Tentative programme
Location
Room Z4, Netherlands Cancer Institute, Amsterdam
| Thu 8th Dec | Room Z4 | |
|---|---|---|
| 08:30 | Registration & coffee/tea – Foyer | |
| 09:00-10:30 |
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| 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)
Programme
Welcome to the SWAT4LS Hackathon 2016 discussion group. We will be discussing ideas here leading up to the hackathon on Thursday Dec.
Themes
Wikidata
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.