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"