1. Visualizing Linked Open Data Andra Waagmeester

2. Overview Context: Pathways Howto: Linked data Make sense of linked data Visualizing linked data

3. Gerhard Michal 1974 Böhringer Mannheim Poster

5. Pathway knowledge in the literature... Insulin inactivates liver phosphorylase, the principal enyzme that causes liver glycogen to split into glucose. This prevents breakdown of the glycogen that has been stored in the liver.

6. Pathway knowledge in databases

7. PathwayLoom Plugin for the pathway editor Pathvisio – Using existing knowledge to guide pathway creation (Click-Search-Grow) – Use online and local data resources for interaction data – Searches for known interaction partners for a target element

8. PathwayLoom

9. Pathvisio Loom

10. Caveats Online resources tend to be volatile Each Resource comes with its own Webservice flavour (REST, SOAP, custom made) The plugin has to deal with multitude of output formats (JSON, CSV, XML, etc)

11. 5 ★ Open Data

12. The Linking Open Data cloud diagram maintained by Richard Cyganiak (DERI, NUI Galway) and Anja Jentzsch (HPI) http://lod-cloud.net

13. Guidelines for exposing data as RDF in Open Phacts

14. Linked Data Elements The triple – The dereferencable Unified Resource Identfier = http://www.linkedin.com/pub/andra- waagmeester/2/579/478http://www.linkedin.com/pub/andra- waagmeester/2/579/478 = http://www.w3.org/2006/vcard/ns#Homehttp://www.w3.org/2006/vcard/ns#Home = http://www.w3.org/2006/vcard/ns#Workhttp://www.w3.org/2006/vcard/ns#Work = http://dbpedia.org/resource/Antwerp

15. Making sense of dereferencable URI’s Who lives in Antwerp SPARQL: PREFIX linkedIn: PREFIX vcard: http://www.w3.org/2006/vcard/ns# PREFIX dbpedia: SELECT * WHERE { ?person vcard:work dbpedia:Antwerp }http://www.w3.org/2006/vcard/ns# Returns a mulitude of the following lines: PREFIX linkedIn …. linkedIn:andra. linkedIn:alex. …… linkedIn:silivius.

16. Processing LOD output can become cumbersome

17. Find compounds, targets and enzmes. Viewing provenance, filtering by species or activity and searching by structure are only a click or two away.

18. Within the OpenPHACTS Explorer data from Chemspider, drugbank, chembl and other sources are combined in an easy to use interface. Download your results as a spreadsheet to your own computer.

19. Visualbox.org

21. With Interaction available as Linked data Online resources remains volatile, but having the data in downloadable format allows local usage. There is a uniform webservice (SPARQL query). The plugin requires only a SPARQL wrapper to consume data.

22. Semscape – Visualizing linked data landscapes with Cytoscape Researchers need to easily and intuitively exploit and query the wealth of data that is available behind SPARQL endpoints. SemScape, a semantic-web enabled plugin for Cytoscape. Allows visualizing Sparql queries in cytoscape. Allows creating link data landscapes, which linked data schemas of distributed SPARQL endpoints

23. Use case 1: Visualizing SPARQL queries

24. Use case 2: creating data landscapes

25. Conclusions Creating linked data is a process where data is described in triples (subject, predicate, object). Each element of a triple should be dereferencable URI SPARQL is a query language for linked data SPARQL is for the technical savvy Different visualization techniques allows the integration of Linked Data in various software frameworks, websites, blogs, etc

26. Google Summer of code 2013 NRNB Google Summer of Code (http://nrnb.org/gsoc/) IDEA 28: Visualizing Pathway RDF with Visualbox IDEA 42: User Interaction on Biomedical Linked Data

27. Acknowledgments Yigang Zhou (GSOC student) Andrea Splendiani (DERI, Galway) Carina Haupt (Bonn-Aachen Institute for Information Technology) Helena Deus (DERI, Galway) Ian Dunlop (Manchester University) Alvaro Graves (Rensselaer Polytechnic Institute)