}[ ]*$",
@@ -2213,6 +2232,18 @@
             "title": "TomogramProcessingEnum",
             "type": "string"
         },
+        "TomogramReconstructionMethodEnum": {
+            "description": "Tomogram reconstruction method",
+            "enum": [
+                "SART",
+                "Fourier Space",
+                "SIRT",
+                "WBP",
+                "Unknown"
+            ],
+            "title": "TomogramReconstructionMethodEnum",
+            "type": "string"
+        },
         "TomogramSize": {
             "additionalProperties": false,
             "description": "The size of a tomogram in voxels in each dimension.",
@@ -2277,18 +2308,6 @@
             "title": "TomogramTypeEnum",
             "type": "string"
         },
-        "TomogromReconstructionMethodEnum": {
-            "description": "Tomogram reconstruction method",
-            "enum": [
-                "SART",
-                "Fourier Space",
-                "SIRT",
-                "WBP",
-                "Unknown"
-            ],
-            "title": "TomogromReconstructionMethodEnum",
-            "type": "string"
-        },
         "VoxelSpacingEntity": {
             "additionalProperties": false,
             "description": "A voxel spacing entity.",

schema/v1.1.0/metadata-docs/AlignmentTypeEnum.md

@@ -0,0 +1,62 @@
+# Enum: AlignmentTypeEnum
+
+
+
+
+_Type of alignment_
+
+
+
+URI: [AlignmentTypeEnum](AlignmentTypeEnum.md)
+
+## Permissible Values
+
+| Value | Meaning | Description |
+| --- | --- | --- |
+| LOCAL | None | per-section non-rigid alignment available |
+| GLOBAL | None | only per-section rigid alignment available |
+
+
+
+
+
+
+
+
+
+## Identifier and Mapping Information
+
+
+
+
+
+
+
+### Schema Source
+
+
+* from schema: metadata
+
+
+
+
+
+
+## LinkML Source
+
+<details>
+```yaml
+name: alignment_type_enum
+description: Type of alignment
+from_schema: metadata
+rank: 1000
+permissible_values:
+  LOCAL:
+    text: LOCAL
+    description: per-section non-rigid alignment available
+  GLOBAL:
+    text: GLOBAL
+    description: only per-section rigid alignment available
+
+```
+</details>

schema/v1.1.0/metadata-docs/Annotation.md

@@ -24,76 +24,76 @@ URI: [cdp-meta:Annotation](metadataAnnotation)
         click DateStampedEntity href "../DateStampedEntity"
       AuthoredEntity <|-- Annotation
         click AuthoredEntity href "../AuthoredEntity"
-
+      
       Annotation : annotation_method
-
+        
       Annotation : annotation_object
-
-
-
-
+        
+          
+    
+    
     Annotation --> "1" AnnotationObject : annotation_object
     click AnnotationObject href "../AnnotationObject"
 
-
+        
       Annotation : annotation_publications
-
+        
       Annotation : annotation_software
-
+        
       Annotation : authors
-
-
-
-
+        
+          
+    
+    
     Annotation --> "1..*" Author : authors
     click Author href "../Author"
 
-
+        
       Annotation : confidence
-
-
-
-
+        
+          
+    
+    
     Annotation --> "0..1" AnnotationConfidence : confidence
     click AnnotationConfidence href "../AnnotationConfidence"
 
-
+        
       Annotation : dates
-
-
-
-
+        
+          
+    
+    
     Annotation --> "1" DateStamp : dates
     click DateStamp href "../DateStamp"
 
-
+        
       Annotation : files
-
-
-
-
+        
+          
+    
+    
     Annotation --> "*" AnnotationSourceFile : files
     click AnnotationSourceFile href "../AnnotationSourceFile"
 
-
+        
       Annotation : ground_truth_status
-
+        
       Annotation : is_curator_recommended
-
+        
       Annotation : method_type
-
-
-
-
+        
+          
+    
+    
     Annotation --> "1" AnnotationMethodTypeEnum : method_type
     click AnnotationMethodTypeEnum href "../AnnotationMethodTypeEnum"
 
-
+        
       Annotation : object_count
-
+        
       Annotation : version
-
-
+        
+      
 ```
 
 
@@ -590,4 +590,4 @@ attributes:
     minimum_cardinality: 1
 
 ```
-</details>
+</details>