Guittari

emannotationschemas/schemas/braincircuits.py

@@ -11,3 +11,9 @@ class BrainCircuitsBoundTagAnnotationUser(AnnotationSchema):
         required=True,
         description=f"User who created the tag.",
     )
+
+class RegionsOfInterest(AnnotationSchema):
+    layer = fields.Boolean(description="Layer regions")
+    brain_regions = fields.Boolean(description="Brain regions")
+    cylinder = fields.Boolean(description="Cylinder regions")
+    other = fields.String(description="Other regions of interest")

emannotationschemas/schemas/extended_classical_cell_type.py

@@ -29,3 +29,8 @@
     schema_type_name,
     class_name,
 )
+
+# Adding classes from https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/CAVE-implemented-annotation-metadata-version-1.2.plantuml
+# With explanations from here: https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/required-field-names.md
+
+

emannotationschemas/schemas/functional_coregistration.py

@@ -49,6 +49,17 @@ class FunctionalUnitCoregistrationExtended(ReferenceAnnotation):
         required=False, description="confidence score associated with match"
     )
 
+# Adding classes from https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/CAVE-implemented-annotation-metadata-version-1.2.plantuml
+# With explanations from here: https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/required-field-names.md
 
+class CoRegistration(ReferenceAnnotation):
+    valid = fields.Boolean(description="Indicates if the co-registration is valid")
+    pt = fields.Nested('PointSchema', description="Point schema for location data")
+    valid_id = fields.Float(description="Validation ID")
+    status_dendrite = fields.String(description="Status of the dendrite")
+    object_id = fields.String(description="Object ID for co-registration")
+    other = fields.String(description="Other co-registration-related information")
+
+# Moving this to the bottom/after BENCHMARK additions:
 class FunctionalUnitCoregistrationQC(ReferenceAnnotation):
     pass

emannotationschemas/schemas/nucleus_detection.py

@@ -23,3 +23,7 @@ class NucleusDetection(AnnotationSchema):
         required=False,
         description="high corner of the bounding box",
     )
+
+class NucleusProperties(AnnotationSchema):
+    nucleolus = fields.Boolean(description="Presence of nucleolus")
+    other = fields.String(description="Other nucleus properties")

emannotationschemas/schemas/proofreading.py

@@ -71,4 +71,43 @@ class CompartmentProofreadStatusStrategy(PointWithValid):
     strategy_axon = fields.String(
         required=True,
         description=f"Strategy used when proofreading axon. See table description for more details.",
-    )
+    )
+
+# Adding classes from https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/CAVE-implemented-annotation-metadata-version-1.2.plantuml
+# With explanations from here: https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/required-field-names.md
+
+class AnnotationProvenance(PointWithValid):
+    valid = fields.Boolean(description="Indicates if the annotation is valid")
+    pt = fields.Nested('PointSchema', description="Point schema for location data")
+    valid_id = fields.Float(description="Validation ID")
+    status = fields.String(description="Status of the annotation")
+
+
+class Annotator(PointWithValid):
+    valid = fields.Boolean(description="Indicates if the annotator data is valid")
+    pt = fields.Nested('PointSchema', description="Point schema for location data")
+    valid_id = fields.Float(description="Validation ID")
+    contributor_method = fields.String(description="Method used by the contributor")
+    novice_annotator = fields.Boolean(description="Indicates if the annotator is a novice")
+    expert_annotator = fields.Boolean(description="Indicates if the annotator is an expert")
+    novice_proofreader = fields.Boolean(description="Indicates if the proofreader is a novice")
+    expert_proofreader = fields.Boolean(description="Indicates if the proofreader is an expert")
+    contributor = fields.String(description="Name of the contributor")
+    other = fields.String(description="Other annotator-related information")
+
+class Score(PointWithValid):
+    valid = fields.Boolean(description="Indicates if the score is valid")
+    pt = fields.Nested('PointSchema', description="Point schema for location data")
+    valid_id = fields.Float(description="Validation ID")
+    annotation_reviewed = fields.Integer(description="Number of annotations reviewed")
+    review_time_hours = fields.Integer(description="Time spent reviewing annotations (in hours)")
+    confidence_value = fields.Integer(description="Confidence value of the annotation")
+    other = fields.Integer(description="Other score-related information")
+
+class Versioning(PointWithValid):
+    valid = fields.Boolean(description="Indicates if the versioning is valid")
+    pt = fields.Nested('PointSchema', description="Point schema for location data")
+    valid_id = fields.Float(description="Validation ID")
+    version_checkpoint_value = fields.Integer(description="Version checkpoint value")
+    version_checkpoint_updates = fields.String(description="Updates made in this version")
+    other = fields.String(description="Other versioning-related information")

emannotationschemas/schemas/synapse.py

@@ -6,7 +6,6 @@
     ReferenceAnnotation,
 )
 
-
 class BaseSynapseSchema(AnnotationSchema):
     pre_pt = mm.fields.Nested(
         BoundSpatialPoint,
@@ -36,13 +35,11 @@ def check_root_id(self, data, **kwargs):
             data.pop("valid", None)
         return data
 
-
 class NoCleftSynapse(BaseSynapseSchema):
     score = mm.fields.Float(
         description="synapse score (see table metadata for description of score)"
     )
 
-
 class SynapseSchema(BaseSynapseSchema):
     ctr_pt = mm.fields.Nested(
         SpatialPoint, required=True, description="central point", order=1
@@ -92,3 +89,27 @@ class ValidSynapse(ReferenceAnnotation):
         required=True,
         description="Valid annotation for synapses",
     )
+
+# Adding classes from https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/CAVE-implemented-annotation-metadata-version-1.2.plantuml
+# With explanations from here: https://github.com/aplbrain/BENCHMARK-Metadata/blob/1.1-and-1.2-annotation-metadata-for-review/annotation-metadata/required-field-names.md
+class Chemical(BaseSynapseSchema):
+        presynaptic = mm.fields.Float(
+        description="Specialized sites that transmit signals between presynaptic neurons and their respective postsynaptic targets"
+    )
+        postsynaptic = mm.fields.Float(
+        description="Specialized sites that transmit signals between presynaptic neurons and their respective postsynaptic targets"
+    )
+
+class Electrical(BaseSynapseSchema):
+        gap_junction_location = mm.fields.Float(
+        description="The location where channels that allow for cell to cell transfers between ions and small molecules"
+    )
+        gap_junction_id = mm.fields.Float(
+        description="The identification tag for gap junctions"
+    )
+
+class SynapseSite(BaseSynapseSchema):
+    type = fields.String(description="Synapse site type")
+    class_label = fields.String(description="Class label")
+    neuron_id = fields.String(description="Neuron ID")
+    other = fields.String(description="Other synapse site information")