Extend ontology to phenotyping

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/release.yml

@@ -0,0 +1,25 @@
+---
+name: Prepare release files
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    container: obolibrary/odklite
+    permissions:
+      contents: write
+      packages: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Generate artifacts
+        run: robot convert --input cop.owl --output cop.ttl
+      - uses: svenstaro/upload-release-action@v2
+        with:
+          tag: ${{ github.ref }}
+          file: cop.*
+          file_glob: true
+          overwrite: true

.github/workflows/test.yml

@@ -0,0 +1,20 @@
+---
+name: Check ontology
+
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches:
+      - master
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    container: obolibrary/odklite
+    steps:
+      - uses: actions/checkout@v4
+      - run: check-rdfxml cop.owl

CITATION.cff

@@ -1,38 +1,34 @@
-title: "Core Ontology of Phenotypes (COP)"
-abstract: "The Core Ontology of Phenotypes is a core ontology, which can be used to specify phenotype algorithms as ontologies (Phenotype Algorithm Specification Ontology)."
+cff-version: "1.1.0"
+message: "If you use the content of this repository, please cite it using these metadata."
+title: "Core Ontology of Phenotyping (COP)"
+abstract: "The Core Ontology of Phenotyping (COP) defines core entities and their relationships that are relevant for modelling phenotypic knowledge and developing phenotyping software."
 authors:
-  -
-    affiliation: "University of Leipzig"
+  - affiliation: "Leipzig University"
     family-names: Uciteli
     given-names: Alexandr
     orcid: "https://orcid.org/0000-0001-9558-5352"
-  -
-    affiliation: "University of Leipzig"
+  - affiliation: "Leipzig University"
     family-names: Beger
     given-names: Christoph
     orcid: "https://orcid.org/0000-0002-1166-0368"
-  -
-    affiliation: "University of Leipzig"
-    family-names: Kirsten
-    given-names: Toralf
-    orcid: "https://orcid.org/0000-0001-7117-4268"
-  -
-    affiliation: "University of Leipzig"
-    family-names: Meineke
-    given-names: Frank
-    orcid: "https://orcid.org/0000-0002-9256-7543"
-  -
-    affiliation: "University of Leipzig"
-    family-names: Herre
-    given-names: Heinrich
-cff-version: "1.1.0"
+  - affiliation: "Leipzig University"
+    family-names: Matthies
+    given-names: Franz
+    orcid: "https://orcid.org/0000-0001-7196-506X"
+  - affiliation: "Leipzig University"
+    family-names: Höffner
+    given-names: Konrad
+    orcid: "https://orcid.org/0000-0001-7358-3217"
+  - affiliation: "Leipzig University"
+    family-names: Schäfermeier
+    given-names: Ralph
+    orcid: "https://orcid.org/0000-0002-4349-6726"
 date-released: 2021-04-19
 keywords: 
   - ontology
+  - phenotyping
   - phenotype
-  - "inference-engine"
   - "phenotype-exchange-format"
-license: "GPL-3.0"
-doi: 10.5281/zenodo.5205498
-message: "If you use the content of this repository, please cite it using these metadata."
-version: "v0.2.1"
+  - "phenotyping-algorithms"
+license: "CC-BY-4.0"
+doi: 10.5281/zenodo.5205497

CONTRIBUTING.md

@@ -0,0 +1,24 @@
+# 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/COP/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/) to modify the ontology [cop.owl](cop.owl).
+If you want to contribute changes, please do so by:
+
+1. cloning this repository (forking for external contributors)
+2. creating a new feature branch
+3. applying your changes
+4. committing and pushing all changes
+5. creating a [pull request](https://github.com/Onto-Med/COP/pulls)