SPARQLing Biology: a beginners course.

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This website includes the workshop material for:

• BioSB conference BreakOut Session taking place at the 3th of April 2019 in Lunteren.
• Nanosafety and the semantic web: from natural language to computational processing workshop taking place online on the 8th and 9th of December 2021.

Program

This workshop consists out of four parts:

• 30 minutes: Introduction to RDF and SPARQL (presentation)

• 25 minutes: Gene variants in Wikidata
  • Understanding the Basics
  • Execute the query and retain results
  • Expand and change Query
• 25 minutes: Drug Targets in Wikidata
  • A more complicated query
  • Answering Biological Questions
• 10 minutes: Recap
  • Other Biological databases with RDF (presentation)
  • Update your SPARQL query here

An addendum is available, where we added:

• Answers to questions asked during the tutorial.
• More information on where to find Biological and Chemical properties (aka relationships) to expand your query.
• More detailed explanation of the SERVICE statement (since this is not directly part of SPARQL, but constructed by Wikidata for easier querying).

We added a second addendum, discussing federated query from Wikidata to WikiPathways and converting IRIs

We want to thank all the participants of our workshop, and if you have any more questions and/or comments, feel free to use our issue tracker (if you are new to GitHub, please follow the instructions in the addendum to create an account and add an issue).

The material for this workshop is available under CC-BY-SA 4.0 International licence.