generate another formats

brain-bican · Oct 4, 2024 · c30dd97 · c30dd97
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diff --git a/erdiagram-autogen/bican_core.md b/erdiagram-autogen/bican_core.md
@@ -0,0 +1,262 @@
+```mermaid
+erDiagram
+OntologyClass {
+ string id 
+}
+Annotation {
+
+}
+QuantityValue {
+ unit has_unit 
+ double has_numeric_value 
+}
+Attribute {
+ string id 
+ uriorcurieList category 
+ stringList type 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+ label type attribute_name 
+ iri type iri 
+ label type name 
+}
+Entity {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+}
+NamedThing {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+}
+TaxonomicRank {
+ string id 
+}
+OrganismTaxon {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+}
+InformationContentEntity {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+ string license 
+ string rights 
+ string format 
+ date creation_date 
+}
+Dataset {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+ string license 
+ string rights 
+ string format 
+ date creation_date 
+}
+PhysicalEssenceOrOccurrent {
+
+}
+PhysicalEssence {
+
+}
+PhysicalEntity {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+}
+Occurrent {
+
+}
+ActivityAndBehavior {
+
+}
+Activity {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+}
+Procedure {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+}
+SubjectOfInvestigation {
+
+}
+MaterialSample {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+}
+ThingWithTaxon {
+ label type in_taxon_label 
+}
+BiologicalEntity {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+ label type in_taxon_label 
+}
+GenomicEntity {
+ biological sequence has_biological_sequence 
+}
+ChemicalEntityOrGeneOrGeneProduct {
+
+}
+MacromolecularMachineMixin {
+ label type name 
+}
+GeneOrGeneProduct {
+ label type name 
+}
+Gene {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ label type full_name 
+ label typeList synonym 
+ label type in_taxon_label 
+ string symbol 
+ uriorcurieList xref 
+ biological sequence has_biological_sequence 
+}
+Genome {
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label type full_name 
+ label typeList synonym 
+ label type in_taxon_label 
+ biological sequence has_biological_sequence 
+}
+Checksum {
+ DigestType checksum_algorithm 
+ string value 
+ string id 
+ iri type iri 
+ uriorcurieList category 
+ stringList type 
+ label type name 
+ narrative text description 
+ boolean deprecated 
+}
+
+Attribute ||--}o Attribute : "has attribute"
+Attribute ||--|| OntologyClass : "has attribute type"
+Attribute ||--}o QuantityValue : "has quantitative value"
+Attribute ||--|o NamedThing : "has qualitative value"
+Entity ||--}o Attribute : "has attribute"
+NamedThing ||--}o Attribute : "has attribute"
+OrganismTaxon ||--}o Attribute : "has attribute"
+OrganismTaxon ||--|o TaxonomicRank : "has taxonomic rank"
+InformationContentEntity ||--}o Attribute : "has attribute"
+Dataset ||--}o Attribute : "has attribute"
+PhysicalEntity ||--}o Attribute : "has attribute"
+Activity ||--}o Attribute : "has attribute"
+Procedure ||--}o Attribute : "has attribute"
+MaterialSample ||--}o Attribute : "has attribute"
+ThingWithTaxon ||--}o OrganismTaxon : "in taxon"
+BiologicalEntity ||--}o Attribute : "has attribute"
+BiologicalEntity ||--}o OrganismTaxon : "in taxon"
+Gene ||--}o Attribute : "has attribute"
+Gene ||--}o OrganismTaxon : "in taxon"
+Genome ||--}o Attribute : "has attribute"
+Genome ||--}o OrganismTaxon : "in taxon"
+Checksum ||--}o Attribute : "has attribute"
+
+```
+
diff --git a/erdiagram-autogen/bican_prov.md b/erdiagram-autogen/bican_prov.md
@@ -0,0 +1,15 @@
+```mermaid
+erDiagram
+ProvActivity {
+
+}
+ProvEntity {
+
+}
+
+ProvActivity ||--|o ProvEntity : "used"
+ProvEntity ||--|o ProvEntity : "was_derived_from"
+ProvEntity ||--|o ProvActivity : "was_generated_by"
+
+```
+
diff --git a/erdiagram-autogen/genome_annotation.md b/erdiagram-autogen/genome_annotation.md
@@ -58,17 +58,6 @@ GeneAnnotation {
  uriorcurieList xref 
  biological_sequence has_biological_sequence 
 }
-Checksum {
- DigestType checksum_algorithm 
- string value 
- string id 
- iri_type iri 
- uriorcurieList category 
- stringList type 
- label_type name 
- narrative_text description 
- boolean deprecated 
-}
 
 AnnotationCollection ||--}o GeneAnnotation : "annotations"
 AnnotationCollection ||--}o GenomeAnnotation : "genome_annotations"
@@ -79,7 +68,6 @@ GenomeAnnotation ||--}o Attribute : "has attribute"
 GenomeAnnotation ||--}o OrganismTaxon : "in taxon"
 GeneAnnotation ||--}o Attribute : "has attribute"
 GeneAnnotation ||--}o OrganismTaxon : "in taxon"
-Checksum ||--}o Attribute : "has attribute"
 
 ```
 
diff --git a/erdiagram-autogen/library_generation.md b/erdiagram-autogen/library_generation.md
@@ -1,10 +1,30 @@
 ```mermaid
 erDiagram
-ProvEntity {
-
+DigitalAsset {
+ stringList digest 
+ string content_url 
+ string data_type 
+ string id 
+ iri_type iri 
+ uriorcurieList category 
+ stringList type 
+ label_type name 
+ narrative_text description 
+ boolean deprecated 
+ stringList provided_by 
+ uriorcurieList xref 
+ label_type full_name 
+ label_typeList synonym 
+ string license 
+ string rights 
+ string format 
+ date creation_date 
 }
 ProvActivity {
 
+}
+ProvEntity {
+
 }
 DissectionRoiPolygon {
  label_type name 
@@ -301,9 +321,12 @@ Donor {
  label_typeList synonym 
 }
 
+DigitalAsset ||--|o LibraryPool : "was_derived_from"
+DigitalAsset ||--|o ProvActivity : "was_generated_by"
+DigitalAsset ||--}o Attribute : "has attribute"
+ProvActivity ||--|o ProvEntity : "used"
 ProvEntity ||--|o ProvEntity : "was_derived_from"
 ProvEntity ||--|o ProvActivity : "was_generated_by"
-ProvActivity ||--|o ProvEntity : "used"
 DissectionRoiPolygon ||--|o DissectionRoiDelineation : "was_generated_by"
 DissectionRoiPolygon ||--|o BrainSlab : "annotates"
 DissectionRoiPolygon ||--|o ProvEntity : "was_derived_from"
@@ -352,7 +375,7 @@ TissueSample ||--|o Donor : "was_derived_from"
 TissueSample ||--|o TissueDissection : "was_generated_by"
 TissueSample ||--|o DissectionRoiPolygon : "dissection_was_guided_by"
 TissueSample ||--}o Attribute : "has attribute"
-BrainSlab ||--|o Donor : "was_derived_from"
+BrainSlab ||--|o ProvEntity : "was_derived_from"
 BrainSlab ||--|o ProvActivity : "was_generated_by"
 BrainSlab ||--}o Attribute : "has attribute"
 Donor ||--}o OrganismTaxon : "in taxon"