release files 2024-09-19

VirtualFlyBrain · Sep 19, 2024 · e809bf3 · e809bf3
1 parent c7b645a
commit e809bf3
Show file tree

Hide file tree

Showing 83 changed files with 30,368 additions and 17,186 deletions.
diff --git a/docs/Assay.md b/docs/Assay.md
@@ -116,7 +116,6 @@ URI: [FBcv:0003025](http://purl.obolibrary.org/obo/FBcv_0003025)
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -128,6 +127,8 @@ URI: [FBcv:0003025](http://purl.obolibrary.org/obo/FBcv_0003025)
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -158,10 +159,10 @@ attributes:
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
     slot_uri: BAO:0000212
-    multivalued: false
     domain_of:
     - Assay
     range: Thing
+    multivalued: false
   associated_sample_for_assay:
     name: associated_sample_for_assay
     annotations:
@@ -173,10 +174,10 @@ attributes:
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
     slot_uri: RO:0002233
-    multivalued: true
     domain_of:
     - Assay
     range: Sample
+    multivalued: true
 class_uri: FBcv:0003025
 
 ```
@@ -205,12 +206,12 @@ attributes:
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
     slot_uri: BAO:0000212
-    multivalued: false
     alias: method
     owner: Assay
     domain_of:
     - Assay
     range: Thing
+    multivalued: false
   associated_sample_for_assay:
     name: associated_sample_for_assay
     annotations:
@@ -222,12 +223,12 @@ attributes:
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
     slot_uri: RO:0002233
-    multivalued: true
     alias: associated_sample_for_assay
     owner: Assay
     domain_of:
     - Assay
     range: Sample
+    multivalued: true
   associated_dataset:
     name: associated_dataset
     annotations:

diff --git a/docs/Boolean.md b/docs/Boolean.md
@@ -37,3 +37,14 @@ URI: [xsd:boolean](http://www.w3.org/2001/XMLSchema#boolean)
 
 
 
+
+## Mappings
+
+| Mapping Type | Mapped Value |
+| ---  | ---  |
+| self | xsd:boolean |
+| native | http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq/:boolean |
+| exact | schema:Boolean |
+
+
+
diff --git a/docs/Class.md b/docs/Class.md
@@ -100,7 +100,6 @@ URI: [http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq/:Class](http://gi
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -112,6 +111,8 @@ URI: [http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq/:Class](http://gi
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->

diff --git a/docs/Cluster.md b/docs/Cluster.md
@@ -51,6 +51,8 @@ URI: [FBcv:0009003](http://purl.obolibrary.org/obo/FBcv_0009003)
         
       Cluster : expression_level
         
+      Cluster : filtered_gene_count
+        
       Cluster : gene
         
           
@@ -88,6 +90,8 @@ URI: [FBcv:0009003](http://purl.obolibrary.org/obo/FBcv_0009003)
         
       Cluster : title
         
+      Cluster : total_gene_count
+        
       
 ```
 
@@ -114,6 +118,8 @@ URI: [FBcv:0009003](http://purl.obolibrary.org/obo/FBcv_0009003)
 | [expression_level](expression_level.md) | 0..1 <br/> [Float](Float.md) | Level of expression of the given gene | direct |
 | [expression_extent](expression_extent.md) | 0..1 <br/> [Float](Float.md) | Extent of expression of the given gene | direct |
 | [hide_in_terminfo](hide_in_terminfo.md) | 0..1 <br/> [String](String.md) | Flag to hide expression edges in VFB Term Info pane | direct |
+| [total_gene_count](total_gene_count.md) | 0..1 <br/> [Integer](Integer.md) | Total number of distinct genes associated with the entity before filtering by... | direct |
+| [filtered_gene_count](filtered_gene_count.md) | 0..1 <br/> [Integer](Integer.md) | Total number of distinct genes associated with the entity after filtering by ... | direct |
 | [associated_clustering](associated_clustering.md) | 0..1 <br/> [Clustering](Clustering.md) | Clustering (FBlc ID) that the Cluster belongs to | direct |
 | [cell_number](cell_number.md) | 0..1 <br/> [Integer](Integer.md) | The number of cells in the Cluster (as integer) | direct |
 | [cell_type](cell_type.md) | * <br/> [Thing](Thing.md) | Anatomy (FBbt IDs) for the Cluster | direct |
@@ -151,7 +157,6 @@ URI: [FBcv:0009003](http://purl.obolibrary.org/obo/FBcv_0009003)
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -163,6 +168,8 @@ URI: [FBcv:0009003](http://purl.obolibrary.org/obo/FBcv_0009003)
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -187,6 +194,8 @@ slots:
 - expression_level
 - expression_extent
 - hide_in_terminfo
+- total_gene_count
+- filtered_gene_count
 attributes:
   associated_clustering:
     name: associated_clustering
@@ -204,9 +213,9 @@ attributes:
   cell_number:
     name: cell_number
     annotations:
-      owl.fstring:
-        tag: owl.fstring
-        value: AnnotationAssertion( neo_custom:cell_count {id} {cell_number} )
+      owl:
+        tag: owl
+        value: AnnotationProperty
     description: The number of cells in the Cluster (as integer).
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
@@ -225,10 +234,10 @@ attributes:
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
     slot_uri: RO:0002473
-    multivalued: true
     domain_of:
     - Cluster
     range: Thing
+    multivalued: true
 class_uri: FBcv:0009003
 
 ```
@@ -264,9 +273,9 @@ attributes:
   cell_number:
     name: cell_number
     annotations:
-      owl.fstring:
-        tag: owl.fstring
-        value: AnnotationAssertion( neo_custom:cell_count {id} {cell_number} )
+      owl:
+        tag: owl
+        value: AnnotationProperty
     description: The number of cells in the Cluster (as integer).
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
@@ -287,12 +296,12 @@ attributes:
     from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
     rank: 1000
     slot_uri: RO:0002473
-    multivalued: true
     alias: cell_type
     owner: Cluster
     domain_of:
     - Cluster
     range: Thing
+    multivalued: true
   stage:
     name: stage
     annotations:
@@ -418,6 +427,40 @@ attributes:
     domain_of:
     - Cluster
     range: string
+  total_gene_count:
+    name: total_gene_count
+    annotations:
+      owl:
+        tag: owl
+        value: AnnotationProperty
+    description: Total number of distinct genes associated with the entity before
+      filtering by extent.
+    from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
+    rank: 1000
+    slot_uri: neo_custom:total_gene_count
+    alias: total_gene_count
+    owner: Cluster
+    domain_of:
+    - Dataset
+    - Cluster
+    range: integer
+  filtered_gene_count:
+    name: filtered_gene_count
+    annotations:
+      owl:
+        tag: owl
+        value: AnnotationProperty
+    description: Total number of distinct genes associated with the entity after filtering
+      by extent.
+    from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
+    rank: 1000
+    slot_uri: neo_custom:filtered_gene_count
+    alias: filtered_gene_count
+    owner: Cluster
+    domain_of:
+    - Dataset
+    - Cluster
+    range: integer
   name:
     name: name
     annotations:

diff --git a/docs/Clustering.md b/docs/Clustering.md
@@ -103,7 +103,6 @@ URI: [FBcv:0009002](http://purl.obolibrary.org/obo/FBcv_0009002)
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -115,6 +114,8 @@ URI: [FBcv:0009002](http://purl.obolibrary.org/obo/FBcv_0009002)
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->

diff --git a/docs/Curie.md b/docs/Curie.md
@@ -42,3 +42,13 @@ URI: [xsd:string](http://www.w3.org/2001/XMLSchema#string)
 
 
 
+
+## Mappings
+
+| Mapping Type | Mapped Value |
+| ---  | ---  |
+| self | xsd:string |
+| native | http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq/:curie |
+
+
+
diff --git a/docs/Dataset.md b/docs/Dataset.md
@@ -29,6 +29,8 @@ URI: [FBcv:0003023](http://purl.obolibrary.org/obo/FBcv_0003023)
     click Thing href "../Thing"
 
         
+      Dataset : filtered_gene_count
+        
       Dataset : id
         
       Dataset : licence
@@ -64,6 +66,8 @@ URI: [FBcv:0003023](http://purl.obolibrary.org/obo/FBcv_0003023)
         
       Dataset : title
         
+      Dataset : total_gene_count
+        
       
 ```
 
@@ -83,6 +87,8 @@ URI: [FBcv:0003023](http://purl.obolibrary.org/obo/FBcv_0003023)
 | Name | Cardinality and Range | Description | Inheritance |
 | ---  | --- | --- | --- |
 | [neo_label](neo_label.md) | 0..1 <br/> [String](String.md) | neo4j node label to add to entity | direct |
+| [total_gene_count](total_gene_count.md) | 0..1 <br/> [Integer](Integer.md) | Total number of distinct genes associated with the entity before filtering by... | direct |
+| [filtered_gene_count](filtered_gene_count.md) | 0..1 <br/> [Integer](Integer.md) | Total number of distinct genes associated with the entity after filtering by ... | direct |
 | [publication](publication.md) | 0..1 <br/> [Publication](Publication.md) | Publication associated with the Dataset | direct |
 | [licence](licence.md) | 0..1 <br/> [Thing](Thing.md) | Licence for the Dataset (all CC-BY 4 | direct |
 | [assay_type](assay_type.md) | 0..1 <br/> [Thing](Thing.md) | Assay type (FBcv ID) for the Dataset, this will probably be 'FBcv:0009000' ('... | direct |
@@ -132,7 +138,6 @@ URI: [FBcv:0003023](http://purl.obolibrary.org/obo/FBcv_0003023)
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -144,6 +149,8 @@ URI: [FBcv:0003023](http://purl.obolibrary.org/obo/FBcv_0003023)
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -161,6 +168,8 @@ from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
 is_a: Class
 slots:
 - neo_label
+- total_gene_count
+- filtered_gene_count
 attributes:
   publication:
     name: publication
@@ -338,6 +347,40 @@ attributes:
     - Cluster
     - Publication
     range: string
+  total_gene_count:
+    name: total_gene_count
+    annotations:
+      owl:
+        tag: owl
+        value: AnnotationProperty
+    description: Total number of distinct genes associated with the entity before
+      filtering by extent.
+    from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
+    rank: 1000
+    slot_uri: neo_custom:total_gene_count
+    alias: total_gene_count
+    owner: Dataset
+    domain_of:
+    - Dataset
+    - Cluster
+    range: integer
+  filtered_gene_count:
+    name: filtered_gene_count
+    annotations:
+      owl:
+        tag: owl
+        value: AnnotationProperty
+    description: Total number of distinct genes associated with the entity after filtering
+      by extent.
+    from_schema: http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq
+    rank: 1000
+    slot_uri: neo_custom:filtered_gene_count
+    alias: filtered_gene_count
+    owner: Dataset
+    domain_of:
+    - Dataset
+    - Cluster
+    range: integer
   name:
     name: name
     annotations:

diff --git a/docs/Date.md b/docs/Date.md
@@ -37,3 +37,14 @@ URI: [xsd:date](http://www.w3.org/2001/XMLSchema#date)
 
 
 
+
+## Mappings
+
+| Mapping Type | Mapped Value |
+| ---  | ---  |
+| self | xsd:date |
+| native | http://github.org/vfb/vfb-scRNAseq-ontology/VFB_scRNAseq/:date |
+| exact | schema:Date |
+
+
+