SPARQLing Plant Metabolic Pathways Wiki

This repository contains the SPARQLing Plant Metabolic Pathways Wiki tutorial material, adapted from the original SPARQLing Biology workshop so that it can be reused in other workshops.

• 🌱 Online tutorial: https://pathway-lod.github.io/SPARQLTutorials/
• 🌐 PlantMetWiki SPARQL Explorer: https://plantmetwiki.bioinformatics.nl/

This tutorial was adapted from the course materials available at
https://DeniseSl22.github.io/SPARQLTutorials/.

License for this tutorial and source code:
CC-BY-SA 4.0 International

Credits

Authors of the original SPARQLing Biology material:

• Egon Willighagen
• Marvin Martens
• Denise Slenter

We would like to acknowledge the material provided at
https://github.com/egonw/fvtworkshop by Egon Willighagen, Ruud Steltenpool and Lars Willighagen, which has been used to construct this workshop (material is only available in Dutch).

Part of this material has been tested at the
BioSB conference breakout session taking place on the 3rd of April 2019 in Lunteren.
The specific material for this workshop can be found at
https://bigcat-um.github.io/SPARQLTutorialBioSB2019/.

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Serve this website locally for development (macOS, tested)

These instructions assume:

• macOS
• Homebrew installed
• You are in this repository (e.g. cd /path/to/SPARQLTutorials)

The site uses Jekyll with the GitHub Pages theme jekyll-theme-tactile and is best run via Bundler, so the local environment matches GitHub Pages.

1. Install Ruby (via Homebrew)

brew install ruby

2. Ensure Homebrew Ruby is on your PATH

For Apple Silicon (M1/M2/M3):

echo 'export PATH="/opt/homebrew/opt/ruby/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

For Intel Macs:

echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

You can check Ruby with:

ruby -v

3. Install Bundler

gem install bundler

4. Install the site dependencies with Bundler

From the repo root (SPARQLTutorials):

cd /path/to/SPARQLTutorials
bundle install

This uses the Gemfile in the repository to install:

• jekyll
• jekyll-theme-tactile
• jekyll-seo-tag
• and any other required gems.

5. Serve the site locally

bundle exec jekyll serve --port 4001

Jekyll will print something like:

Server address: http://127.0.0.1:4001/
Server running... press ctrl-c to stop.

Open the URL in your browser (usually http://127.0.0.1:4000/). You should see the tutorial rendered with the same tactile theme as on GitHub Pages.

Feedback

If you have feedback on this tutorial or find an issue, please open a GitHub issue in this repository:

https://github.com/pathway-lod/SPARQLTutorials/issues