Added a new creation time attribute for the annotations class

BioImage-Archive · Aug 3, 2023 · 4ed1d8f · 4ed1d8f
1 parent 015e5db
commit 4ed1d8f
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Showing 14 changed files with 240 additions and 176 deletions.
diff --git a/examples/Annotations_template.yaml b/examples/Annotations_template.yaml
@@ -40,10 +40,12 @@ file_metadata:
     source_image_id: 
     transformations:
     spatial_information: 
+    annotation_creation_time:
   - annotation_id: 
     annotation_type: 
       - 
       - 
     source_image_id: 
     transformations:
-    spatial_information: 
+    spatial_information: 
+    annotation_creation_time:
diff --git a/project/bia_faim_models.py b/project/bia_faim_models.py
@@ -1,5 +1,5 @@
 # Auto generated from bia_faim_models.yaml by pythongen.py version: 0.9.0
-# Generation date: 2023-07-17T15:22:23
+# Generation date: 2023-08-03T15:23:17
 # Schema: bia-faim-models
 #
 # id: https://w3id.org/BioImage-Archive/bia-faim-models
@@ -419,6 +419,7 @@ class FileLevelMetadata(YAMLRoot):
     source_image_id: str = None
     transformations: Optional[str] = None
     spatial_information: Optional[str] = None
+    annotation_creation_time: Optional[Union[str, XSDDateTime]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.annotation_id):
@@ -443,6 +444,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.spatial_information is not None and not isinstance(self.spatial_information, str):
             self.spatial_information = str(self.spatial_information)
 
+        if self.annotation_creation_time is not None and not isinstance(self.annotation_creation_time, XSDDateTime):
+            self.annotation_creation_time = XSDDateTime(self.annotation_creation_time)
+
         super().__post_init__(**kwargs)
 
 
@@ -575,7 +579,7 @@ class AnnotationType(EnumDefinitionImpl):
         description="""graphical representations of the morphology, connectivity, or spatial arrangement of biological structures in an image. Graphs, such as skeletons or connectivity diagrams, typically consist of nodes and edges, where nodes represent individual elements or regions and edges represent the connections or interactions between them""")
     point_annotations = PermissibleValue(
         text="point_annotations",
-        description="X, Y, and Z coordinates of a point of interest in an image (for example an object's centroid).")
+        description="""X, Y, and Z coordinates of a point of interest in an image (for example an object's centroid  or landmarks).""")
     segmentation_mask = PermissibleValue(
         text="segmentation_mask",
         description="""an image, the same size as the source image, with the value of each pixel representing some biological identity or background region""")
@@ -715,6 +719,9 @@ class slots:
 slots.transformations = Slot(uri=BIA_FAIM_MODELS.transformations, name="transformations", curie=BIA_FAIM_MODELS.curie('transformations'),
                    model_uri=BIA_FAIM_MODELS.transformations, domain=None, range=Optional[str])
 
+slots.annotation_creation_time = Slot(uri=PAV.authoredOn, name="annotation_creation_time", curie=PAV.curie('authoredOn'),
+                   model_uri=BIA_FAIM_MODELS.annotation_creation_time, domain=None, range=Optional[Union[str, XSDDateTime]])
+
 slots.version = Slot(uri=PAV.version, name="version", curie=PAV.curie('version'),
                    model_uri=BIA_FAIM_MODELS.version, domain=None, range=float)
 

diff --git a/project/excel/bia_faim_models.xlsx b/project/excel/bia_faim_models.xlsx
diff --git a/project/graphql/bia_faim_models.graphql b/project/graphql/bia_faim_models.graphql
@@ -31,6 +31,7 @@ type FileLevelMetadata
     sourceImageId: String!
     transformations: String
     spatialInformation: String
+    annotationCreationTime: Datetime
   }
 
 interface FileLevelMetadataCollection

diff --git a/project/jsonld/bia_faim_models.context.jsonld b/project/jsonld/bia_faim_models.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-07-17T15:22:09",
+      "generation_date": "2023-08-03T15:23:03",
       "source": "bia_faim_models.yaml"
    },
    "@context": {
@@ -23,6 +23,10 @@
       "ai_models_trained": {
          "@type": "@id"
       },
+      "annotation_creation_time": {
+         "@type": "xsd:dateTime",
+         "@id": "pav:authoredOn"
+      },
       "annotation_id": "@id",
       "annotation_type": {
          "@context": {

diff --git a/project/jsonld/bia_faim_models.jsonld b/project/jsonld/bia_faim_models.jsonld
@@ -361,7 +361,7 @@
         },
         {
           "text": "point_annotations",
-          "description": "X, Y, and Z coordinates of a point of interest in an image (for example an object's centroid).",
+          "description": "X, Y, and Z coordinates of a point of interest in an image (for example an object's centroid  or landmarks).",
           "todos": [
             "map this to an ontology"
           ]
@@ -1275,6 +1275,32 @@
       "range": "string",
       "@type": "SlotDefinition"
     },
+    {
+      "name": "annotation_creation_time",
+      "definition_uri": "https://w3id.org/BioImage-Archive/bia-faim-models/annotation_creation_time",
+      "description": "Date and time when the annotation was created",
+      "examples": [
+        {
+          "value": "2021-04-11 11:00:15-05:00",
+          "@type": "Example"
+        },
+        {
+          "value": "2017-01-23 18:22:04+00:00",
+          "@type": "Example"
+        }
+      ],
+      "from_schema": "https://w3id.org/BioImage-Archive/bia-faim-models",
+      "mappings": [
+        "http://purl.org/pav/authoredOn"
+      ],
+      "slot_uri": "http://purl.org/pav/authoredOn",
+      "owner": "FileLevelMetadata",
+      "domain_of": [
+        "FileLevelMetadata"
+      ],
+      "range": "datetime",
+      "@type": "SlotDefinition"
+    },
     {
       "name": "version",
       "definition_uri": "https://w3id.org/BioImage-Archive/bia-faim-models/version",
@@ -1670,7 +1696,8 @@
         "annotation_type",
         "source_image_id",
         "transformations",
-        "spatial_information"
+        "spatial_information",
+        "annotation_creation_time"
       ],
       "slot_usage": {},
       "class_uri": "https://w3id.org/BioImage-Archive/bia-faim-models/FileLevelMetadata",
@@ -1740,9 +1767,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "bia_faim_models.yaml",
-  "source_file_date": "2023-07-17T15:21:27",
-  "source_file_size": 20392,
-  "generation_date": "2023-07-17T15:22:10",
+  "source_file_date": "2023-08-03T15:13:21",
+  "source_file_size": 20678,
+  "generation_date": "2023-08-03T15:23:04",
   "@type": "SchemaDefinition",
   "@context": [
     "project//jsonld/bia_faim_models.context.jsonld",

diff --git a/project/jsonschema/bia_faim_models.schema.json b/project/jsonschema/bia_faim_models.schema.json
@@ -111,6 +111,11 @@
             "additionalProperties": false,
             "description": "metadata atributes that must be detailed at the file level",
             "properties": {
+                "annotation_creation_time": {
+                    "description": "Date and time when the annotation was created",
+                    "format": "date-time",
+                    "type": "string"
+                },
                 "annotation_id": {
                     "description": "The identifier for the annotation",
                     "type": "string"