Merge pull request #3 from materialdigital/fresh-seed-20250828-141423

ODK Seed: hto

Author: ThHanke

.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
+
+/hto.owl
+/hto.obo
+/hto.json
+/hto.db
+/hto-base.*
+/hto-basic.*
+/hto-full.*
+/hto-simple.*
+/hto-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/hto.owl
+src/ontology/hto.obo
+src/ontology/hto.json
+src/ontology/hto.db
+src/ontology/hto-base.*
+src/ontology/hto-basic.*
+src/ontology/hto-full.*
+src/ontology/hto-simple.*
+src/ontology/hto-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-hto-edit.owl
+src/ontology/hto-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 My Application Ontology
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to HTO. 
+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/heat-treatment-application-ontology/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/hto).
+- **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/heat-treatment-application-ontology/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/heat-treatment-application-ontology/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/hto-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

@@ -1,22 +1,29 @@
-# application-ontology-template
 
-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).
+![Build Status](https://github.com/materialdigital/heat-treatment-application-ontology/actions/workflows/qc.yml/badge.svg)
+# My Application Ontology
 
-## how to use
+Description: None
 
-1. Fork this repository
-2. Run the seed workflow under github actions, set the id and uribase_suffix. It will override the default values in seed-template.yaml
+More information can be found at http://obofoundry.org/ontology/hto
 
-```yaml
-id: <change here>
-title: <ontology title>
-github_org: materialdigital
-git_main_branch: main
-repo: <repo name>
-uribase: https://w3id.org/pmd/ao
-uribase_suffix: xxx
-```
+## Versions
 
-3. Check the pul request create! If everything is fine merge to main
-4. Put ur ontology work into the \*-edit.owl file in src folder, after pushing changes to the repository the build_with imports workflow will run and integrate your changes into the release types defined
-5. Documentation of the application ontology is created via widoco and github pages, when the docs workflow runs
+### Stable release versions
+
+The latest version of the ontology can always be found at:
+
+https://w3id.org/pmd/ao/hto.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/hto-edit.owl](src/ontology/hto-edit.owl)
+
+## Contact
+
+Please use this GitHub repository's [Issue tracker](https://github.com/materialdigital/heat-treatment-application-ontology/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).