WikiPathways SPARQL Book

This repository contains the pre-Markdown sources of a book detailing everything you can do with SPARQL in WikiPathways, as well as the compiled Markdown sources.

Requirements

• Groovy
• nodejs
• citation-js (see doi:10.7717/peerj-cs.214)
• make
• curl (optional, but handy)

Install

The requirements can be installed on Debian GNU/Linux with:

sudo apt install groovy make nodejs curl
npm install citation-js

Compile

cd sparql
make
cd ..
make

The website makes use of GitHub pages, and GitHub automatically converts the .md files in the docs/ folder to HTML when you push to the repository.

Adding content

1. develop a new SPARQL query (and test it)
2. create a new .rq file in the sparql/ folder
3. add content to one of the .i.md files and embed the SPARQL with the instruction <sparql>foo</sparql> for the sparql/foo.rq query
4. compile the code (see above)
5. make a pull request

Pre-Markdown instructions

The following instructions can be used in the .i.md files:

• <topic></topic> to mark a word or term as topic, making it appear in the indexList
• <sparql></sparql> on a single line embeds the SPARQL query at that position
• <cite></cite> for adding a reference, using the Wikidata Q-identifier for that paper (or book or ...)
• <section label="intro" level="#">Introduction</section> to make a section referencable, and use <xref>intro</xref> to refer to that section.