Add descriptive meta data (#39)

* Reformat owl files

* Add ontology descriptions

* Add proper license to gfo-base.owl

* Update gfo-base.owl

- Rename base/Instantanuous_change to base/Instantaneous_change
- Add labels
- Replace rdfs:comment with skos:definition
- Fix typos
- Add deprecations

* Update test workflow

- Create workflow annotations from robot report

* Add contributing guide

.github/workflows/test.yml

@@ -25,7 +25,16 @@ jobs:
     container: obolibrary/odklite
     steps:
       - uses: actions/checkout@v4
+
       - run: check-rdfxml gfo-light.owl
       - run: check-rdfxml modules/gfo-base.owl
+
       - run: robot reason --input gfo-light.owl
       - run: robot reason --input modules/gfo-base.owl
+
+      # - run: |
+      #     result=$(robot report --input gfo-light.owl --profile qc_report/profile.txt)
+      #     echo "::notice file=gfo-light.owl::$result"
+      - run: |
+          result=$(robot report --input modules/gfo-base.owl --profile qc_report/profile.txt)
+          echo "::notice file=modules/gfo-base.owl::$result"

CONTRIBUTING.md

@@ -0,0 +1,40 @@
+# Contributing Guide
+
+Thank you for investing your time in contributing to our project!
+
+Read our [Code of Conduct](CODE_OF_CONDUCT.md) to keep our community approachable and respectable.
+
+## Issues and Support
+
+If you find a problem or have a question about the content in this repository and how to use it,
+please create an issue in the [Issues Tracker](https://github.com/Onto-Med/GFO/issues).
+Make sure you describe the problem as clearly as possible.
+
+## Workflow to Make Contributions
+
+We are very happy about contributions!
+
+It is recommended to use an ontology editor such as [Protégé](https://protege.stanford.edu/).
+If you want to contribute changes, please do so by:
+
+1. Clone this repository ([fork](https://github.com/Onto-Med/GFO/fork) for external contributors).
+2. Creating a new feature branch.
+3. Apply your changes.
+
+   Edit the ontology files using a suitable ontology editor or text editor.
+   Adhere to the GFO's existing coding style and conventions.
+   Ensure your changes are well-documented and understandable.
+   You can run the following command with docker to check your changes locally (in this case `modules/gfo-base.owl` is checked):
+
+       docker run -it -v .:/gfo -w /gfo obolibrary/odklite robot report --input modules/gfo-base.owl --profile qc_report/profile.txt
+
+4. Commit and push all changes.
+5. Create a [pull request](https://github.com/Onto-Med/GFO/pulls).
+
+   On GitHub, create a pull request from your branch to the main branch of the official GFO repository.
+   Provide a clear description of your changes and the rationale behind them.
+
+6. Review and Feedback.
+
+   Be prepared to address feedback and suggestions from the GFO community and maintainers.
+   Work collaboratively with other contributors to refine your changes.

README.md

@@ -17,6 +17,9 @@ The entire GFO ontology can be imported via IRI https://w3id.org/gfo. GFO is div
 
 **GFO-light** is a simplified view of the entire GFO. It does not build on single modules but combines all basic concepts and simplified axioms of the GFO. It is primarily intended to found domain or application ontologies and can be imported via IRI https://w3id.org/gfo/light.
 
+## How to Contribute
+Please see our [Contributing Guide](CONTRIBUTING.md).
+
 ## Brief History
 Work on GFO has started in 1999 in the context of the GOL project (General Ontological Language). Meanwhile, several directions of research have been recognized and divided the initial project, such that GFO is now one component of a larger framework. Work on GFO remains in progress, because the development of top-level ontologies is a long-term research effort.
 

gfo.owl

@@ -1,31 +1,34 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <rdf:RDF xmlns="https://w3id.org/gfo" xml:base="https://w3id.org/gfo"
-    xmlns:gfo="https://w3id.org/gfo"
-    xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-    xmlns:dc="http://purl.org/dc/elements/1.1/"
-    xmlns:vann="http://purl.org/vocab/vann/"
-    xmlns:foaf="http://xmlns.com/foaf/0.1/"
-    xmlns:doap="http://usefulinc.com/ns/doap#"
-    xmlns:bibo="http://purl.org/ontology/bibo/"
-    xmlns:terms="http://purl.org/dc/terms/">
+  xmlns:gfo="https://w3id.org/gfo"
+  xmlns:owl="http://www.w3.org/2002/07/owl#"
+  xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+  xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
+  xmlns:vann="http://purl.org/vocab/vann/"
+  xmlns:foaf="http://xmlns.com/foaf/0.1/"
+  xmlns:doap="http://usefulinc.com/ns/doap#"
+  xmlns:bibo="http://purl.org/ontology/bibo/"
+  xmlns:terms="http://purl.org/dc/terms/">
 
-    <owl:Ontology rdf:about="https://w3id.org/gfo">
-        <dc:modified rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-11-18</dc:modified>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-11-18</owl:versionInfo>
-        <owl:versionIRI rdf:resource="https://w3id.org/gfo/release/2024-11-18"/>
-        <owl:priorVersion rdf:resource="https://w3id.org/gfo/release/2024-07-05"/>
-        <owl:imports rdf:resource="https://w3id.org/gfo/base/"/>
-        <dc:title xml:lang="en">General Formal Ontology (GFO)</dc:title>
-        <rdfs:label xml:lang="en">General Formal Ontology (GFO)</rdfs:label>
-        <dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2006-08-28</dc:created>
-        <vann:preferredNamespaceURI>https://w3id.org/gfo/</vann:preferredNamespaceURI>
-        <vann:preferredNamespacePrefix>gfo</vann:preferredNamespacePrefix>
-        <foaf:homepage>https://github.com/Onto-Med/GFO</foaf:homepage>
-        <doap:repository rdf:resource="https://github.com/Onto-Med/GFO"/>
-        <bibo:doi rdf:resource="https://zenodo.org/doi/10.5281/zenodo.5205419"/>
-        <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
-    </owl:Ontology>
+  <owl:Ontology rdf:about="https://w3id.org/gfo">
+    <dc:modified rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-11-18</dc:modified>
+    <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2024-11-18</owl:versionInfo>
+    <owl:versionIRI rdf:resource="https://w3id.org/gfo/release/2024-11-18" />
+    <owl:priorVersion rdf:resource="https://w3id.org/gfo/release/2024-07-05" />
+    <owl:imports rdf:resource="https://w3id.org/gfo/base/" />
+    <dc:title xml:lang="en">General Formal Ontology (GFO)</dc:title>
+    <rdfs:label xml:lang="en">General Formal Ontology (GFO)</rdfs:label>
+    <dc:description xml:lang="en">The General Formal Ontology is a top-level ontology for conceptual
+      modeling. It includes elaborations of categories like objects, processes, time and space,
+      properties, relations, roles, functions, facts, and situations.</dc:description>
+    <dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2006-08-28</dc:created>
+    <vann:preferredNamespaceURI>https://w3id.org/gfo/</vann:preferredNamespaceURI>
+    <vann:preferredNamespacePrefix>gfo</vann:preferredNamespacePrefix>
+    <foaf:homepage>https://github.com/Onto-Med/GFO</foaf:homepage>
+    <doap:repository rdf:resource="https://github.com/Onto-Med/GFO" />
+    <bibo:doi rdf:resource="https://zenodo.org/doi/10.5281/zenodo.5205419" />
+    <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/" />
+  </owl:Ontology>
 </rdf:RDF>