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Merge pull request #203 from puja-trivedi/fix_bke_taxonomy_model_20250924
Fix incorrect 'type' assignment for slots in jsonld context for bke_taxonomy model
2 parents 9da4531 + 65a9399 commit aa22f33

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10 files changed

+949
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‎erdiagram-autogen/bke_taxonomy.md‎

Lines changed: 14 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,8 @@
22
erDiagram
33
DisplayColor {
44
string id
5-
string color_hex_triplet
65
uriorcurieList xref
6+
string color_hex_triplet
77
iri_type iri
88
uriorcurieList category
99
stringList type
@@ -49,10 +49,10 @@ MatrixFile {
4949
}
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Abbreviation {
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string id
52+
uriorcurieList xref
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string term
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string meaning
54-
string entity_type
55-
uriorcurieList xref
55+
AbbreviationEntityType entity_type
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iri_type iri
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uriorcurieList category
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stringList type
@@ -77,8 +77,8 @@ CellSpecimen {
7777
label_typeList synonym
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}
7979
ObservationRow {
80-
string label
8180
uriorcurieList xref
81+
string label
8282
string id
8383
iri_type iri
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uriorcurieList category
@@ -121,8 +121,8 @@ Cluster {
121121
string id
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string accession_id
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string name
124-
integer number_of_observations
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uriorcurieList xref
125+
integer number_of_observations
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iri_type iri
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uriorcurieList category
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stringList type
@@ -134,11 +134,11 @@ Cluster {
134134
}
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ClusterSet {
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string id
137-
datetime created_at
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string accession_id
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string name
140139
string description
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uriorcurieList xref
141+
date creation_date
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iri_type iri
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uriorcurieList category
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stringList type
@@ -166,8 +166,8 @@ CellTypeTaxon {
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string name
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integer order
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string description
169-
integer number_of_cells
170169
uriorcurieList xref
170+
integer number_of_cells
171171
iri_type iri
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uriorcurieList category
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stringList type
@@ -181,9 +181,9 @@ CellTypeSet {
181181
string accession_id
182182
string name
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string description
184-
string cell_type_set_type
185184
integer order
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uriorcurieList xref
186+
CellTypeSetType cell_type_set_type
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iri_type iri
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uriorcurieList category
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stringList type
@@ -194,7 +194,7 @@ CellTypeSet {
194194
}
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CellTypeTaxonomy {
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string id
197-
datetime created_at
197+
date creation_date
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string accession_id
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string name
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string description
@@ -239,21 +239,22 @@ MatrixFile ||--|o ProvActivity : "was_generated_by"
239239
MatrixFile ||--}o Attribute : "has attribute"
240240
Abbreviation ||--}o GeneAnnotation : "denotes_gene_annotation"
241241
Abbreviation ||--}o ParcellationTerm : "denotes_parcellation_term"
242+
Abbreviation ||--}o CellTypeTaxon : "denotes_cell_type"
242243
Abbreviation ||--|o ProvEntity : "was_derived_from"
243244
Abbreviation ||--|o ProvActivity : "was_generated_by"
244245
Abbreviation ||--}o Attribute : "has attribute"
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CellSpecimen ||--|o ProvEntity : "was_derived_from"
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CellSpecimen ||--|o ProvActivity : "was_generated_by"
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CellSpecimen ||--}o Attribute : "has attribute"
249+
ObservationRow ||--|o CellSpecimen : "was_derived_from"
248250
ObservationRow ||--|o ObservationMatrix : "part_of_matrix"
249251
ObservationRow ||--|o MatrixFile : "represented_in"
250-
ObservationRow ||--|o CellSpecimen : "was_derived_from"
251252
ObservationRow ||--|o ProvActivity : "was_generated_by"
252253
ObservationRow ||--}o Attribute : "has attribute"
253254
ObservationMatrix ||--|o ObservationMatrixCreationProcess : "was_generated_by"
255+
ObservationMatrix ||--}o CellSpecimen : "was_derived_from"
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ObservationMatrix ||--}o MatrixFile : "represented_by"
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ObservationMatrix ||--}o GeneAnnotation : "has_variable"
256-
ObservationMatrix ||--}o CellSpecimen : "was_derived_from"
257258
ObservationMatrix ||--}o Attribute : "has attribute"
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ObservationMatrixCreationProcess ||--|o ProvEntity : "used"
259260
ObservationMatrixCreationProcess ||--}o Attribute : "has attribute"
@@ -270,16 +271,16 @@ ClusterSet ||--}o Attribute : "has attribute"
270271
ClusteringProcess ||--}o ObservationMatrix : "used"
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ClusteringProcess ||--}o Attribute : "has attribute"
272273
CellTypeTaxon ||--|o CellTypeTaxonomy : "part_of_taxonomy"
273-
CellTypeTaxon ||--}o Cluster : "contains_cluster"
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CellTypeTaxon ||--|o CellTypeTaxon : "has_parent"
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CellTypeTaxon ||--}o Abbreviation : "has_abbreviation"
276+
CellTypeTaxon ||--}o Cluster : "contains_cluster"
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CellTypeTaxon ||--|o ProvEntity : "was_derived_from"
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CellTypeTaxon ||--|o ProvActivity : "was_generated_by"
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CellTypeTaxon ||--}o Attribute : "has attribute"
279280
CellTypeSet ||--|o CellTypeTaxonomy : "part_of_taxonomy"
280-
CellTypeSet ||--}o CellTypeTaxon : "contains_taxon"
281281
CellTypeSet ||--|o CellTypeSet : "has_parent"
282282
CellTypeSet ||--}o Abbreviation : "has_abbreviation"
283+
CellTypeSet ||--}o CellTypeTaxon : "contains_taxon"
283284
CellTypeSet ||--|o ProvEntity : "was_derived_from"
284285
CellTypeSet ||--|o ProvActivity : "was_generated_by"
285286
CellTypeSet ||--}o Attribute : "has attribute"

‎json-schema-autogen/bke_taxonomy.json‎

Lines changed: 38 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -29,6 +29,16 @@
2929
"null"
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]
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},
32+
"denotes_cell_type": {
33+
"description": "One of potentially many cell type terms which the abbreviation denotes.",
34+
"items": {
35+
"type": "string"
36+
},
37+
"type": [
38+
"array",
39+
"null"
40+
]
41+
},
3242
"denotes_gene_annotation": {
3343
"description": "One of potentially many gene annotation terms to which the abbreviation denotes.",
3444
"items": {
@@ -64,11 +74,8 @@
6474
]
6575
},
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"entity_type": {
67-
"description": "The entity type which the abbreviation term denotes.",
68-
"type": [
69-
"string",
70-
"null"
71-
]
77+
"$ref": "#/$defs/AbbreviationEntityType",
78+
"description": "The entity type which the abbreviation term denotes."
7279
},
7380
"full_name": {
7481
"description": "a long-form human readable name for a thing",
@@ -187,6 +194,16 @@
187194
"title": "Abbreviation",
188195
"type": "object"
189196
},
197+
"AbbreviationEntityType": {
198+
"description": "",
199+
"enum": [
200+
"cell_type",
201+
"gene",
202+
"anatomical"
203+
],
204+
"title": "AbbreviationEntityType",
205+
"type": "string"
206+
},
190207
"Activity": {
191208
"additionalProperties": false,
192209
"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 @@
931948
]
932949
},
933950
"cell_type_set_type": {
934-
"description": "A tag denoting the type or purpose of the cell type set.",
935-
"type": [
936-
"string",
937-
"null"
938-
]
951+
"$ref": "#/$defs/CellTypeSetType",
952+
"description": "A tag denoting the type or purpose of the cell type set."
939953
},
940954
"contains_taxon": {
941955
"description": "One of potentially many cell types taxons which together defines the cell type set.",
@@ -1096,6 +1110,15 @@
10961110
"title": "CellTypeSet",
10971111
"type": "object"
10981112
},
1113+
"CellTypeSetType": {
1114+
"description": "",
1115+
"enum": [
1116+
"taxonomic_level",
1117+
"neighborhood"
1118+
],
1119+
"title": "CellTypeSetType",
1120+
"type": "string"
1121+
},
10991122
"CellTypeTaxon": {
11001123
"additionalProperties": false,
11011124
"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 @@
13111334
"null"
13121335
]
13131336
},
1314-
"created_at": {
1337+
"creation_date": {
13151338
"description": "The creation date of the cell type taxonomy.",
1316-
"format": "date-time",
1339+
"format": "date",
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"type": [
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"string",
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"null"
@@ -1846,9 +1869,9 @@
18461869
"null"
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]
18481871
},
1849-
"created_at": {
1872+
"creation_date": {
18501873
"description": "The creation date of the cluster set.",
1851-
"format": "date-time",
1874+
"format": "date",
18521875
"type": [
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"string",
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"null"
@@ -3462,7 +3485,6 @@
34623485
},
34633486
"x_resolution": {
34643487
"description": "The resolution (length / pixel) in along the x axis (numerical value part).",
3465-
"pattern": "{PositiveFloat}",
34663488
"type": [
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"number",
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"null"
@@ -3492,7 +3514,6 @@
34923514
},
34933515
"y_resolution": {
34943516
"description": "The resolution (length / pixel) in along the y axis (numerical value part).",
3495-
"pattern": "{PositiveFloat}",
34963517
"type": [
34973518
"number",
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"null"
@@ -3512,7 +3533,6 @@
35123533
},
35133534
"z_resolution": {
35143535
"description": "The resolution (length / pixel) in along the z axis (numerical value part).",
3515-
"pattern": "{PositiveFloat}",
35163536
"type": [
35173537
"number",
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"null"
@@ -4711,7 +4731,6 @@
47114731
"properties": {
47124732
"color": {
47134733
"description": "A string representing to hex triplet code of a color",
4714-
"pattern": "{ColorHexTriplet}",
47154734
"type": [
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"string",
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"null"
@@ -5607,7 +5626,7 @@
56075626
"type": "object"
56085627
}
56095628
},
5610-
"$id": "https:/w3id.org/brain-bican/bke-taxonomy",
5629+
"$id": "https://w3id.org/brain-bican/bke-taxonomy",
56115630
"$schema": "https://json-schema.org/draft/2019-09/schema",
56125631
"additionalProperties": true,
56135632
"description": "",
@@ -5645,4 +5664,3 @@
56455664
"type": "object",
56465665
"version": null
56475666
}
5648-

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