Integrate taxonomy with semantic enumerations

schema/README.md

@@ -12,5 +12,9 @@
 - Create separate schema files for each logical schema class and `import` into the root `schemas.yaml` file.
 - Generated markdown from schemas:
     ```shell
-    gen-doc schema/src/schemas.yml --directory schema/generated --diagram-type er_diagram
+    gen-doc schema/src/schemas.yaml --directory schema/generated --example-directory schema/examples --diagram-type er_diagram
+    ```
+- Generate linkml enums for taxonomy terms:
+    ```shell
+    python populateSemanticEnums.py
     ```

schema/generated/ActivityTypes.md

@@ -2,19 +2,38 @@
 
 
 
-
-_The type of activity_
-
-
-
 URI: [ActivityTypes](ActivityTypes.md)
 
 ## Permissible Values
 
 | Value | Meaning | Description |
 | --- | --- | --- |
-| conservation | rfs:Conservation | a conservation activity |
-| ecosystemRestoration | rfs:EcosystemRestoration | an ecosystem restoration activity |
+| ResidueTillageManagement | rft:ResidueTillageManagement |  |
+| BiocharProduction | rft:BiocharProduction |  |
+| ImprovedForestManagement | rft:ImprovedForestManagement |  |
+| Agroforestry | rft:Agroforestry |  |
+| PrescribedGrazing | rft:PrescribedGrazing |  |
+| RiparianForestBuffers | rft:RiparianForestBuffers |  |
+| SoilAmendments | rft:SoilAmendments |  |
+| Conservation | rft:Conservation |  |
+| Ecotourism | rft:Ecotourism |  |
+| CoverCropping | rft:CoverCropping |  |
+| TreePlanting | rft:TreePlanting |  |
+| PhotocatalystApplication | rft:PhotocatalystApplication |  |
+| EcosystemRestoration | rft:EcosystemRestoration |  |
+| IndustrialBiocharProduction | rft:IndustrialBiocharProduction |  |
+| ArtisanalBiocharProduction | rft:ArtisanalBiocharProduction |  |
+| Biochar | rft:Biochar |  |
+| EnhancedRockWeathering | rft:EnhancedRockWeathering |  |
+| CompostAmendments | rft:CompostAmendments |  |
+| KeystoneSpeciesConservation | rft:KeystoneSpeciesConservation |  |
+| UmbrellaSpeciesConservation | rft:UmbrellaSpeciesConservation |  |
+| Silvopasture | rft:Silvopasture |  |
+| ForestFarming | rft:ForestFarming |  |
+| NonUrbanForestImprovement | rft:NonUrbanForestImprovement |  |
+| UrbanForestImprovement | rft:UrbanForestImprovement |  |
+| Afforestation | rft:Afforestation |  |
+| Reforestation | rft:Reforestation |  |
 
 
 
@@ -23,7 +42,7 @@ URI: [ActivityTypes](ActivityTypes.md)
 
 | Name | Description |
 | ---  | --- |
-| [activity](activity.md) | the activity |
+| [activity](activity.md) | The types of activities being implemented in projects |
 
 
 
@@ -53,18 +72,113 @@ URI: [ActivityTypes](ActivityTypes.md)
 <details>
 ```yaml
 name: ActivityTypes
-description: The type of activity
 from_schema: https://framework.regen.network/schema/
 rank: 1000
 permissible_values:
-  conservation:
-    text: conservation
-    description: a conservation activity
-    meaning: rfs:Conservation
-  ecosystemRestoration:
-    text: ecosystemRestoration
-    description: an ecosystem restoration activity
-    meaning: rfs:EcosystemRestoration
+  ResidueTillageManagement:
+    text: ResidueTillageManagement
+    meaning: rft:ResidueTillageManagement
+    title: ResidueTillageManagement
+  BiocharProduction:
+    text: BiocharProduction
+    meaning: rft:BiocharProduction
+    title: BiocharProduction
+  ImprovedForestManagement:
+    text: ImprovedForestManagement
+    meaning: rft:ImprovedForestManagement
+    title: ImprovedForestManagement
+  Agroforestry:
+    text: Agroforestry
+    meaning: rft:Agroforestry
+    title: Agroforestry
+  PrescribedGrazing:
+    text: PrescribedGrazing
+    meaning: rft:PrescribedGrazing
+    title: PrescribedGrazing
+  RiparianForestBuffers:
+    text: RiparianForestBuffers
+    meaning: rft:RiparianForestBuffers
+    title: RiparianForestBuffers
+  SoilAmendments:
+    text: SoilAmendments
+    meaning: rft:SoilAmendments
+    title: SoilAmendments
+  Conservation:
+    text: Conservation
+    meaning: rft:Conservation
+    title: Conservation
+  Ecotourism:
+    text: Ecotourism
+    meaning: rft:Ecotourism
+    title: Ecotourism
+  CoverCropping:
+    text: CoverCropping
+    meaning: rft:CoverCropping
+    title: CoverCropping
+  TreePlanting:
+    text: TreePlanting
+    meaning: rft:TreePlanting
+    title: TreePlanting
+  PhotocatalystApplication:
+    text: PhotocatalystApplication
+    meaning: rft:PhotocatalystApplication
+    title: PhotocatalystApplication
+  EcosystemRestoration:
+    text: EcosystemRestoration
+    meaning: rft:EcosystemRestoration
+    title: EcosystemRestoration
+  IndustrialBiocharProduction:
+    text: IndustrialBiocharProduction
+    meaning: rft:IndustrialBiocharProduction
+    title: IndustrialBiocharProduction
+  ArtisanalBiocharProduction:
+    text: ArtisanalBiocharProduction
+    meaning: rft:ArtisanalBiocharProduction
+    title: ArtisanalBiocharProduction
+  Biochar:
+    text: Biochar
+    meaning: rft:Biochar
+    title: Biochar
+  EnhancedRockWeathering:
+    text: EnhancedRockWeathering
+    meaning: rft:EnhancedRockWeathering
+    title: EnhancedRockWeathering
+  CompostAmendments:
+    text: CompostAmendments
+    meaning: rft:CompostAmendments
+    title: CompostAmendments
+  KeystoneSpeciesConservation:
+    text: KeystoneSpeciesConservation
+    meaning: rft:KeystoneSpeciesConservation
+    title: KeystoneSpeciesConservation
+  UmbrellaSpeciesConservation:
+    text: UmbrellaSpeciesConservation
+    meaning: rft:UmbrellaSpeciesConservation
+    title: UmbrellaSpeciesConservation
+  Silvopasture:
+    text: Silvopasture
+    meaning: rft:Silvopasture
+    title: Silvopasture
+  ForestFarming:
+    text: ForestFarming
+    meaning: rft:ForestFarming
+    title: ForestFarming
+  NonUrbanForestImprovement:
+    text: NonUrbanForestImprovement
+    meaning: rft:NonUrbanForestImprovement
+    title: NonUrbanForestImprovement
+  UrbanForestImprovement:
+    text: UrbanForestImprovement
+    meaning: rft:UrbanForestImprovement
+    title: UrbanForestImprovement
+  Afforestation:
+    text: Afforestation
+    meaning: rft:Afforestation
+    title: Afforestation
+  Reforestation:
+    text: Reforestation
+    meaning: rft:Reforestation
+    title: Reforestation
 
 ```
 </details>

schema/generated/AdministrativeArea.md

@@ -1,39 +1,46 @@
 
 
-# Slot: administrativeArea
+# Class: AdministrativeArea
 
 
-_The administrative area associated with the project._
 
+URI: [schema:AdministrativeArea](http://schema.org/AdministrativeArea)
 
 
 
+```mermaid
+erDiagram
+AdministrativeArea {
+    string name  
+    string url  
+}
 
-URI: [rfs:administrativeArea](https://framework.regen.network/schema/administrativeArea)
 
 
-
-<!-- no inheritance hierarchy -->
-
+```
 
 
 
+<!-- no inheritance hierarchy -->
 
-## Applicable Classes
 
-| Name | Description | Modifies Slot |
-| --- | --- | --- |
-| [Project](Project.md) |  |  no  |
+## Slots
 
+| Name | Cardinality and Range | Description | Inheritance |
+| ---  | --- | --- | --- |
+| [name](name.md) | 1 <br/> [String](String.md) | Name of the project | direct |
+| [url](url.md) | 0..1 <br/> [String](String.md) |  | direct |
 
 
 
 
 
+## Usages
 
-## Properties
+| used by | used in | type | used |
+| ---  | --- | --- | --- |
+| [Project](Project.md) | [administrativeArea](administrativeArea.md) | range | [AdministrativeArea](AdministrativeArea.md) |
 
-* Range: [AdministrativeArea](AdministrativeArea.md)
 
 
 
@@ -59,24 +66,68 @@ URI: [rfs:administrativeArea](https://framework.regen.network/schema/administrat
 
 | Mapping Type | Mapped Value |
 | ---  | ---  |
-| self | rfs:administrativeArea |
-| native | rfs:administrativeArea |
+| self | schema:AdministrativeArea |
+| native | rfs:AdministrativeArea |
+
+
+
 
 
 
 
 ## LinkML Source
 
+<!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->
+
+### Direct
+
+<details>
+```yaml
+name: AdministrativeArea
+from_schema: https://framework.regen.network/schema/
+slots:
+- name
+- url
+class_uri: schema:AdministrativeArea
+
+```
+</details>
+
+### Induced
+
 <details>
 ```yaml
-name: administrativeArea
-description: The administrative area associated with the project.
+name: AdministrativeArea
 from_schema: https://framework.regen.network/schema/
-rank: 1000
-alias: administrativeArea
-domain_of:
-- Project
-range: AdministrativeArea
+attributes:
+  name:
+    name: name
+    description: Name of the project.
+    from_schema: https://framework.regen.network/schema/
+    rank: 1000
+    slot_uri: schema:name
+    alias: name
+    owner: AdministrativeArea
+    domain_of:
+    - Project
+    - ProjectRole
+    - Organization
+    - AdministrativeArea
+    - File
+    range: string
+    required: true
+  url:
+    name: url
+    from_schema: https://framework.regen.network/schema/
+    rank: 1000
+    alias: url
+    owner: AdministrativeArea
+    domain_of:
+    - ProjectRole
+    - Organization
+    - AdministrativeArea
+    range: string
+class_uri: schema:AdministrativeArea
 
 ```
 </details>