Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

…models into notebook_additions
brain-bican · Nov 7, 2023 · 536e4c8 · 536e4c8
2 parents f97cb9c + a05fdbe
commit 536e4c8
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Showing 3 changed files with 18 additions and 63 deletions.
diff --git a/erdiagram-autogen/kbmodel.md b/erdiagram-autogen/kbmodel.md
@@ -193,6 +193,7 @@ CellBarcoding {
  narrative_text description 
 }
 EnrichedCellSample {
+ string source_barcode_name 
  string histone_modification_marker 
  string population 
  string id 
@@ -202,7 +203,7 @@ EnrichedCellSample {
  label_type name 
  narrative_text description 
 }
-Activity {
+CellEnrichment {
  stringList provided_by 
  uriorcurieList xref 
  label_type full_name 
@@ -345,27 +346,27 @@ RoiDelineation {
 ProvEntity {
 
 }
-Entity {
+Activity {
+ stringList provided_by 
+ uriorcurieList xref 
+ label_type full_name 
+ label_typeList synonym 
  string id 
  iri_type iri 
  category_typeList category 
  stringList type 
  label_type name 
  narrative_text description 
 }
-Split {
- stringList provided_by 
- uriorcurieList xref 
- label_type full_name 
- label_typeList synonym 
+Entity {
  string id 
  iri_type iri 
  category_typeList category 
  stringList type 
  label_type name 
  narrative_text description 
 }
-CellEnrichment {
+Split {
  stringList provided_by 
  uriorcurieList xref 
  label_type full_name 
@@ -503,12 +504,14 @@ CellBarcoding ||--}o EnrichedCellSample : "used"
 CellBarcoding ||--}o BarcodedCellSample : "generated"
 CellBarcoding ||--}o Agent : "wasAssociatedWith"
 CellBarcoding ||--}o Attribute : "has attribute"
-EnrichedCellSample ||--|o CellEnrichment : "source barcode name"
 EnrichedCellSample ||--}o DissociatedCellSample : "wasDerivedFrom"
-EnrichedCellSample ||--}o Activity : "wasGeneratedBy"
+EnrichedCellSample ||--}o CellEnrichment : "wasGeneratedBy"
 EnrichedCellSample ||--}o Agent : "wasAttributedTo"
 EnrichedCellSample ||--}o Attribute : "has attribute"
-Activity ||--}o Attribute : "has attribute"
+CellEnrichment ||--}o DissociatedCellSample : "used"
+CellEnrichment ||--}o EnrichedCellSample : "generated"
+CellEnrichment ||--}o Agent : "wasAssociatedWith"
+CellEnrichment ||--}o Attribute : "has attribute"
 DissociatedCellSample ||--}o TissueSample : "wasDerivedFrom"
 DissociatedCellSample ||--}o CellDissociation : "wasGeneratedBy"
 DissociatedCellSample ||--}o Agent : "wasAttributedTo"
@@ -554,15 +557,12 @@ RoiDelineation ||--}o Attribute : "has attribute"
 ProvEntity ||--}o Entity : "wasDerivedFrom"
 ProvEntity ||--}o Activity : "wasGeneratedBy"
 ProvEntity ||--}o Agent : "wasAttributedTo"
+Activity ||--}o Attribute : "has attribute"
 Entity ||--}o Attribute : "has attribute"
 Split ||--}o EnrichedCellSample : "used"
 Split ||--}o EnrichedCellSample : "generated"
 Split ||--}o Agent : "wasAssociatedWith"
 Split ||--}o Attribute : "has attribute"
-CellEnrichment ||--}o DissociatedCellSample : "used"
-CellEnrichment ||--}o EnrichedCellSample : "generated"
-CellEnrichment ||--}o Agent : "wasAssociatedWith"
-CellEnrichment ||--}o Attribute : "has attribute"
 ProvActivity ||--}o Entity : "used"
 ProvActivity ||--}o Entity : "generated"
 ProvActivity ||--}o Agent : "wasAssociatedWith"

diff --git a/json-schema-autogen/kbmodel.json b/json-schema-autogen/kbmodel.json
@@ -12238,7 +12238,7 @@
  "type": "string"
  },
  "source_barcode_name": {
- "description": "Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes]. wasGeneratedBy:",
+ "description": "Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes].",
  "type": "string"
  },
  "type": {
@@ -12273,53 +12273,8 @@
  "wasGeneratedBy": {
  "items": {
  "anyOf": [
- {
- "$ref": "#/$defs/Activity"
- },
- {
- "$ref": "#/$defs/BrainExtraction"
- },
- {
- "$ref": "#/$defs/BrainSegmentSectioning"
- },
- {
- "$ref": "#/$defs/RoiDelineation"
- },
- {
- "$ref": "#/$defs/TissueDissection"
- },
- {
- "$ref": "#/$defs/CellDissociation"
- },
  {
  "$ref": "#/$defs/CellEnrichment"
- },
- {
- "$ref": "#/$defs/Split"
- },
- {
- "$ref": "#/$defs/CellBarcoding"
- },
- {
- "$ref": "#/$defs/CdnaAmplification"
- },
- {
- "$ref": "#/$defs/LibraryConstruction"
- },
- {
- "$ref": "#/$defs/LibraryAliquoting"
- },
- {
- "$ref": "#/$defs/LibraryPooling"
- },
- {
- "$ref": "#/$defs/Sequencing"
- },
- {
- "$ref": "#/$defs/Alignment"
- },
- {
- "$ref": "#/$defs/Study"
  }
  ]
  },

diff --git a/models_py-autogen/kbmodel.py b/models_py-autogen/kbmodel.py
@@ -696,11 +696,11 @@ class DissociatedCellSample(Entity, ProvEntity):
 
 class EnrichedCellSample(Entity, ProvEntity):
 
- source_barcode_name: Optional[str] = Field(None, description="""Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes]. wasGeneratedBy:""")
+ source_barcode_name: Optional[str] = Field(None, description="""Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes].""")
  histone_modification_marker: Optional[str] = Field(None, description="""Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. Each of the Histone antibodies captures an essential part of the epigenome.""")
  population: str = Field(..., description="""Actual percentage of cells as a result of using set of fluorescent marker label(s) to enrich dissociated_cell_sample with desired mix of cell populations. This plan can also be used to describe 'No FACS' where no enrichment was performed. This is a property of enriched_cell_prep_container.""")
  wasDerivedFrom: Optional[List[DissociatedCellSample]] = Field(default_factory=list)
- wasGeneratedBy: Optional[List[Union[Activity,BrainExtraction,BrainSegmentSectioning,RoiDelineation,TissueDissection,CellDissociation,CellEnrichment,Split,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Sequencing,Alignment,Study]]] = Field(default_factory=list)
+ wasGeneratedBy: Optional[List[CellEnrichment]] = Field(default_factory=list)
  wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list)
  id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""")
  iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""")