Fix incorrect 'type' assignment for slots in jsonld context for bke_taxonomy model

erdiagram-autogen/bke_taxonomy.md

@@ -2,8 +2,8 @@
 erDiagram
 DisplayColor {
     string id  
-    string color_hex_triplet  
     uriorcurieList xref  
+    string color_hex_triplet  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -49,10 +49,10 @@ MatrixFile {
 }
 Abbreviation {
     string id  
+    uriorcurieList xref  
     string term  
     string meaning  
-    string entity_type  
-    uriorcurieList xref  
+    AbbreviationEntityType entity_type  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -77,8 +77,8 @@ CellSpecimen {
     label_typeList synonym  
 }
 ObservationRow {
-    string label  
     uriorcurieList xref  
+    string label  
     string id  
     iri_type iri  
     uriorcurieList category  
@@ -121,8 +121,8 @@ Cluster {
     string id  
     string accession_id  
     string name  
-    integer number_of_observations  
     uriorcurieList xref  
+    integer number_of_observations  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -134,11 +134,11 @@ Cluster {
 }
 ClusterSet {
     string id  
-    datetime created_at  
     string accession_id  
     string name  
     string description  
     uriorcurieList xref  
+    date creation_date  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -166,8 +166,8 @@ CellTypeTaxon {
     string name  
     integer order  
     string description  
-    integer number_of_cells  
     uriorcurieList xref  
+    integer number_of_cells  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -181,9 +181,9 @@ CellTypeSet {
     string accession_id  
     string name  
     string description  
-    string cell_type_set_type  
     integer order  
     uriorcurieList xref  
+    CellTypeSetType cell_type_set_type  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -194,7 +194,7 @@ CellTypeSet {
 }
 CellTypeTaxonomy {
     string id  
-    datetime created_at  
+    date creation_date  
     string accession_id  
     string name  
     string description  
@@ -239,21 +239,22 @@ MatrixFile ||--|o ProvActivity : "was_generated_by"
 MatrixFile ||--}o Attribute : "has attribute"
 Abbreviation ||--}o GeneAnnotation : "denotes_gene_annotation"
 Abbreviation ||--}o ParcellationTerm : "denotes_parcellation_term"
+Abbreviation ||--}o CellTypeTaxon : "denotes_cell_type"
 Abbreviation ||--|o ProvEntity : "was_derived_from"
 Abbreviation ||--|o ProvActivity : "was_generated_by"
 Abbreviation ||--}o Attribute : "has attribute"
 CellSpecimen ||--|o ProvEntity : "was_derived_from"
 CellSpecimen ||--|o ProvActivity : "was_generated_by"
 CellSpecimen ||--}o Attribute : "has attribute"
+ObservationRow ||--|o CellSpecimen : "was_derived_from"
 ObservationRow ||--|o ObservationMatrix : "part_of_matrix"
 ObservationRow ||--|o MatrixFile : "represented_in"
-ObservationRow ||--|o CellSpecimen : "was_derived_from"
 ObservationRow ||--|o ProvActivity : "was_generated_by"
 ObservationRow ||--}o Attribute : "has attribute"
 ObservationMatrix ||--|o ObservationMatrixCreationProcess : "was_generated_by"
+ObservationMatrix ||--}o CellSpecimen : "was_derived_from"
 ObservationMatrix ||--}o MatrixFile : "represented_by"
 ObservationMatrix ||--}o GeneAnnotation : "has_variable"
-ObservationMatrix ||--}o CellSpecimen : "was_derived_from"
 ObservationMatrix ||--}o Attribute : "has attribute"
 ObservationMatrixCreationProcess ||--|o ProvEntity : "used"
 ObservationMatrixCreationProcess ||--}o Attribute : "has attribute"
@@ -270,16 +271,16 @@ ClusterSet ||--}o Attribute : "has attribute"
 ClusteringProcess ||--}o ObservationMatrix : "used"
 ClusteringProcess ||--}o Attribute : "has attribute"
 CellTypeTaxon ||--|o CellTypeTaxonomy : "part_of_taxonomy"
-CellTypeTaxon ||--}o Cluster : "contains_cluster"
 CellTypeTaxon ||--|o CellTypeTaxon : "has_parent"
 CellTypeTaxon ||--}o Abbreviation : "has_abbreviation"
+CellTypeTaxon ||--}o Cluster : "contains_cluster"
 CellTypeTaxon ||--|o ProvEntity : "was_derived_from"
 CellTypeTaxon ||--|o ProvActivity : "was_generated_by"
 CellTypeTaxon ||--}o Attribute : "has attribute"
 CellTypeSet ||--|o CellTypeTaxonomy : "part_of_taxonomy"
-CellTypeSet ||--}o CellTypeTaxon : "contains_taxon"
 CellTypeSet ||--|o CellTypeSet : "has_parent"
 CellTypeSet ||--}o Abbreviation : "has_abbreviation"
+CellTypeSet ||--}o CellTypeTaxon : "contains_taxon"
 CellTypeSet ||--|o ProvEntity : "was_derived_from"
 CellTypeSet ||--|o ProvActivity : "was_generated_by"
 CellTypeSet ||--}o Attribute : "has attribute"

json-schema-autogen/bke_taxonomy.json

@@ -29,6 +29,16 @@
                         "null"
                     ]
                 },
+                "denotes_cell_type": {
+                    "description": "One of potentially many cell type terms  which the abbreviation denotes.",
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": [
+                        "array",
+                        "null"
+                    ]
+                },
                 "denotes_gene_annotation": {
                     "description": "One of potentially many gene annotation terms to which the abbreviation denotes.",
                     "items": {
@@ -64,11 +74,8 @@
                     ]
                 },
                 "entity_type": {
-                    "description": "The entity type which the abbreviation term denotes.",
-                    "type": [
-                        "string",
-                        "null"
-                    ]
+                    "$ref": "#/$defs/AbbreviationEntityType",
+                    "description": "The entity type which the abbreviation term denotes."
                 },
                 "full_name": {
                     "description": "a long-form human readable name for a thing",
@@ -187,6 +194,16 @@
             "title": "Abbreviation",
             "type": "object"
         },
+        "AbbreviationEntityType": {
+            "description": "",
+            "enum": [
+                "cell_type",
+                "gene",
+                "anatomical"
+            ],
+            "title": "AbbreviationEntityType",
+            "type": "string"
+        },
         "Activity": {
             "additionalProperties": false,
             "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.",
@@ -931,11 +948,8 @@
                     ]
                 },
                 "cell_type_set_type": {
-                    "description": "A tag denoting the type or purpose of the cell type set.",
-                    "type": [
-                        "string",
-                        "null"
-                    ]
+                    "$ref": "#/$defs/CellTypeSetType",
+                    "description": "A tag denoting the type or purpose of the cell type set."
                 },
                 "contains_taxon": {
                     "description": "One of potentially many cell types taxons which together defines the cell type set.",
@@ -1096,6 +1110,15 @@
             "title": "CellTypeSet",
             "type": "object"
         },
+        "CellTypeSetType": {
+            "description": "",
+            "enum": [
+                "taxonomic_level",
+                "neighborhood"
+            ],
+            "title": "CellTypeSetType",
+            "type": "string"
+        },
         "CellTypeTaxon": {
             "additionalProperties": false,
             "description": "A cell type taxon is a node in a taxonomy. Taxons represents a unit of cell type classification and is defined by a set of clusters. Taxons may be organized into a heirarchy and levels. Taxons at higher levels represents broader cell type classes and partitioned into more specific types at lower levels. Additionally, taxons may be organized into neighborhoods or related groups.",
@@ -1311,9 +1334,9 @@
                         "null"
                     ]
                 },
-                "created_at": {
+                "creation_date": {
                     "description": "The creation date of the cell type taxonomy.",
-                    "format": "date-time",
+                    "format": "date",
                     "type": [
                         "string",
                         "null"
@@ -1846,9 +1869,9 @@
                         "null"
                     ]
                 },
-                "created_at": {
+                "creation_date": {
                     "description": "The creation date of the cluster set.",
-                    "format": "date-time",
+                    "format": "date",
                     "type": [
                         "string",
                         "null"
@@ -3462,7 +3485,6 @@
                 },
                 "x_resolution": {
                     "description": "The resolution (length / pixel) in along the x axis (numerical value part).",
-                    "pattern": "{PositiveFloat}",
                     "type": [
                         "number",
                         "null"
@@ -3492,7 +3514,6 @@
                 },
                 "y_resolution": {
                     "description": "The resolution (length / pixel) in along the y axis (numerical value part).",
-                    "pattern": "{PositiveFloat}",
                     "type": [
                         "number",
                         "null"
@@ -3512,7 +3533,6 @@
                 },
                 "z_resolution": {
                     "description": "The resolution (length / pixel) in along the z axis (numerical value part).",
-                    "pattern": "{PositiveFloat}",
                     "type": [
                         "number",
                         "null"
@@ -4711,7 +4731,6 @@
             "properties": {
                 "color": {
                     "description": "A string representing to hex triplet code of a color",
-                    "pattern": "{ColorHexTriplet}",
                     "type": [
                         "string",
                         "null"
@@ -5607,7 +5626,7 @@
             "type": "object"
         }
     },
-    "$id": "https:/w3id.org/brain-bican/bke-taxonomy",
+    "$id": "https://w3id.org/brain-bican/bke-taxonomy",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "",
@@ -5645,4 +5664,3 @@
     "type": "object",
     "version": null
 }
-