chore: Setup BWMD ontology (end-to-end complete)

Auto-generated via Setup New Ontology workflow:
- Configured project-odk.yaml (URIs: https://w3id.org/pmd/bwmd/)
- Initialized components, imports (SLME), ID ranges
- Generated bwmd-edit.owl and bwmd-idranges.owl
- Customized README.md with development guides

Author: github-actions[bot]

.gitignore

@@ -1,15 +1,69 @@
-# ODK-managed rules, do not modify
-# If you need to add your own ignore rules, you may do so below
-# the "End ODK-managed rules" marker at the end of this file.
-.DS_Store
-semantic.cache
-bin/
-.trunk/
-*.tmp
-*.tmp.obo
-*.tmp.owl
-*.tmp.json
-*-relation-graph.tsv.gz
-.template.db
-
-.github/token.txt
+# ODK-managed rules, do not modify
+# If you need to add your own ignore rules, you may do so below
+# the "End ODK-managed rules" marker at the end of this file.
+.DS_Store
+semantic.cache
+bin/
+
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+*-relation-graph.tsv.gz
+.template.db
+
+.github/token.txt
+
+/bwmd.owl
+/bwmd.obo
+/bwmd.json
+/bwmd.db
+/bwmd-base.*
+/bwmd-basic.*
+/bwmd-full.*
+/bwmd-simple.*
+/bwmd-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/bwmd.owl
+src/ontology/bwmd.obo
+src/ontology/bwmd.json
+src/ontology/bwmd.db
+src/ontology/bwmd-base.*
+src/ontology/bwmd-basic.*
+src/ontology/bwmd-full.*
+src/ontology/bwmd-simple.*
+src/ontology/bwmd-simple-non-classified.*
+
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-bwmd-edit.owl
+src/ontology/bwmd-edit.properties
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/.gitkeep
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+src/ontology/imports/*_terms_combined.txt
+
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt
+
+# End of ODK-managed rules

CONTRIBUTING.md

@@ -0,0 +1,86 @@
+# Contributing to BWMD Ontology
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to BWMD. 
+These guidelines are not strict rules. Use your best judgment, and feel free to propose 
+changes to this document in a pull request.
+
+## Table Of Contents
+
+- [Guidelines for Contributions and Requests](#contributions)
+    * [Reporting problems with the ontology](#reporting-bugs)
+    * [Requesting new terms](#requesting-terms)
+    * [Adding new terms by yourself](#adding-terms)
+- [Best practices](#best-practices)
+    * [How to write a great issue?](#great-issues)
+    * [How to create a great pull/merge request?](#great-pulls)
+
+<a id="contributions"></a>
+
+## Guidelines for Contributions and Requests
+
+<a id="reporting-bugs"></a>
+
+### Reporting problems with the ontology
+
+Please use our [Issue Tracker](https://github.com/materialdigital/materialdigital/pmdco-bwmd/issues/) for reporting problems with the ontology. 
+To learn how to write a good issue [see here](#great-issues).
+
+<a id="requesting-terms"></a>
+
+### Requesting new terms
+
+Before you write a new request, please consider the following: 
+
+- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, 
+either as a primary term or a synonym term. You can search for your term using [OLS](http://www.ebi.ac.uk/ols/ontologies/bwmd).
+- **Can you provide a definition for the term?** It should be very clear what the term means, and you should be
+able to provide a concise definition, ideally with a scientific reference.
+- **Is the ontology in scope for the term?** Sometimes, it is hard to tell whether a term "belongs" in
+and ontology. A rule of thumb is "if a similar term already exists, the new term is probably in scope."
+It can be very helpful to mention a very similar concept as part of the term request!
+
+#### Who can request a term?
+
+Anyone can request new terms. However, there is not guarantee that your term will be added automatically. Since this is a 
+community resource, it is often necessary to do at least some of the work of adding the term yourself, see below.
+
+#### How to write a new term request
+
+Request a new term _via_ the GitHub [Issue Tracker](https://github.com/materialdigital/materialdigital/pmdco-bwmd/issues/).
+
+It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker.
+To make this work easier, please always use issue templates if they are available (https://github.com/materialdigital/materialdigital/pmdco-bwmd/issues/new/choose).
+
+For how to write a good term request, please read the [best practices carefully](#great-issues).
+
+<a id="adding-terms"></a>
+
+### How to add a new term
+
+If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies)
+
+**Process**:
+
+1. Clone the repository (In case you are not an offical team member, create a fork first)
+1. Create new branch in git, for example `git checkout -b issue123`
+1. Open src/ontology/bwmd-edit.owl in your favourite editor, i.e. [Protege](https://protege.stanford.edu/). **Careful:** double check you are editing the correct file. There are many ontology files in this repository, but only one _editors file_!
+1. Perform your edit and save your changes
+1. Commit changes to branch
+1. Push changes upstream
+1. Create pull request
+
+## Best Practices
+
+<a id="great-issues"></a>
+
+### How to write great issues?
+
+Please refer to the [OBO Academy term request guide](https://oboacademy.github.io/obook/howto/term-request/).
+
+<a id="great-pulls"></a>
+
+### How to create a great pull/merge request?
+
+Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/)

README.md

@@ -1,17 +1,66 @@
-# application-ontology-template
+# BWMD Ontology
 
-template repository for starting a PMDCo application ontology. iT comes preconfigured with github workflows using [ontology development kit](https://github.com/INCATools/ontology-development-kit).
+Description: PMD Core application ontology generated via ODK Template.
 
-## How to use
 
-1. Click use as Template Repository
-2. Documentation of the application ontology is created via widoco and GitHub Pages when the docs workflow runs.
+More information can be found at http://obofoundry.org/ontology/bwmd
 
-   To enable the documentation, you have to activate GitHub Pages in the repository settings. Set it to GitHub Actions instead of branch; the doc action will upload      the artifacts needed after each push to the repository.
-3. You need to give GitHub Actions the permissions to read write and create pull requests (checkbox) in the repository settings at actions -> general
-4. Run the seed workflow under GitHub Actions, and set the id and uribase_suffix. It will override the default values in [seed-template.yaml](./seed-template.yaml)
-   
-    Id and uribase_suffix are usually set to the same lowercase acronym that will be used with this ontology; examples are pmdco, tto, hto ...
-    Github org and repo name will be set automatically by the seed workflow. To run the workflow, switch to GitHub Actions, select the seed workflow, and dispatch the  job manually.
-5. Check the pull request created! If everything is fine, merge into main.
-6. Put your ontology work into the \*-edit.owl file in the src folder; after pushing changes to the repository, the build will run and integrate your changes into the release types defined.
+## Versions
+
+### Stable release versions
+
+The latest version of the ontology can always be found at:
+
+https://w3id.org/pmd/bwmd.owl
+
+(note this will not show up until the request has been approved by obofoundry.org)
+
+### Editors' version
+
+Editors of this ontology should use the edit version, [src/ontology/bwmd-edit.owl](src/ontology/bwmd-edit.owl)
+
+## Contact
+
+Please use this GitHub repository's [Issue tracker](https://github.com/materialdigital/materialdigital/pmdco-bwmd/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+
+## Acknowledgements
+
+This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).
+## Development
+This ontology is developed using OWL and managed with the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit). To edit:
+- Open `bwmd-edit.owl` (located in `src/ontology/`) in [Protégé](https://protege.stanford.edu/) or your preferred OWL editor.
+- Create new entities (classes, properties) within the namespace `https://w3id.org/pmd/bwmd/`.
+  - Example class ID: `https://w3id.org/pmd/bwmd/BWMD_0000001` (PREFIX is uppercase).
+- Use the `Makefile` for automation:
+  - `make test`: Run quality control (OWL reasoner checks, syntax validation).
+  - `make refresh-imports`: Update imported ontologies (e.g., PMD Core, LOGO) with SLME extraction.
+  - `make release`: Build release artifacts (full, base, etc.) in TTL/OWL/JSON formats.
+  - `make update_repo`: Sync changes to the repo structure.
+Quick start: After setup, edit in Protégé, commit, and push to trigger CI builds.
+## Repository Structure
+This repository provides the modular implementation of BWMD Ontology, developed and maintained using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).
+### Top-level directories
+* **.github/:** GitHub configuration files, including CI workflows and templates.
+* **docs/:** Documentation sources for the ontology website and user guides (optional; add as needed).
+* **patterns/:** Logical patterns and SHACL shapes used to maintain consistent ontology design (optional).
+* **src/:** Main development folder generated and managed through ODK.
+  * **ontology/components/:** – Modular ontology components (classes, properties, axioms).
+  * **ontology/bwmd-edit.owl:** – Primary editable ontology file used during development (ontology editors' version).
+  * **ontology/imports/:** Extracted terms from imported ontologies (via SLME).
+### Ontology versions (generated on release)
+* **bwmd-full.owl/ttl:** Complete ontology with all imports and full axiomatization.
+* **bwmd-base.owl/ttl:** Core entities without extended imports.
+* **bwmd-simple.owl/ttl:** Simplified version with basic subclass and existential axioms.
+* **bwmd-minimal.owl/ttl:** Lightweight minimal version for quick onboarding (recommended for beginners).
+* **bwmd.owl/ttl:** Main ontology file contains the full version.
+### Other files
+* README.md, LICENSE.txt, CONTRIBUTING.md – Project overview, license, and contribution guidelines.
+* imports.txt, components.txt, creators.txt – Configuration for setup (optional edits).
+## Contribution
+We welcome contributions to the BWMD Ontology ontology!
+To get involved:
+- Please use this GitHub repository's **[Issue tracker](https://github.com/materialdigital/pmdco-bwmd/issues)** to request new terms/classes or report errors or specific concerns related to the ontology.
+- For creation of application ontologies using PMD core ontologies, we advise using the **[application-ontology-template](https://github.com/materialdigital/application-ontology-template/)**. It applies the same framework used here and mirrors the pmdco with all its modules.
+- Write about your specific modeling concerns or any other discussable topics in the **[discussion forum](https://github.com/materialdigital/pmdco-bwmd/discussions)**.
+- Participate in our **PMD Playground Meetings**: Our Ontology Playground, organized online every second Friday from 1-2 pm (CET), is a great opportunity to connect with developers and our proactive community to shape the PMDco. Please register via our [mailing list](https://www.lists.kit.edu/sympa/subscribe/ontology-playground?previous_action=info).
+- If you need further information, please feel free to contact us via **[info@material-digital.de](mailto:info@material-digital.de)**