SPARQL example template repository

.github/workflows/check.yml

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+name: Check SPARQL queries
+on: [push, pull_request, workflow_call, workflow_dispatch]
+
+jobs:
+
+  check:
+    name: Run SPARQL checks
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-java@v4
+      with:
+        distribution: 'temurin'
+        java-version: '21'
+
+    - name: Install tester
+      run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.6/sparql-examples-utils-2.0.6-uber.jar" -O sparql-examples-utils.jar
+
+    - name: Run tests
+      run: java -jar sparql-examples-utils.jar test --input-directory=examples/

.github/workflows/publish_github_pages.yml

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+# Publishes the Markdown pages.
+name: Publish to github-pages
+
+on:
+  push:
+    branches: [ "master" ]
+
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  publish_html:
+    name: "publish html"
+    runs-on: ubuntu-latest 
+    steps: 
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-java@v4
+      with:
+        distribution: 'temurin'
+        java-version: '21'
+
+    - name: Install tester
+      run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.6/sparql-examples-utils-2.0.6-uber.jar" -O sparql-examples-utils-uber.jar
+
+    - name: generate markdown
+      run: java -jar sparql-examples-utils-uber.jar convert -i examples/ -m 
+
+    - name: generate rq files
+      run: java -jar sparql-examples-utils-uber.jar convert -i examples/ -r
+
+    - name: Setup Pages
+      id: pages
+      uses: actions/configure-pages@v5
+
+    - name: Build with Jekyll
+      uses: actions/jekyll-build-pages@v1
+      with:
+        source: ./
+        destination: ./_site
+
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: publish_html
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications"
+repository-code: https://github.com/sib-swiss/sparql-examples-utils
+date-released: 2024-10-08
+doi: 10.48550/arXiv.2410.06010
+license: MIT
+authors:
+  - given-names: Jerven
+    family-names: Bolleman
+    orcid: https://orcid.org/0000-0002-7449-1266,
+    email: [email protected]
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Vincent
+    family-names: Emonet
+    orcid: https://orcid.org/0000-0002-1501-1082
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Adrian
+    family-names: Altenhoff
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Amos
+    family-names: Bairoch
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Marie-Claude
+    family-names: Blatter
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Alan
+    family-names: Bridge
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Severine
+    family-names: Duvaud
+    orcid: https://orcid.org/0000-0001-7892-9678
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Elisabeth
+    family-names: Gasteiger
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Dmitry
+    family-names: Kuznetsov
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Sebastien
+    family-names: Moretti
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Pierre-Andre
+    family-names: Michel
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Anne
+    family-names: Morgat
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Marco
+    family-names: Pagni
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Nicole
+    family-names: Redaschi
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Monique
+    family-names: Zahn-Zabal
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Tarcisio
+    family-names: Mendes de Farias
+    orcid: https://orcid.org/0000-0002-3175-5372
+    affiliation: SIB Swiss Institute of Bioinformatics
+  - given-names: Ana Claudia
+    family-names: Sima
+    orcid: https://orcid.org/0000-0003-3213-4495
+    affiliation: SIB Swiss Institute of Bioinformatics

LICENSE.md

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+All example queries are dual licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)  and the MIT license as included below. The code arround the sparql-examples under src/ is only licensed under the MIT license included below. 
+
+The MIT License (MIT)
+
+Copyright (c) 2024 SIB Swiss Institute of Bioinformatics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+# SPARQL examples template repository
+
+This is a template repository to help you get started with sharing your sparql examples in a structured maner.
+
+
+The idea comes from the [SIB SPARQL Examples](https://github.com/sib-swiss/sparql-examples/) project. 
+
+# Upon forking
+
+Change YOUR\_PROJECT to what you need it to be, adapt the index.md files.
+Add your prefixes.ttl and examples in \*.ttl files.
+Correct the LICSENSE.md and CITATION.cff to account for your project.
+
+
+# For more inspiration see
+
+ * [SIB Sparql Examples](https://github.com/sib-swiss/sparql-examples/)
+ * [Wikibase Examples](https://github.com/JervenBolleman/wikibase-sparql-examples/)
+ * [BiGCAT-UM](https://github.com/BiGCAT-UM/sparql-examples)
+
+# The QA and markdown 
+
+Can be found in the project [SIB SPARQL Examples Utils](https://github.com/sib-swiss/sparql-examples-utils/
+

_includes/mermaid.html

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+<script type="module">
+  import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
+
+  mermaid.initialize({ startOnLoad: false });
+  await mermaid.run({
+      querySelector: '.language-mermaid',
+  });
+</script>

_layouts/default.html

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+<!DOCTYPE html>
+<html lang="{{ site.lang | default: "en-US" }}">
+  <head>
+    <meta charset="UTF-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+
+{% seo %}
+    <link rel="stylesheet" href="{{ "/assets/css/style.css?v=" | append: site.github.build_revision | relative_url }}">
+    <!--[if lt IE 9]>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
+    <![endif]-->
+    {% include head-custom.html %}
+  </head>
+  <body>
+    <div class="wrapper">
+      <header>
+        <h1><a href="{{ "/" | absolute_url }}">{{ site.title | default: site.github.repository_name }}</a></h1>
+
+        {% if site.logo %}
+          <img src="{{site.logo | relative_url}}" alt="Logo" />
+        {% endif %}
+
+        <p>{{ site.description | default: site.github.project_tagline }}</p>
+
+        {% if site.github.is_project_page %}
+        <p class="view"><a href="{{ site.github.repository_url }}">View the Project on GitHub <small>{{ site.github.repository_nwo }}</small></a></p>
+        {% endif %}
+
+        {% if site.github.is_user_page %}
+        <p class="view"><a href="{{ site.github.owner_url }}">View My GitHub Profile</a></p>
+        {% endif %}
+
+        {% if site.show_downloads %}
+        <ul class="downloads">
+          <li><a href="{{ site.github.zip_url }}">Download <strong>ZIP File</strong></a></li>
+          <li><a href="{{ site.github.tar_url }}">Download <strong>TAR Ball</strong></a></li>
+          <li><a href="{{ site.github.repository_url }}">View On <strong>GitHub</strong></a></li>
+        </ul>
+        {% endif %}
+      </header>
+      <section>
+
+      {{ content }}
+
+      </section>
+      <footer>
+        {% if site.github.is_project_page %}
+        <p>This project is maintained by <a href="{{ site.github.owner_url }}">{{ site.github.owner_name }}</a></p>
+        {% endif %}
+        <p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
+      </footer>
+    </div>
+    {% include mermaid.html %}
+    <script src="{{ "/assets/js/scale.fix.js" | relative_url }}"></script>
+  </body>
+</html>

examples/prefixes.ttl

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+prefix sh: <http://www.w3.org/ns/shacl#>
+prefix xsd: <http://www.w3.org/2001/XMLSchema#>
+prefix owl: <http://www.w3.org/2002/07/owl#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+_:sparql_examples_prefixes
+  a owl:Ontology ;
+  owl:imports sh: .
+
+_:sparql_examples_prefixes sh:declare _:prefix_rdf .
+_:prefix_rdf
+  sh:prefix "rdf" ;
+  sh:namespace "http://www.w3.org/1999/02/22-rdf-syntax-ns#"^^xsd:anyURI .
+
+_:sparql_examples_prefixes sh:declare _:prefix_rdfs .
+_:prefix_rdfs
+  sh:prefix "rdfs" ;
+  sh:namespace "http://www.w3.org/2000/01/rdf-schema#"^^xsd:anyURI .
+
+_:sparql_examples_prefixes sh:declare _:prefix_skos .
+_:prefix_skos
+  sh:prefix "skos" ;
+  sh:namespace "http://www.w3.org/2004/02/skos/core#"^^xsd:anyURI .
+
+_:sparql_examples_prefixes sh:declare _:prefix_owl .
+_:prefix_owl
+  sh:prefix "owl" ;
+  sh:namespace "http://www.w3.org/2002/07/owl#"^^xsd:anyURI .
+
+_:sparql_examples_prefixes sh:declare _:prefix_xsd .
+_:prefix_xsd
+  sh:prefix "xsd" ;
+  sh:namespace "http://www.w3.org/2001/XMLSchema#"^^xsd:anyURI .

index.md

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+# SPARQL examples
+
+Edit this file to change YOUR\_PROJECT to the name of your actual project.
+In YOUR\_PROJECT. In that directory keep your project specific prefixes.ttl and 
+the ttl files containing your example queries.
+
+ * [YOUR PROJECT](./examples/YOUR_PROJECT/)
+
+# Examples
+
+* [SIB Swiss Institute of Bioinformatics](https://sib-swiss.github.io/sparql-examples/)