Enhanced heatmap functionality (#798)

* Enhanced heatmap functionality * format * format * ruff * fixed sparql queries * poetry * Fix for gilda/nltk/punkt. Fixes #802 See nltk/nltk#3293
INCATools · Aug 29, 2024 · d58eede · d58eede
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diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -92,7 +92,7 @@ jobs:
 
       - name: Get Gilda resources
         run: |
-          poetry run python -c "import nltk; nltk.download('punkt'); nltk.download('stopwords')"
+          poetry run python -c "import nltk; nltk.download('punkt_tab'); nltk.download('stopwords')"
           poetry run python -m adeft.download
 
       #----------------------------------------------

diff --git a/docs/datamodels/obograph/Axiom.md b/docs/datamodels/obograph/Axiom.md
@@ -1,6 +1,12 @@
+
+
 # Class: Axiom
-_A generic grouping for any OWL axiom or group of axioms that is not captured by existing constructs in this standard.
-_
+
+
+_A generic grouping for any OWL axiom or group of axioms that is not captured by existing constructs in this standard._
+
+__
+
 
 
 
@@ -11,17 +17,32 @@ URI: [owl:Axiom](http://www.w3.org/2002/07/owl#Axiom)
 
 
 
-```{mermaid}
+
+
+
+```mermaid
  classDiagram
     class Axiom
+    click Axiom href "../Axiom"
       Axiom <|-- DomainRangeAxiom
+        click DomainRangeAxiom href "../DomainRangeAxiom"
       Axiom <|-- EquivalentNodesSet
+        click EquivalentNodesSet href "../EquivalentNodesSet"
       Axiom <|-- LogicalDefinitionAxiom
+        click LogicalDefinitionAxiom href "../LogicalDefinitionAxiom"
+      Axiom <|-- DisjointClassExpressionsAxiom
+        click DisjointClassExpressionsAxiom href "../DisjointClassExpressionsAxiom"
       Axiom <|-- PropertyChainAxiom
+        click PropertyChainAxiom href "../PropertyChainAxiom"
       
       Axiom : meta
         
-          Axiom ..> Meta : meta
+          
+    
+    
+    Axiom --> "0..1" Meta : meta
+    click Meta href "../Meta"
+
         
       
 ```
@@ -35,6 +56,7 @@ URI: [owl:Axiom](http://www.w3.org/2002/07/owl#Axiom)
     * [DomainRangeAxiom](DomainRangeAxiom.md)
     * [EquivalentNodesSet](EquivalentNodesSet.md)
     * [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md)
+    * [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md)
     * [PropertyChainAxiom](PropertyChainAxiom.md)
 
 
@@ -69,7 +91,6 @@ URI: [owl:Axiom](http://www.w3.org/2002/07/owl#Axiom)
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -81,6 +102,8 @@ URI: [owl:Axiom](http://www.w3.org/2002/07/owl#Axiom)
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -95,7 +118,6 @@ description: 'A generic grouping for any OWL axiom or group of axioms that is no
 
   '
 from_schema: https://github.com/geneontology/obographs
-rank: 1000
 abstract: true
 slots:
 - meta
@@ -114,7 +136,6 @@ description: 'A generic grouping for any OWL axiom or group of axioms that is no
 
   '
 from_schema: https://github.com/geneontology/obographs
-rank: 1000
 abstract: true
 attributes:
   meta:

diff --git a/docs/datamodels/obograph/BasicPropertyValue.md b/docs/datamodels/obograph/BasicPropertyValue.md
@@ -1,23 +1,38 @@
+
+
 # Class: BasicPropertyValue
+
+
 _A property value that represents an assertion about an entity that is not a definition, synonym, or xref_
 
 
 
 
+
 URI: [obographs:BasicPropertyValue](https://github.com/geneontology/obographs/BasicPropertyValue)
 
 
 
-```{mermaid}
+
+
+
+```mermaid
  classDiagram
     class BasicPropertyValue
+    click BasicPropertyValue href "../BasicPropertyValue"
       PropertyValue <|-- BasicPropertyValue
+        click PropertyValue href "../PropertyValue"
       
       BasicPropertyValue : lang
         
       BasicPropertyValue : meta
         
-          BasicPropertyValue ..> Meta : meta
+          
+    
+    
+    BasicPropertyValue --> "0..1" Meta : meta
+    click Meta href "../Meta"
+
         
       BasicPropertyValue : pred
         
@@ -46,7 +61,7 @@ URI: [obographs:BasicPropertyValue](https://github.com/geneontology/obographs/Ba
 | ---  | --- | --- | --- |
 | [pred](pred.md) | 0..1 <br/> [String](String.md) | the predicate of an edge | [PropertyValue](PropertyValue.md) |
 | [val](val.md) | 0..1 <br/> [String](String.md) | the value of a property | [PropertyValue](PropertyValue.md) |
-| [xrefs](xrefs.md) | 0..* <br/> [XrefString](XrefString.md) | A list of cross references to other entities represented in other ontologies,... | [PropertyValue](PropertyValue.md) |
+| [xrefs](xrefs.md) | * <br/> [XrefString](XrefString.md) | A list of cross references to other entities represented in other ontologies,... | [PropertyValue](PropertyValue.md) |
 | [meta](meta.md) | 0..1 <br/> [Meta](Meta.md) | A collection of metadata about either an ontology (graph), an entity, or an a... | [PropertyValue](PropertyValue.md) |
 | [valType](valType.md) | 0..1 <br/> [String](String.md) | the datatype of a property value | [PropertyValue](PropertyValue.md) |
 | [lang](lang.md) | 0..1 <br/> [String](String.md) | the language of a property value | [PropertyValue](PropertyValue.md) |
@@ -82,7 +97,6 @@ URI: [obographs:BasicPropertyValue](https://github.com/geneontology/obographs/Ba
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -94,6 +108,8 @@ URI: [obographs:BasicPropertyValue](https://github.com/geneontology/obographs/Ba
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -106,7 +122,6 @@ name: BasicPropertyValue
 description: A property value that represents an assertion about an entity that is
   not a definition, synonym, or xref
 from_schema: https://github.com/geneontology/obographs
-rank: 1000
 is_a: PropertyValue
 
 ```
@@ -120,7 +135,6 @@ name: BasicPropertyValue
 description: A property value that represents an assertion about an entity that is
   not a definition, synonym, or xref
 from_schema: https://github.com/geneontology/obographs
-rank: 1000
 is_a: PropertyValue
 attributes:
   pred:
@@ -161,13 +175,13 @@ attributes:
     close_mappings:
     - rdfs:seeAlso
     rank: 1000
-    multivalued: true
     alias: xrefs
     owner: BasicPropertyValue
     domain_of:
     - Meta
     - PropertyValue
     range: XrefString
+    multivalued: true
   meta:
     name: meta
     description: A collection of metadata about either an ontology (graph), an entity,

diff --git a/docs/datamodels/obograph/DefinitionPropertyValue.md b/docs/datamodels/obograph/DefinitionPropertyValue.md
@@ -1,23 +1,38 @@
+
+
 # Class: DefinitionPropertyValue
+
+
 _A property value that represents an assertion about the textual definition of an entity_
 
 
 
 
+
 URI: [obographs:DefinitionPropertyValue](https://github.com/geneontology/obographs/DefinitionPropertyValue)
 
 
 
-```{mermaid}
+
+
+
+```mermaid
  classDiagram
     class DefinitionPropertyValue
+    click DefinitionPropertyValue href "../DefinitionPropertyValue"
       PropertyValue <|-- DefinitionPropertyValue
+        click PropertyValue href "../PropertyValue"
       
       DefinitionPropertyValue : lang
         
       DefinitionPropertyValue : meta
         
-          DefinitionPropertyValue ..> Meta : meta
+          
+    
+    
+    DefinitionPropertyValue --> "0..1" Meta : meta
+    click Meta href "../Meta"
+
         
       DefinitionPropertyValue : pred
         
@@ -46,7 +61,7 @@ URI: [obographs:DefinitionPropertyValue](https://github.com/geneontology/obograp
 | ---  | --- | --- | --- |
 | [pred](pred.md) | 0..1 <br/> [String](String.md) | the predicate of an edge | [PropertyValue](PropertyValue.md) |
 | [val](val.md) | 0..1 <br/> [String](String.md) | The textual string representing the definition | [PropertyValue](PropertyValue.md) |
-| [xrefs](xrefs.md) | 0..* <br/> [XrefString](XrefString.md) | A list of identifiers that support the definition | [PropertyValue](PropertyValue.md) |
+| [xrefs](xrefs.md) | * <br/> [XrefString](XrefString.md) | A list of identifiers that support the definition | [PropertyValue](PropertyValue.md) |
 | [meta](meta.md) | 0..1 <br/> [Meta](Meta.md) | A collection of metadata about either an ontology (graph), an entity, or an a... | [PropertyValue](PropertyValue.md) |
 | [valType](valType.md) | 0..1 <br/> [String](String.md) | the datatype of a property value | [PropertyValue](PropertyValue.md) |
 | [lang](lang.md) | 0..1 <br/> [String](String.md) | the language of a property value | [PropertyValue](PropertyValue.md) |
@@ -82,7 +97,6 @@ URI: [obographs:DefinitionPropertyValue](https://github.com/geneontology/obograp
 
 
 
-
 ## Mappings
 
 | Mapping Type | Mapped Value |
@@ -94,6 +108,8 @@ URI: [obographs:DefinitionPropertyValue](https://github.com/geneontology/obograp
 
 
 
+
+
 ## LinkML Source
 
 <!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
@@ -106,7 +122,6 @@ name: DefinitionPropertyValue
 description: A property value that represents an assertion about the textual definition
   of an entity
 from_schema: https://github.com/geneontology/obographs
-rank: 1000
 is_a: PropertyValue
 slot_usage:
   val:
@@ -138,7 +153,6 @@ name: DefinitionPropertyValue
 description: A property value that represents an assertion about the textual definition
   of an entity
 from_schema: https://github.com/geneontology/obographs
-rank: 1000
 is_a: PropertyValue
 slot_usage:
   val:
@@ -194,14 +208,14 @@ attributes:
       a contributing role in the definition.
     from_schema: https://github.com/geneontology/obographs
     rank: 1000
-    multivalued: true
     alias: xrefs
     owner: DefinitionPropertyValue
     domain_of:
     - Meta
     - PropertyValue
     role: supporting identifiers
     range: XrefString
+    multivalued: true
   meta:
     name: meta
     description: A collection of metadata about either an ontology (graph), an entity,