remove outdated troubleshooting guide, fix review comments

Author: lukaspie

.github/workflows/build_docs.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master  # Triggers deployment on push to the main branch
-      - 405-move-readme-content-to-documentation
 
 env:
   UV_SYSTEM_PYTHON: true

docs/index.md

@@ -27,7 +27,6 @@ A series of tutorials giving you an overview on how to store or convert your dat
 
 - [Converting your data to NeXus](tutorial/converting-data-to-nexus.md)
 - [Uploading NeXus data to NOMAD](tutorial/nexus-to-nomad.md)
-- [Troubleshooting guide](tutorial/troubleshooting.md)
 
 </div>
 <div markdown="block">
@@ -72,6 +71,8 @@ How-to guides provide step-by-step instructions for a wide range of tasks.
 Or go directly to the [official NIAC](https://manual.nexusformat.org/classes/index.html)
  or [latest FAIRmat](https://fairmat-nfdi.github.io/nexus_definitions/) definitions.
 
+Note: To connect NeXus concepts with semantic web tools, efforts are underway to represent them using the [W3C Web Ontology Language (OWL)](https://www.w3.org/OWL/). See the [NeXusOntology](https://github.com/FAIRmat-NFDI/NeXusOntology) for more details.
+
 #### pynxtools
 
 `pynxtools` has a number of command line tools that can be used to convert data and verify NeXus files. You can find more information about the API [here](reference/cli-api.md).

docs/learn/nexus-validation.md

@@ -7,11 +7,11 @@ One of the main advantages of using pynxtools is that it comes with its own vali
 During [data conversion](./dataconverter-and-readers.md), before writing the HDF5 file, the data is first checked against the provided application definition.
 
 <!--## verify-nexus: Testing existing NeXus/HDF5 files
-This CLI tool can be used to validate _existing_ HDF5 files that claim to be NeXus-compliant. See [here](reference/cli-api.html#verify-nexus) for the API documentation.-->
+This CLI tool can be used to validate _existing_ HDF5 files that claim to be NeXus-compliant. See [here](reference/cli-api.md#verify-nexus) for the API documentation.-->
 
 ## read_nexus: NeXus file reader and debugger
 
-This utility outputs a debug log for a given NeXus file by annotating the data and metadata entries with the schema definitions from the respective NeXus base classes and application definitions to which the file refers to. See [here](../reference/cli-api.html#read_nexus) for the API documentation.
+This utility outputs a debug log for a given NeXus file by annotating the data and metadata entries with the schema definitions from the respective NeXus base classes and application definitions to which the file refers to. See [here](../reference/cli-api.md#read_nexus) for the API documentation.
 
 The following example dataset can be used to test the `read_nexus` module: [src/pynxtools/data/201805_WSe2_arpes.nxs](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/data/201805_WSe2_arpes.nxs).
 

docs/reference/definitions.md

@@ -10,3 +10,7 @@ The FAIRmat definitions are regularly contributed to NIAC (around every 6 months
 a state which is still under development and may contain new or improved application definitions or base classes.
 Consider it as the public review stage of these application definitions.
 However, there might be some parts which are still under discussion and will be subject to change.
+
+Note: To connect NeXus concepts with semantic web tools, efforts are underway to represent them using the [W3C Web Ontology Language (OWL)](https://www.w3.org/OWL/). See the [NeXusOntology](https://github.com/FAIRmat-NFDI/NeXusOntology) for more details.
+
+

docs/tutorial/troubleshooting.md

@@ -10,7 +10,6 @@ nav:
   - Tutorials:
     - tutorial/converting-data-to-nexus.md
     - tutorial/nexus-to-nomad.md
-    - tutorial/troubleshooting.md
   - How-tos:
     - how-tos/writing-an-appdef.md
     - how-tos/using-multiple-appdefs.md