materialdigital · joergwa · Feb 27, 2026 · Feb 23, 2026 · Feb 23, 2026 · Feb 23, 2026
diff --git a/docs/docs_HTML/HTML_Docs/acknowledgements.html b/docs/docs_HTML/HTML_Docs/acknowledgements.html
diff --git a/docs/docs_HTML/HTML_Docs/glossary-and-tools.html b/docs/docs_HTML/HTML_Docs/glossary-and-tools.html
diff --git a/docs/docs_HTML/HTML_Docs/index.html b/docs/docs_HTML/HTML_Docs/index.html
diff --git a/docs/docs_HTML/HTML_Docs/intro.html b/docs/docs_HTML/HTML_Docs/intro.html
diff --git a/docs/docs_HTML/HTML_Docs/introduction-to-ontologies.html b/docs/docs_HTML/HTML_Docs/introduction-to-ontologies.html
diff --git a/docs/docs_HTML/HTML_Docs/migration.html b/docs/docs_HTML/HTML_Docs/migration.html
diff --git a/docs/docs_HTML/HTML_Docs/obsolete-ontology-terms.html b/docs/docs_HTML/HTML_Docs/obsolete-ontology-terms.html
diff --git a/docs/docs_HTML/HTML_Docs/ontology-structure.html b/docs/docs_HTML/HTML_Docs/ontology-structure.html
diff --git a/docs/docs_HTML/HTML_Docs/patterns.html b/docs/docs_HTML/HTML_Docs/patterns.html
diff --git a/docs/docs_HTML/HTML_Docs/pmdco-user-guide.html b/docs/docs_HTML/HTML_Docs/pmdco-user-guide.html
diff --git a/docs/docs_HTML/HTML_Docs/publications.html b/docs/docs_HTML/HTML_Docs/publications.html
diff --git a/docs/docs_HTML/HTML_Docs/references.html b/docs/docs_HTML/HTML_Docs/references.html
diff --git a/docs/docs_HTML/HTML_Docs/reused-ontologies.html b/docs/docs_HTML/HTML_Docs/reused-ontologies.html
diff --git a/docs/docs_HTML/HTML_Docs/search-index.json b/docs/docs_HTML/HTML_Docs/search-index.json
diff --git a/docs/docs_HTML/HTML_Docs/versions.html b/docs/docs_HTML/HTML_Docs/versions.html
diff --git a/docs/docs_HTML/HTML_Docs/who-we-are.html b/docs/docs_HTML/HTML_Docs/who-we-are.html
diff --git a/docs/docs_HTML/README.md b/docs/docs_HTML/README.md
@@ -14,6 +14,7 @@ Markdown + TTL/OWL  ──▶  Interactive HTML Documentation
 |---------|-------------|
 | **Ontology Trees** | Auto-generate expandable class hierarchies from OWL files |
 | **Graph Diagrams** | Render TTL/SHACL as interactive Graphviz diagrams |
+| **Hierarchy Views** | Switch between Full, Upper, and File views per diagram |
 | **Full-Text Search** | Cross-page search with relevance ranking |
 | **Dark/Light Themes** | Auto-detects system preference |
 | **Zero Config** | Define pages in YAML, run one command |
@@ -158,12 +159,24 @@ Special HTML comments trigger dynamic content generation during build.
 
 ### `@Graphviz_renderer` — TTL to Interactive Diagram
 
-Converts Turtle/SHACL files into pan-zoom-export graph viewers.
+Converts Turtle/SHACL files into pan-zoom-export graph viewers with three hierarchy views.
 
 ```markdown
 <!--@Graphviz_renderer:URL_OR_PATH-->
 ```
 
+**Hierarchy Views:**
+
+Each diagram automatically includes three switchable views via toggle buttons:
+
+| View | Description |
+|------|-------------|
+| **Full** | Complete class hierarchy from the PMD core ontology |
+| **Upper** | One superclass level above each class |
+| **File** | File content only — no hierarchy expansion |
+
+Users can switch between views using the **Full / Upper / File** toggle buttons in the diagram header. The same toggle is available in fullscreen mode.
+
 **Supported Input Types:**
 
 | Type | Extension | What It Renders |
@@ -183,8 +196,9 @@ Converts Turtle/SHACL files into pan-zoom-export graph viewers.
 **Generated Features:**
 - Mouse wheel zoom / drag to pan
 - Click nodes for URI tooltips
+- Switch between Full / Upper / File hierarchy views
 - Export as SVG or PNG
-- Fullscreen mode
+- Fullscreen mode with view toggle
 
 ---
 
@@ -287,7 +301,7 @@ Auto-detects language from extension (`.ttl`, `.py`, `.json`, etc.)
 
 | Tag | Input | Output |
 |-----|-------|--------|
-| `@Graphviz_renderer` | TTL/OWL URL | Interactive graph |
+| `@Graphviz_renderer` | TTL/OWL URL | Interactive graph (Full/Upper/File views) |
 | `@module_indicator` | OWL URL | Class tree |
 | `@property_indicator` | `object`/`data`/`annotation` | Property tree |
 | `@Graphviz_renderer_manual` | DOT code block | Interactive graph |

diff --git a/docs/docs_HTML/scripts/build_all.py b/docs/docs_HTML/scripts/build_all.py
diff --git a/docs/obsolete ontology terms.md b/docs/obsolete ontology terms.md
@@ -1,30 +1,32 @@
 # Obsoleting and deprecating ontology terms
 <!--@Document_indicator: Text,links -->
 
-Ontologies evolve, terms are revised, split into more detailed terms or deprecated. For proper reusablity of the ontology and traceability of the reason why it was deleted and what is a possible replacement term that should be used instead, the following steps should be adopted.
-*(These steps are largely based on the [GO](https://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term) and [ODK](https://ontology-development-kit.readthedocs.io/en/latest/ObsoleteTerm.html) pages for term obsoletion but adjusted for the PMDco.)*
+Ontologies evolve, terms are revised, split into more detailed terms or deprecated. For proper reusablity of the ontology and traceability of the reason why it was deleted and what is a possible replacement term that should be used instead, the following obsoletion procedure should be followed.
+*(These steps are largely based on the [GO](https://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term) and [ODK](https://ontology-development-kit.readthedocs.io/en/latest/ObsoleteTerm.html) pages for term obsoletion but adopted for the PMDco.)*
 
 ## Check for the PMDco deprecation profile
 1. Navigate to your local Protégé installation folder and further to '..\conf\deprecation\'
-2. Check whether the file 'PMDco.yaml' is present
-	- if not, download it from [here](https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/PMDco.yaml) and move it into the Protégé installation folder
+2. Check whether the file `PMDco.yaml` is present
+	- if not, download it from [here](https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/src/ontology/PMDco.yaml) and move it into the Protégé installation folder
 
 <!--- In the future this should be done without the need for users to manually copy files on their machines. The PMDco deprecation profile may be added to the official protege release or be moved into the respective folder when editing the core or application ontologies. For now this shoould suffice.--->
 
 
 ## Check the usage of the term
 1. Check where in the ontology the term is used
-	- In Protégé, navigate to the term you want to obsolete, go to the ‘Usage’ tab to see if that ID is used elsewhere.
+	- In Protégé, navigate to the term you want to obsolete, go to the `Usage` tab to see if that ID is used elsewhere.
 	- If the term is a parent term or used in logical definitions, **create a substitute term** that replaces the obsolete term.
 	- Is the obsolete term itself is the replacement or in consideration for other obsoleted terms, update these (with a substitute term) or delete them.
-2. Navigate to the term you want to obsolete agin
-3. Right-click on the term and select 'Deprecate...' **or** click the 'Edit'-Tab -> 'Deprecrate entity...'
-4. Choose the PMDco deprecation profile -> continue
-5. Give a reason for deprecation from the list below -> continue 
-6. (If applicable) Search the substitute term you created earlier, else continue
-7. If no substitute term was defined, give one or more terms that can be used as an alternative when possible (if applicable) -> continue -> finish
+2. Navigate to the term you want to obsolete again
+3. Right-click on the term and select `Deprecate...` **or** click the `Edit`-tab → `Deprecrate entity...`
+4. Choose the PMDco deprecation profile from the dropdown menu → continue
+	- If no PMDco deprecation profile is present, the `PMDco.yaml` is missing from your Protégé installation folder. Checkout the previous section, then return here.
+6. Give a reason for deprecation from the list below → continue 
+7. (If applicable) Search the substitute term you created earlier, else continue
+8. If no substitute term was defined, give one or more terms that can be used as an alternative when possible (if applicable) → continue → finish
 
 ## Reasons for deprecation
+Copy&paste these into the corresponding dialog during the obsoletion procedure.
 
 - original meaning has split and more specific terms were created
 - outside of the scope of the ontology

diff --git a/docs/patterns.md b/docs/patterns.md
@@ -7,7 +7,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 
 ## Pattern 1 - Duality of object and material
 <!--Please provide the link to the pattern (raw data ttl file) in the repository-->
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/duality%20object%20material/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/duality%20object%20material/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/duality%20object%20material/pattern.md-->
 
@@ -20,7 +20,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 2 - Temporal Region
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/temporal%20region/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/temporal%20region/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/temporal%20region/pattern.md-->
 
@@ -33,7 +33,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 3 - Process Chain
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/process%20chain/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/process%20chain/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/process%20chain/pattern.md-->
 
@@ -46,7 +46,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 4 - Process Inputs and Outputs
-<!--@Graphviz_renderer_upper:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/input%20and%20output%20of%20processes/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/input%20and%20output%20of%20processes/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/input%20and%20output%20of%20processes/pattern.md-->
 
@@ -59,7 +59,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 5 - Realizable Entities (Role)
-<!--@Graphviz_renderer_file:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/realizable%20entity%20(role)/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/realizable%20entity%20(role)/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/realizable%20entity%20(role)/pattern.md-->
 
@@ -72,7 +72,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 6 - Material Properties (Qualities)
-<!--@Graphviz_renderer_file:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/material%20property%20(quality)/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/material%20property%20(quality)/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/material%20property%20(quality)/pattern.md-->
 
@@ -85,7 +85,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 7 - Measurement
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/measurement/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/measurement/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/measurement/pattern.md-->
 
@@ -98,7 +98,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 8 - Scalar Value Specification
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/scalar%20value%20specification/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/scalar%20value%20specification/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/scalar%20value%20specification/pattern.md-->
 
@@ -111,7 +111,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 9 - Categorical Value Specification
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/categorical%20value%20specification/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/categorical%20value%20specification/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/categorical%20value%20specification/pattern.md-->
 
@@ -124,7 +124,7 @@ The sections below illustrate how to read and apply these patterns. Each pattern
 ---
 
 ## Pattern 10 - Simulation input/output
-<!--@Graphviz_renderer_full:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/simulation%20inout%20simple/shape-data.ttl-->
+<!--@Graphviz_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/simulation%20inout%20simple/shape-data.ttl-->
 
 <!--@md_file_renderer:https://raw.githubusercontent.com/materialdigital/core-ontology/refs/heads/main/patterns/simulation%20inout%20simple/pattern.md-->