schenging directory structure for schema, adding mermaid

.github/workflows/publishdocs.yaml

@@ -27,8 +27,8 @@ jobs:
 
       - name: Generating docs
         run: |
-          gen-doc -d docs/model linkml-schema/reproschema.yaml
-          gen-erdiagram linkml-schema/reproschema.yaml > docs/model/erdiagram.md
+          gen-doc -d docs/schema/doc-linkml-autogen linkml-schema/reproschema.yaml
+          gen-erdiagram linkml-schema/reproschema.yaml > docs/schema/erdiagram-autogen.md
 
       - name: Deploy docs
         uses: mhausenblas/mkdocs-deploy-gh-pages@master

docs/schema.md → docs/schema/schema.md

@@ -80,7 +80,14 @@ Protocol
 The [ReproSchema-UI](https://repronim.org/reproschema-ui) is a prototype implementation of an UI that leverages these
 different elements of the schema.
 
-## Properties of ReproSchema objects
+## ReproSchema Model
 
-- Description of the model automatically generated by LinkML tools is [here](./model/index.md)
-- ER diagram to visualize the model is [here](./model/erdiagram.md)
+The model was written using a linked data modeling language [LinkML](https://linkml.io/linkml/).
+
+There are multiple ways of accessing the content
+- [The LinkML YAML file that defines the model](https://github.com/ReproNim/reproschema/blob/main/linkml-schema/reproschema.yaml)
+- [Automatically generated documentation](./doc-linkml-autogen/index.md) using LinkML tools
+- [Automatically generated Entity-Relationship (ER) Diagrams](./erdiagram-autogen.md)) to visualize the model.
+
+The context was created semi-automatically: the initial version was generated using LinkML tools,
+but manual curation was necessary to support all Reeproschema features.

mkdocs.yml

@@ -39,7 +39,7 @@ nav:
   - Welcome: "index.md"
   - Introduction: "introduction.md"
   - Project structure: "project-structure.md"
-  - Schema: "schema.md"
+  - Schema: "schema/schema.md"
   - User Guide:
       - Create a research protocol: "user-guide/create-new-protocol.md"
       - Adopt assessments from the library: "user-guide/adopt-assessments.md"
@@ -84,3 +84,4 @@ watch:
 plugins:
   - search
   - tags
+  - mermaid2