Nanosafety and the semantic web: from natural language to computational processing

A NanoCommons Training Workshop, 8-9 November 2021

The workshop was covering the whole range of Semantic Approaches developed and used at the Department of Bioinformatics at Maastricht University (BiGCaT) within the nanosafety-projects. The setting was alternating between introductory presentations and hands on exercises starting with more general questions like “what is a triple and what is the link with ontologies and RDF?” all the way to writing SPARQL queries and exploring their capabilities. By the end of the workshop the participants were able to apply to tools and possibly implement them in their own work.

1. Introduction to RDF and SPARQL

2. SPARQLing Biology: a beginners course

Hands-on training covering a general introduction to RDF and SPARQL, gene variants and drug targets on Wikidata and federated query from Wikidata to WikiPathways

3. Overview of SPARQL Endpoints

4. Querying the SPARQL endpoint of your choice

Hands-on training covering WikiPathways, AOP-Wiki, Nanosafety RDF and ChEMBL RDF queries

5. Introduction to Ontologies

6. Ontology Walkthrough and Workshop

Hands-on training covering browsing the eNanoMapper ontology, adding a nanomaterial and creating an eNanoMapper data set in RDF