Hackathon – 8th December

Tentative programme


Room Z4, Netherlands Cancer Institute, Amsterdam

Thu 8th Dec Room Z4
08:30 Registration & coffee/tea – Foyer
  •  Arrive
  • Welcome and Introduction
  • Short presentations on activities per cluster


10:30-11:00 Break with coffee/tea – Foyer
11:00-12:00 hack hack hack
12:00-13:30 Lunch – Foyer
13:30-15:00  hack hack hack
15:00-15:30 Break with coffee/tea – Foyer
15:30-17:30  hack hack hack
~17:30 Close
Hackathon details (Googledoc snapshot):

SWAT4LS Hackathon Ideas and Programme

Instructions for contributing to this document:

  • Please go to the designated google document to add idea’s for themes or topics.
  • Provide an elevator pitch
  • Add Datasets that we can use in an activity with sample SPARQL queries
  • Add proposals for Activities
  • We will create a poll leading up to the day of the Hackathon to sign up for activities of interest (possibly more than one)



Welcome to the SWAT4LS Hackathon 2016 discussion group. We will be discussing ideas here leading up to the hackathon on Thursday Dec.



Wikidata is the linked database of the mediawiki foundation. It features a powerful WikiData Query Service (WDQS) which supports SPARQL queries and various visualization filters on the SPARQL results (http://query.wikidata.org). Wikidata provides a powerful hub in the Semantic Web. This hackathon provides an ideal opportunity to explore the value of Wikidata in the life science & Health section of the semantic web. The following angles could be good starting points to explore the value of Wikidata.
Main page: http://www.wikidata.org
SPARQL endpoint: http://query.wikidata.org

Clinical interpretation of Variants in Cancer

Contact: Andra Waagmeester

Preceding this hackathon (1&2 December), the CIViC Hackathon  & Jamboree (https://itcr.nci.nih.gov/about-itcr/news/civic-hackathon-and-curation-jamboree-nki-amsterdam-nov-30-dec-2)  shares the same venue. During that hackathon a Wikidata model on genetic variants will be implemented and populated from the CIViC database. These CIViC entries provide valuable hubs between genes, diseases and drugs. During the SWAT4LS hackathon the linked data originating from CIViC, available as linked data in Wikidata, could extended, linked with other relevant resources.

 Applying shape expressions on Wikidata subsets.

Contact: Eric Prud’hommeaux

The Shape Expressions (ShEx) language describes RDF graph structures. A shape describes the triples touching nodes in RDF graphs. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces. We would like to see if shape expressions can be of value in validating additions to Wikidata from external sources

 Model a novel open life science/health resource in Wikidata

Contact: Andra Waagmeester

The semantics of Wikidata content remains completely within the Wikidata space. Using external ontologies is not immediately possible. Adding novel data to Wikidata requires it to be completely covered by the existing Wikidata datamodel of items, properties, qualifiers, and references. Extending the Wikidata model with new semantic layers is possible by involving the community at large. With enough interest (and novel datasource), we explore the proposal process used to do so.